Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 15 of 91
Found at i:2682983 original size:16 final size:16
Alignment explanation
Indices: 2682919--2682996 Score: 52
Period size: 17 Copynumber: 4.7 Consensus size: 16
2682909 GTTTATTTAA
* *
2682919 TATTGTTTTTA-TCTT
1 TATTTTTTTTATTATT
2682934 TATTTTATTTTATT-TT
1 TATTTT-TTTTATTATT
* *
2682950 TGTTTTACTTTTCTTTATT
1 TATTTT--TTTT-ATTATT
2682969 TATTTTTTTTATTATT
1 TATTTTTTTTATTATT
*
2682985 CTATTTTCTTTA
1 -TATTTTTTTTA
2682997 AATAAAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 5 0.10
16 17 0.34
17 19 0.38
18 2 0.04
19 7 0.14
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (16 bp):
TATTTTTTTTATTATT
Found at i:2683166 original size:60 final size:58
Alignment explanation
Indices: 2683001--2683411 Score: 469
Period size: 58 Copynumber: 6.9 Consensus size: 58
2682991 TCTTTAAATA
*
2683001 AAAAT-AAAAATTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAATCAAAATTTCC-AAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTT
* ***
2683060 AAAAAC-AAATTT-C-AAAAAGGCTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCTCTT
1 AAAATCAAAATTTCCAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTC-CTT
2683116 AAAGATCAAAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAA-ATCAAAATTTCCAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTT
* **
2683176 AGAAAT--AAATTTTCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 A-AAATCAAAATTTCCAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTT
* * *
2683234 GAAAATCAAAATTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAATTATCAATTTTCCTAAAA
1 -AAAATCAAAATTTC-CAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCT---T
* *
2683298 AAAATCAAAATTTCCAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAATCAAAATTTCCAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTT
** *
2683357 AAAAAAATAAATTTTC-AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTT
1 AAAATCA-AAATTTCCAAAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTT
2683412 TCCTACACAA
Statistics
Matches: 304, Mismatches: 27, Indels: 42
0.82 0.07 0.11
Matches are distributed among these distances:
55 5 0.02
56 36 0.12
57 3 0.01
58 60 0.20
59 51 0.17
60 49 0.16
61 47 0.15
62 38 0.12
63 15 0.05
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (58 bp):
AAAATCAAAATTTCCAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTT
Found at i:2683329 original size:181 final size:174
Alignment explanation
Indices: 2683017--2683411 Score: 546
Period size: 181 Copynumber: 2.2 Consensus size: 174
2683007 AAAATTCCAA
* * *
2683017 AAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAATTTCAAAAAGGC
1 AAAAAAGATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAATTTCAAAAAAGA
* *
2683081 TTTTTGAGGAAAAGTTGAAAGTATCAATTTCTCTTAAAGATCAAAATTTCCAAAAAAATATTTTT
65 TTTTTGAGGAAAAGTTGAAAGTATCAATTTCTCTAAAAAATCAAAATTTCCAAAAAAATATTTTT
* *
2683146 AGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTTC
130 AGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTC
*
2683190 AAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCAAAAAA
1 AAAAAA-GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAAC-AAATTTC---AAA
* *
2683255 AAATATTTTTGAGGAAAAGTTGAAATTATCAATTT-TCCTAAAAAAAATCAAAATTTCCAAAAAA
60 AAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTCT-CT--AAAAAATCAAAATTTCCAAAAAA
*
2683319 ATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAATAAATTTTC
122 ATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTT-AAAAAATAAATTTTC
*
2683373 AAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAGATTTTTGAG-GAAAAGTTGAAAGTATCAATTTT
2683412 TCCTACACAA
Statistics
Matches: 197, Mismatches: 12, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
173 6 0.03
174 34 0.17
175 6 0.03
176 7 0.04
178 1 0.01
179 36 0.18
181 58 0.29
182 30 0.15
183 19 0.10
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (174 bp):
AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAATTTCAAAAAAGAT
TTTTGAGGAAAAGTTGAAAGTATCAATTTCTCTAAAAAATCAAAATTTCCAAAAAAATATTTTTA
GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTC
Found at i:2686896 original size:4 final size:4
Alignment explanation
Indices: 2686880--2686927 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
2686870 ATCATTTGTG
* * * *
2686880 CATT CATT TATT CATT CATT CATC CATT TATT CATT CATT CATC CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
2686928 TATGTATCAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CATT
Found at i:2686907 original size:20 final size:20
Alignment explanation
Indices: 2686884--2686930 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2686874 TTTGTGCATT
2686884 CATTTATTCATTCATTCATC
1 CATTTATTCATTCATTCATC
2686904 CATTTATTCATTCATTCATC
1 CATTTATTCATTCATTCATC
2686924 CATTTAT
1 CATTTAT
2686931 GTATCAACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (20 bp):
CATTTATTCATTCATTCATC
Found at i:2688663 original size:14 final size:14
Alignment explanation
Indices: 2688612--2688679 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
2688602 GAAATGCCTT
2688612 AAAAA-AAAAAAGA
1 AAAAAGAAAAAAGA
* * *
2688625 GAAAAGAGAAAGGA
1 AAAAAGAAAAAAGA
** *
2688639 AAAGTGGAAAAAGA
1 AAAAAGAAAAAAGA
2688653 AAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
*
2688667 CAAAAGACAAAAA
1 AAAAAGA-AAAAA
2688680 AGGGAAAAAA
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
13 4 0.10
14 31 0.77
15 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.01
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:2688671 original size:21 final size:20
Alignment explanation
Indices: 2688612--2688679 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
2688602 GAAATGCCTT
2688612 AAAAA-AAAAAAGAGAAAAGA
1 AAAAAGAAAAAAGA-AAAAGA
* * **
2688632 GAAAGGAAAAGTGGAAAAAGA
1 AAAAAGAAAA-AAGAAAAAGA
2688653 AAAAAGAAAAAAGACAAAAGA
1 AAAAAGAAAAAAGA-AAAAGA
2688674 CAAAAA
1 -AAAAA
2688680 AGGGAAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
20 5 0.14
21 24 0.67
22 7 0.19
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAAGAAAAAGA
Found at i:2689262 original size:24 final size:25
Alignment explanation
Indices: 2689212--2689262 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
2689202 CCCTAAACAG
*
2689212 ATTTATTCCACATGATCCTTTTCTT
1 ATTTATTCCACATGATCCTTTTATT
** *
2689237 ATTTATTCTGCATGA-CTTTTTATT
1 ATTTATTCCACATGATCCTTTTATT
2689261 AT
1 AT
2689263 AATAACTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.55
Consensus pattern (25 bp):
ATTTATTCCACATGATCCTTTTATT
Found at i:2689906 original size:16 final size:16
Alignment explanation
Indices: 2689886--2689941 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
2689876 AAAGTTAAGA
* *
2689886 AAAAGAAATGAATAATT
1 AAAAGAAAAGAA-AAAT
*
2689903 AAAGGAAAAGAAAAAT
1 AAAAGAAAAGAAAAAT
* *
2689919 AAAAG-AAGGAAAAAG
1 AAAAGAAAAGAAAAAT
2689934 AAAAGAAA
1 AAAAGAAA
2689942 TGAATGGGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 13 0.41
16 9 0.28
17 10 0.31
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAT
Found at i:2691987 original size:141 final size:140
Alignment explanation
Indices: 2691806--2692119 Score: 328
Period size: 141 Copynumber: 2.2 Consensus size: 140
2691796 ACTCAGTCTT
* * *
2691806 GATCATCTTTA-TTCTCTGACTTATAGTTCAGTCATGGTCATCTTTGTTCTCTAACTAGTGGTTC
1 GATCATCTTTATTTCTC-GACTTATAGCTCAGTCATAGTCATCTTTATTCTCTAACTAGTGGTTC
** * * ** * *
2691870 AGTCTCAATCATCTTTATTCTCTGACTCGTTG-TTCAGTCCTGGTCATTTCTATCCTTCGACTTA
65 AACCTCAATCATCTTTATTCTCTAACTCG-TGATTCAATCCCAGTCATCTCTAACCTTCGACTTA
*
2691934 AGGTTCAATCCTA
129 AGATTCAAT-CTA
* * * * *
2691947 G-TCATCATTTATTTCTCGACTTGTGGCTCAGTCTTAGTCATCTTTATTCTCTGACTTGTGGTTC
1 GATCATC-TTTATTTCTCGACTTATAGCTCAGTCATAGTCATCTTTATTCTCTAACTAGTGGTTC
*** * * *
2692011 AACCTTGCTCATCTTTATTCTCTAACTTGTGATTCAATCCCAGTCATCTCTAACCTTTGACTTAC
65 AACCTCAATCATCTTTATTCTCTAACTCGTGATTCAATCCCAGTCATCTCTAACCTTCGACTTAA
*
2692076 GATTCAATCTC
130 GATTCAATCTA
* *
2692087 GATCATTCTTTATTTCTCGACTAATAGTTCAGT
1 GATCA-TCTTTATTTCTCGACTTATAGCTCAGT
2692120 TTCGGTTATT
Statistics
Matches: 140, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
140 10 0.07
141 123 0.88
142 7 0.05
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (140 bp):
GATCATCTTTATTTCTCGACTTATAGCTCAGTCATAGTCATCTTTATTCTCTAACTAGTGGTTCA
ACCTCAATCATCTTTATTCTCTAACTCGTGATTCAATCCCAGTCATCTCTAACCTTCGACTTAAG
ATTCAATCTA
Found at i:2692000 original size:176 final size:176
Alignment explanation
Indices: 2691700--2692046 Score: 403
Period size: 176 Copynumber: 2.0 Consensus size: 176
2691690 GTTTAGTCCT
* * ** * * *
2691700 AATCAGCTTTATTCTTTGACTCGTGGTTTAGTTTTGATCATCTCTATCCTTTAACTTACGGTTTA
1 AATCAGCTTTATTCTCTGACTCGTGGTTCAGTCCTGATCATCTCTATCCTTCAACTTAAGGTTCA
* * *
2691765 ATCCCAGTTATCTTTTATTTTCTTATGTGTAACTCAGTCTTGATCATCTTTATTCTCTGACTTAT
66 ATCCCAGTCATCATTTATTTTCTGATGTGTAACTCAGTCTTGATCATCTTTATTCTCTGACTTAT
** * * *
2691830 AGTTCAGTCATGGTCATCTTTGTTCTCTAACTAGTGGTTCAGTCTC
131 AGTTCAACCATGCTCATCTTTATTCTCTAACTAGTGATTCAGTCTC
* * * * *
2691876 AATCATCTTTATTCTCTGACTCGTTGTTCAGTCCTGGTCATTTCTATCCTTCGACTTAAGGTTCA
1 AATCAGCTTTATTCTCTGACTCGTGGTTCAGTCCTGATCATCTCTATCCTTCAACTTAAGGTTCA
* **
2691941 ATCCTAGTCATCATTTA-TTTCTCGACT-TGTGGCTCAGTCTT-AGTCATCTTTATTCTCTGACT
66 ATCCCAGTCATCATTTATTTTCT-GA-TGTGTAACTCAGTCTTGA-TCATCTTTATTCTCTGACT
* * * *
2692003 TGTGGTTCAACCTTGCTCATCTTTATTCTCTAACTTGTGATTCA
128 TATAGTTCAACCATGCTCATCTTTATTCTCTAACTAGTGATTCA
2692047 ATCCCAGTCA
Statistics
Matches: 141, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
175 6 0.04
176 134 0.95
177 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.46
Consensus pattern (176 bp):
AATCAGCTTTATTCTCTGACTCGTGGTTCAGTCCTGATCATCTCTATCCTTCAACTTAAGGTTCA
ATCCCAGTCATCATTTATTTTCTGATGTGTAACTCAGTCTTGATCATCTTTATTCTCTGACTTAT
AGTTCAACCATGCTCATCTTTATTCTCTAACTAGTGATTCAGTCTC
Found at i:2692058 original size:35 final size:35
Alignment explanation
Indices: 2691808--2692059 Score: 199
Period size: 35 Copynumber: 7.2 Consensus size: 35
2691798 TCAGTCTTGA
* * * * *
2691808 TCATCTTTATTCTCTGACTTATAGTTCAGTCATGG
1 TCATCTTTATTCTCTGACTTGTGGTTCAATCCTAG
* * * * *
2691843 TCATCTTTGTTCTCTAACTAGTGGTTCAGT-CTCAA
1 TCATCTTTATTCTCTGACTTGTGGTTCAATCCT-AG
* * * *
2691878 TCATCTTTATTCTCTGACTCGTTGTTCAGTCCTGG
1 TCATCTTTATTCTCTGACTTGTGGTTCAATCCTAG
* **
2691913 TCAT-TTCTATCCT-TCGACTTAAGGTTCAATCCTAG
1 TCATCTT-TATTCTCT-GACTTGTGGTTCAATCCTAG
* * *
2691948 TCATCATTTATT-TCTCGACTTGTGGCTCAGTCTTAG
1 TCATC-TTTATTCTCT-GACTTGTGGTTCAATCCTAG
*
2691984 TCATCTTTATTCTCTGACTTGTGGTTCAA-CCTTG
1 TCATCTTTATTCTCTGACTTGTGGTTCAATCCTAG
* * *
2692018 CTCATCTTTATTCTCTAACTTGTGATTCAATCCCAG
1 -TCATCTTTATTCTCTGACTTGTGGTTCAATCCTAG
2692054 TCATCT
1 TCATCT
2692060 CTAACCTTTG
Statistics
Matches: 172, Mismatches: 35, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
34 7 0.04
35 130 0.76
36 33 0.19
37 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.44
Consensus pattern (35 bp):
TCATCTTTATTCTCTGACTTGTGGTTCAATCCTAG
Found at i:2692537 original size:22 final size:23
Alignment explanation
Indices: 2692496--2692542 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
2692486 TTTTATTAAA
2692496 ATTAATAATCAAATATTAAATAT
1 ATTAATAATCAAATATTAAATAT
*
2692519 ATTAATAAT-AATTATTAAATAT
1 ATTAATAATCAAATATTAAATAT
2692541 AT
1 AT
2692543 GAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAATAATCAAATATTAAATAT
Found at i:2692540 original size:20 final size:21
Alignment explanation
Indices: 2692488--2692540 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
2692478 TTGTTTAATT
2692488 TTATTAAA-ATTAATAATCAA
1 TTATTAAATATTAATAATCAA
*
2692508 ATATTAAATATATTAATAAT-AA
1 TTATT-AA-ATATTAATAATCAA
2692530 TTATTAAATAT
1 TTATTAAATAT
2692541 ATGAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 8 0.29
21 4 0.14
22 7 0.25
23 9 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATTAAATATTAATAATCAA
Found at i:2693489 original size:21 final size:21
Alignment explanation
Indices: 2693448--2693503 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
2693438 TTCAGGTAAT
* *
2693448 ATTTTTTAATTTTTTTATTTA
1 ATTTTTTAATATTATTATTTA
2693469 ATTTTTTAAATATTATT-TTTA
1 ATTTTTT-AATATTATTATTTA
* *
2693490 GTTTTATTATTATT
1 ATTTT-TTAATATT
2693504 TACGCATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTTTAATATTATTATTTA
Found at i:2693559 original size:3 final size:3
Alignment explanation
Indices: 2693553--2693601 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
2693543 TTATTATTTT
* * * *
2693553 TAA TAA TAA TAA TAA TAA TGA GAA AAA TAAA TAA TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
2693599 TAA
1 TAA
2693602 AATTTAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:2693587 original size:19 final size:19
Alignment explanation
Indices: 2693563--2693602 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2693553 TAATAATAAT
*
2693563 AATAATAATGAGAAAAATA
1 AATAATAATAAGAAAAATA
*
2693582 AATAATAATAATAAAAATA
1 AATAATAATAAGAAAAATA
2693601 AA
1 AA
2693603 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AATAATAATAAGAAAAATA
Found at i:2693796 original size:18 final size:17
Alignment explanation
Indices: 2693757--2693799 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
2693747 AATAAGGAAG
2693757 AATAATAATCAAAAAATA
1 AATAA-AATCAAAAAATA
2693775 AATAAAAT-AAAAAATGA
1 AATAAAATCAAAAAAT-A
2693792 TAATAAAA
1 -AATAAAA
2693800 ATCGAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 12 0.52
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
AATAAAATCAAAAAATA
Found at i:2694158 original size:31 final size:32
Alignment explanation
Indices: 2694102--2694174 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 32
2694092 AAACCCTAAA
*
2694102 AAACC-TT-AAACCCTACAACCTCAAAATCTT
1 AAACCTTTAAAACCCTACAACCCCAAAATCTT
*
2694132 AAACCTTTAAAACCCTA-AACCCCAAAATTTT
1 AAACCTTTAAAACCCTACAACCCCAAAATCTT
* *
2694163 AAAACTATAAAA
1 AAACCTTTAAAA
2694175 TCAAAACCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 5 0.14
31 24 0.65
32 8 0.22
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.23
Consensus pattern (32 bp):
AAACCTTTAAAACCCTACAACCCCAAAATCTT
Found at i:2694230 original size:55 final size:56
Alignment explanation
Indices: 2694136--2694244 Score: 132
Period size: 55 Copynumber: 1.9 Consensus size: 56
2694126 AATCTTAAAC
* * *
2694136 CTTTAAAACCCTAAACCCCAAAATTTTAAAACTATAAAA-TCAAAACCCTAAACTT
1 CTTTAAAACCCTAAAACCCAAAATTTTAAAACCACAAAATTCAAAACCCTAAACTT
* * *
2694191 CTTTAAAACCCTAAAAATCC-AAATTTTGAAACCCCAAAATTTCAAAACCCTAAA
1 CTTTAAAACCCT-AAAACCCAAAATTTTAAAACCACAAAA-TTCAAAACCCTAAA
2694245 ATCTAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 27 0.60
56 5 0.11
57 13 0.29
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.25
Consensus pattern (56 bp):
CTTTAAAACCCTAAAACCCAAAATTTTAAAACCACAAAATTCAAAACCCTAAACTT
Found at i:2694414 original size:8 final size:8
Alignment explanation
Indices: 2694403--2694487 Score: 54
Period size: 8 Copynumber: 11.1 Consensus size: 8
2694393 AACCCTAAAT
2694403 CTTAAAAC
1 CTTAAAAC
2694411 CTT-AAAC
1 CTTAAAAC
*
2694418 CCTAAAAC
1 CTTAAAAC
* *
2694426 CAT-AAGC
1 CTTAAAAC
**
2694433 CTTGTAAC
1 CTTAAAAC
*
2694441 CTTAAAAT
1 CTTAAAAC
*
2694449 CTGAAAAC
1 CTTAAAAC
2694457 C--AAAATC
1 CTTAAAA-C
2694464 C-TAAAAC
1 CTTAAAAC
2694471 CTTAAAAC
1 CTTAAAAC
*
2694479 CCTAAAAC
1 CTTAAAAC
2694487 C
1 C
2694488 CTCAAAATCC
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
6 4 0.07
7 15 0.25
8 41 0.68
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (8 bp):
CTTAAAAC
Found at i:2694442 original size:30 final size:29
Alignment explanation
Indices: 2694405--2694487 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
2694395 CCCTAAATCT
*
2694405 TAAAACCTTAAACCCTAAAACCATAAGCC
1 TAAAACCTTAAACCCTAAAACCAAAAGCC
** ** *
2694434 TTGTAACCTTAAAATCTGAAAACCAAAATCC
1 -TAAAACCTTAAACCCT-AAAACCAAAAGCC
2694465 TAAAACCTTAAAACCCTAAAACC
1 TAAAACCTT-AAACCCTAAAACC
2694488 CTCAAAATCC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
30 25 0.61
31 16 0.39
ACGTcount: A:0.48, C:0.28, G:0.04, T:0.20
Consensus pattern (29 bp):
TAAAACCTTAAACCCTAAAACCAAAAGCC
Found at i:2694488 original size:8 final size:8
Alignment explanation
Indices: 2694458--2694502 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
2694448 TCTGAAAACC
*
2694458 AAAATCCT
1 AAAACCCT
*
2694466 AAAACCTT
1 AAAACCCT
2694474 AAAACCCT
1 AAAACCCT
2694482 AAAACCCT
1 AAAACCCT
*
2694490 CAAAATCCT
1 -AAAACCCT
2694499 AAAA
1 AAAA
2694503 TTTCATCAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAACCCT
Found at i:2694499 original size:17 final size:16
Alignment explanation
Indices: 2694457--2694502 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
2694447 ATCTGAAAAC
2694457 CAAAATCCTAAAACCT
1 CAAAATCCTAAAACCT
* *
2694473 TAAAACCCTAAAACCCT
1 CAAAATCCTAAAA-CCT
2694490 CAAAATCCTAAAA
1 CAAAATCCTAAAA
2694503 TTTCATCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.17
Consensus pattern (16 bp):
CAAAATCCTAAAACCT
Found at i:2710966 original size:29 final size:29
Alignment explanation
Indices: 2710929--2710988 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
2710919 AGTTAACAGA
* *
2710929 TTTATAATTCAAATATCATATTAAATATT
1 TTTAAAATTCAAATATCACATTAAATATT
* * *
2710958 TTTAAAATTTAGATATTACATTAAATATT
1 TTTAAAATTCAAATATCACATTAAATATT
2710987 TT
1 TT
2710989 ATTATAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTAAAATTCAAATATCACATTAAATATT
Found at i:2717311 original size:28 final size:29
Alignment explanation
Indices: 2717253--2717311 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 29
2717243 AAAATATAAT
* * *
2717253 AAAATATTTAATGTGGTACTTGAATTTTA
1 AAAATATTTAATGTGATACTTGAACTATA
* *
2717282 AAAATTTTTAATG-GATATTTGAACTATA
1 AAAATATTTAATGTGATACTTGAACTATA
2717310 AA
1 AA
2717312 TCTATTAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (29 bp):
AAAATATTTAATGTGATACTTGAACTATA
Found at i:2718381 original size:2 final size:2
Alignment explanation
Indices: 2718374--2718402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2718364 ACATACATAC
2718374 AT 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 AT A
2718403 AGTCACAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2723924 original size:22 final size:22
Alignment explanation
Indices: 2723883--2723938 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
2723873 TAATGCAAAA
2723883 AAAATTATTAAATTTCATAT-AC
1 AAAATTA-TAAATTTCATATAAC
2723905 AAAATTATAAATTAAT-ATATAAC
1 AAAATTATAAATT--TCATATAAC
*
2723928 ACAATTA-AAAT
1 AAAATTATAAAT
2723939 ATACTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.20
22 15 0.50
23 9 0.30
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATTATAAATTTCATATAAC
Found at i:2725692 original size:3 final size:3
Alignment explanation
Indices: 2725684--2725723 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2725674 CTTAGTTCAA
2725684 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2725724 TTCGTTAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2726324 original size:24 final size:24
Alignment explanation
Indices: 2726278--2726325 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2726268 CGTTAAACCA
*
2726278 ATTTTTTTTCTCTTTTTTCTCTTT
1 ATTTTTTTTCTCTTTTCTCTCTTT
*
2726302 ATTTTTTTTTTGCTTTTCT-TCTTT
1 ATTTTTTTTCT-CTTTTCTCTCTTT
2726326 CTCTTCTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (24 bp):
ATTTTTTTTCTCTTTTCTCTCTTT
Found at i:2734641 original size:139 final size:139
Alignment explanation
Indices: 2734450--2734727 Score: 529
Period size: 139 Copynumber: 2.0 Consensus size: 139
2734440 GCCAAGATCA
*
2734450 ACCAGATTGCTGGTCGTGCATCGGCTATTCGAGCCATGCCACTAGATTTGTTGATGAATTTATGA
1 ACCAGATTGCTGGTCGTGCATCGGCTATTCGAGCCATGCCACTAGATGTGTTGATGAATTTATGA
*
2734515 TATCTCCAGGGAGGAAGCAAGGAGATTTTAGGACAGTAGGAAGGAGGTATCTGTTTTTAGCCCCG
66 TATCTCCAGGGAGGAAGCAAGGAGATTTTAGGACAGTAGGAAGGAGGTATCTGTGTTTAGCCCCG
2734580 GTTCTAGGT
131 GTTCTAGGT
*
2734589 ACCAGATTGCTGGTCGTGTATCGGCTATTCGAGCCATGCCACTAGATGTGTTGATGAATTTATGA
1 ACCAGATTGCTGGTCGTGCATCGGCTATTCGAGCCATGCCACTAGATGTGTTGATGAATTTATGA
2734654 TATCTCCAGGGAGGAAGCAAGGAGATTTTAGGACAGTAGGAAGGAGGTATCTGTGTTTAGCCCCG
66 TATCTCCAGGGAGGAAGCAAGGAGATTTTAGGACAGTAGGAAGGAGGTATCTGTGTTTAGCCCCG
2734719 GTTCTAGGT
131 GTTCTAGGT
2734728 CACAGCATCA
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (139 bp):
ACCAGATTGCTGGTCGTGCATCGGCTATTCGAGCCATGCCACTAGATGTGTTGATGAATTTATGA
TATCTCCAGGGAGGAAGCAAGGAGATTTTAGGACAGTAGGAAGGAGGTATCTGTGTTTAGCCCCG
GTTCTAGGT
Found at i:2753242 original size:35 final size:35
Alignment explanation
Indices: 2753203--2753271 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
2753193 AAAAAATTTC
2753203 ACATGAAAGATACTTTTGTTCAAATAAAATGACAT
1 ACATGAAAGATACTTTTGTTCAAATAAAATGACAT
2753238 ACATGAAAGATACTTTTGTTCAAATAAAATGACA
1 ACATGAAAGATACTTTTGTTCAAATAAAATGACA
2753272 CATTTGAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (35 bp):
ACATGAAAGATACTTTTGTTCAAATAAAATGACAT
Found at i:2755275 original size:51 final size:51
Alignment explanation
Indices: 2755216--2755315 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 51
2755206 TATTTTTTTA
* * *
2755216 TTTTACAAGTTTAATTTCTAAATTTTTCATCATTTGGGTCAATTTAGAATT
1 TTTTACAAGTTTAATTTCTAAAATTTTCACCATTTAGGTCAATTTAGAATT
* **
2755267 TTTTACAAGTTTTATTTCTAAAATTTTCACCATTTAGGTTTATTTAGAA
1 TTTTACAAGTTTAATTTCTAAAATTTTCACCATTTAGGTCAATTTAGAA
2755316 AAAAAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (51 bp):
TTTTACAAGTTTAATTTCTAAAATTTTCACCATTTAGGTCAATTTAGAATT
Found at i:2755918 original size:5 final size:5
Alignment explanation
Indices: 2755908--2755948 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
2755898 GATTTATTAA
*
2755908 TATTT TATTT TGTTT TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
2755949 TTCTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:2765922 original size:88 final size:88
Alignment explanation
Indices: 2765818--2766008 Score: 213
Period size: 88 Copynumber: 2.1 Consensus size: 88
2765808 AGATTTTTTA
* * * * *
2765818 AAAAACAAAACAAAAAAGACATTTACATTTGCATTACTTGCATTTGCACTA-CCATGTGCATCTT
1 AAAAAC-AAA-AAAAAA-ACATTCACATTTGCATCACTTGCATTCGCAC-AGACATGTGCATCAT
* *
2765882 GAGAAAGACATTTAATTTGCATGCTAT
62 GAGAAAGACATTTAATCTGCATACTAT
* * *
2765909 AAAAACAAAAAAAAAACATTCGCATTTGTATCACTTGTATTCGCACAGACATGTGCATCATGAGA
1 AAAAACAAAAAAAAAACATTCACATTTGCATCACTTGCATTCGCACAGACATGTGCATCATGAGA
* * *
2765974 AAGATATTTGATCTGCATACTGT
66 AAGACATTTAATCTGCATACTAT
*
2765997 AAAAATAAAAAA
1 AAAAACAAAAAA
2766009 GACATTCGTA
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
87 1 0.01
88 69 0.81
89 6 0.07
90 3 0.04
91 6 0.07
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (88 bp):
AAAAACAAAAAAAAAACATTCACATTTGCATCACTTGCATTCGCACAGACATGTGCATCATGAGA
AAGACATTTAATCTGCATACTAT
Found at i:2766037 original size:26 final size:26
Alignment explanation
Indices: 2766007--2766077 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
2765997 AAAAATAAAA
* *
2766007 AAGACATTCGTATTTGCATCATAATC
1 AAGACAGTCGCATTTGCATCATAATC
* **
2766033 AAGACAGTCGCATTTGCCTCATAAGA
1 AAGACAGTCGCATTTGCATCATAATC
* *
2766059 AAGACACTTGCATTTGCAT
1 AAGACAGTCGCATTTGCAT
2766078 AATGGCATCT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (26 bp):
AAGACAGTCGCATTTGCATCATAATC
Found at i:2766438 original size:32 final size:33
Alignment explanation
Indices: 2766359--2766464 Score: 130
Period size: 32 Copynumber: 3.3 Consensus size: 33
2766349 ATTTAAGCCC
*
2766359 AGTCAAGCTAACA-CTCAGATCAAACTAA-ACCT
1 AGTCAAGCTGACACCT-AGATCAAACTAAGACCT
* * *
2766391 AGTTAAGTTGACACCTAGATCAAACAAAGACC-
1 AGTCAAGCTGACACCTAGATCAAACTAAGACCT
*
2766423 AGTCAAGCTGGCACCTAGATCAAACTAAG-CCT
1 AGTCAAGCTGACACCTAGATCAAACTAAGACCT
2766455 AGTCAAGCTG
1 AGTCAAGCTG
2766465 TAACTCAATC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.03
32 56 0.89
33 5 0.08
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (33 bp):
AGTCAAGCTGACACCTAGATCAAACTAAGACCT
Found at i:2766491 original size:15 final size:15
Alignment explanation
Indices: 2766436--2766506 Score: 65
Period size: 15 Copynumber: 4.6 Consensus size: 15
2766426 CAAGCTGGCA
2766436 CCTAGATCAAACTAAG
1 CCTA-ATCAAACTAAG
* *
2766452 CCTAGTCAAGCTGTAA-
1 CCTAATCAAAC--TAAG
2766468 -CTCAATCAAACTAAG
1 CCT-AATCAAACTAAG
2766483 CCTAATCAAACTAAG
1 CCTAATCAAACTAAG
*
2766498 CTTAATCAA
1 CCTAATCAA
2766507 GTTAGCACCC
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 3 0.07
15 27 0.60
16 12 0.27
17 3 0.07
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (15 bp):
CCTAATCAAACTAAG
Found at i:2766524 original size:32 final size:32
Alignment explanation
Indices: 2766487--2766592 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 32
2766477 ACTAAGCCTA
* * *
2766487 ATCAAACTAAGCTTAATCAAGTTAGCACCCAG
1 ATCAAACTAAACCTAATCAAGCTAGCACCCAG
* * * *
2766519 ATCAAACCAAACCTAATCTAGCTAGCATCTAG
1 ATCAAACTAAACCTAATCAAGCTAGCACCCAG
* * * **
2766551 ATCAAACAAAACCCAATCAAGCTGGCACTTAG
1 ATCAAACTAAACCTAATCAAGCTAGCACCCAG
*
2766583 ATTAAACTAA
1 ATCAAACTAA
2766593 GCTTAGTCAA
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.21
Consensus pattern (32 bp):
ATCAAACTAAACCTAATCAAGCTAGCACCCAG
Found at i:2766733 original size:97 final size:98
Alignment explanation
Indices: 2766615--2766812 Score: 258
Period size: 99 Copynumber: 2.0 Consensus size: 98
2766605 TAACACCCAA
*
2766615 ATCTCTAAGACATCAAAGCATAATCTTTAAGA-CT-TCCAGGGCAAAACATTTTAAAGTTTCAAG
1 ATCTCTAAGACATCAAAGCATAATCTCTAAGACCTATCCA-GGCAAAACATTTTAAAGTTTCAAG
* * * *
2766678 ACCTCTGATCATAGGAGCTTTCAAATATGTCAAG
65 ACCTCTAATCAAAGGAGCTTTCAAAGATATCAAG
* * * *
2766712 ATCTCTAAGATC-TCCAGGCATAATCTCTAATACCTAATCTAGGCAAAACATTTTAAAGTTTCAA
1 ATCTCTAAGA-CATCAAAGCATAATCTCTAAGACCT-ATCCAGGCAAAACATTTTAAAGTTTCAA
*
2766776 GGCCTCTAATCAAAGGAGCTTTCAAAGATATCAAG
64 GACCTCTAATCAAAGGAGCTTTCAAAGATATCAAG
2766811 AT
1 AT
2766813 TTGTAAAATC
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
97 26 0.30
98 3 0.03
99 55 0.63
100 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (98 bp):
ATCTCTAAGACATCAAAGCATAATCTCTAAGACCTATCCAGGCAAAACATTTTAAAGTTTCAAGA
CCTCTAATCAAAGGAGCTTTCAAAGATATCAAG
Found at i:2766833 original size:99 final size:99
Alignment explanation
Indices: 2766654--2766845 Score: 269
Period size: 99 Copynumber: 1.9 Consensus size: 99
2766644 AGACTTCCAG
* * * *
2766654 GGCAAAACATTTTAAAGTTTCAAGACCTCTGATCATAGGAGCTTTCAAATATGTCAAGATCTCTA
1 GGCAAAACATTTTAAAGTTTCAAGACCTCTAATCAAAGGAGCTTTCAAAGATATCAAGATCTCTA
* *
2766719 AGATCTCCAGGCATAATCTCTAATACCTAATCTA
66 AAATCTCCAGGCATAATCTCTAAGACCTAATCTA
* * *
2766753 GGCAAAACATTTTAAAGTTTCAAGGCCTCTAATCAAAGGAGCTTTCAAAGATATCAAGATTTGTA
1 GGCAAAACATTTTAAAGTTTCAAGACCTCTAATCAAAGGAGCTTTCAAAGATATCAAGATCTCTA
**
2766818 AAATCT-TTGGACATAATCTCTAAGACCT
66 AAATCTCCAGG-CATAATCTCTAAGACCT
2766846 CCGAACGTAA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 2 0.02
99 79 0.98
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (99 bp):
GGCAAAACATTTTAAAGTTTCAAGACCTCTAATCAAAGGAGCTTTCAAAGATATCAAGATCTCTA
AAATCTCCAGGCATAATCTCTAAGACCTAATCTA
Found at i:2767858 original size:28 final size:28
Alignment explanation
Indices: 2767817--2767877 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
2767807 GTCAAATTCC
* *
2767817 TGCACACACCAGCCTCAATCGACCTCCT
1 TGCACACACCAGCCCCAATCAACCTCCT
* * * *
2767845 TGCACATACTAGCCCCAATTAACCTTCT
1 TGCACACACCAGCCCCAATCAACCTCCT
2767873 TGCAC
1 TGCAC
2767878 CACTAACCCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.41, G:0.10, T:0.23
Consensus pattern (28 bp):
TGCACACACCAGCCCCAATCAACCTCCT
Found at i:2773136 original size:15 final size:16
Alignment explanation
Indices: 2773101--2773141 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2773091 TTATCCTAAT
* *
2773101 TTTTATTTCTTTTATA
1 TTTTATTTCTATTAAA
2773117 TTTTATTT-TATTAAA
1 TTTTATTTCTATTAAA
2773132 TTTTATTTCT
1 TTTTATTTCT
2773142 GCAATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTTCTATTAAA
Found at i:2775058 original size:3 final size:3
Alignment explanation
Indices: 2775050--2775084 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2775040 ATTGCTATAA
2775050 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2775085 CCAAATCGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2775799 original size:12 final size:13
Alignment explanation
Indices: 2775782--2775832 Score: 61
Period size: 12 Copynumber: 3.9 Consensus size: 13
2775772 TAATTCATGA
2775782 TTAATT-ATAATT
1 TTAATTAATAATT
2775794 TTAATTAATAATAT
1 TTAATTAATAAT-T
*
2775808 ATTTATT-ATAATT
1 -TTAATTAATAATT
2775821 TTAATTAATAAT
1 TTAATTAATAAT
2775833 ATTTTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 6 0.18
15 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTAATAATT
Found at i:2775839 original size:27 final size:27
Alignment explanation
Indices: 2775785--2775839 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2775775 TTCATGATTA
2775785 ATTATAATTTTAATTAATAATATATTT
1 ATTATAATTTTAATTAATAATATATTT
*
2775812 ATTATAATTTTAATTAATAATATTTTT
1 ATTATAATTTTAATTAATAATATATTT
2775839 A
1 A
2775840 AAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTATAATTTTAATTAATAATATATTT
Found at i:2775848 original size:33 final size:31
Alignment explanation
Indices: 2775785--2775872 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 31
2775775 TTCATGATTA
*
2775785 ATTATAATTTTAATTAATAATA-TATT---T
1 ATTATAATTTTAATTAATAATATTTTTAAAT
2775812 ATTATAATTTTAATTAATAATATTTTTAAAAAT
1 ATTATAATTTTAATTAATAATATTTTT--AAAT
2775845 ATTA-ATATTTTAA-T-AT-ATATTTTTAAAT
1 ATTATA-ATTTTAATTAATAATATTTTTAAAT
2775873 TTTAATCTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
27 22 0.42
28 7 0.13
30 8 0.15
31 2 0.04
32 2 0.04
33 12 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTATAATTTTAATTAATAATATTTTTAAAT
Found at i:2775864 original size:18 final size:18
Alignment explanation
Indices: 2775818--2775865 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2775808 ATTTATTATA
2775818 ATTTTAAT-TA-A-TAAT
1 ATTTTAATATATATTAAT
*
2775833 ATTTTTAA-AAATATTAAT
1 A-TTTTAATATATATTAAT
2775851 ATTTTAATATATATT
1 ATTTTAATATATATT
2775866 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 1 0.04
16 7 0.27
17 7 0.27
18 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATATATATTAAT
Found at i:2775877 original size:28 final size:28
Alignment explanation
Indices: 2775825--2775885 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
2775815 ATAATTTTAA
2775825 TTAATAATATTTTTAAAAATATTAATATT
1 TTAATAATATTTTT-AAAATATTAATATT
* *
2775854 TTAATATATATTTTT-AAATTTTAATCTT
1 TTAATA-ATATTTTTAAAATATTAATATT
2775882 TTAA
1 TTAA
2775886 GTCCAACGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 15 0.52
29 6 0.21
30 8 0.28
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAATAATATTTTTAAAATATTAATATT
Found at i:2780091 original size:12 final size:12
Alignment explanation
Indices: 2780076--2780120 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
2780066 TTTTTATATT
2780076 ATTTTAATATAA
1 ATTTTAATATAA
2780088 ATTTTAATAT--
1 ATTTTAATATAA
2780098 A-TTTAA-ATAA
1 ATTTTAATATAA
*
2780108 ATTTTGATATAA
1 ATTTTAATATAA
2780120 A
1 A
2780121 ATTATTATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
8 2 0.07
9 5 0.18
10 2 0.07
11 4 0.14
12 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
ATTTTAATATAA
Found at i:2780098 original size:25 final size:24
Alignment explanation
Indices: 2780051--2780118 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
2780041 TAATTTATGA
* *
2780051 TATTTAAATTTAAATTTTTTATAT
1 TATTTAAATATAAATTTTATATAT
*
2780075 TATTTTAATATAAATTTTA-ATA-
1 TATTTAAATATAAATTTTATATAT
2780097 TATTT-AA-ATAAATTTTGATATA
1 TATTTAAATATAAATTTT-ATATA
2780119 AAATTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.23
21 3 0.08
22 8 0.21
23 3 0.08
24 16 0.41
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (24 bp):
TATTTAAATATAAATTTTATATAT
Found at i:2780109 original size:20 final size:20
Alignment explanation
Indices: 2780050--2780118 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 20
2780040 TTAATTTATG
*
2780050 ATATTTAAATTTAAATTTTTTAT
1 ATATTTAAA--TAAA-TTTTAAT
2780073 ATTATTTTAATATAAATTTTAAT
1 A-TA-TTTAA-ATAAATTTTAAT
*
2780096 ATATTTAAATAAATTTTGAT
1 ATATTTAAATAAATTTTAAT
2780116 ATA
1 ATA
2780119 AAATTATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 14 0.34
21 5 0.12
22 2 0.05
23 8 0.20
24 6 0.15
25 5 0.12
26 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
ATATTTAAATAAATTTTAAT
Found at i:2780187 original size:5 final size:5
Alignment explanation
Indices: 2780174--2780219 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
2780164 TAATAAAAAT
*
2780174 ATTTA ATTTG ATTTA ATTTA ATTTA ATTTTTA ATTT- -TTTA ATTTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA A--TTTA ATTTA ATTTA ATTTA A
2780220 AATTTAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
3 3 0.09
5 27 0.77
7 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (5 bp):
ATTTA
Found at i:2780225 original size:20 final size:20
Alignment explanation
Indices: 2780190--2780227 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2780180 TTTGATTTAA
**
2780190 TTTAATTTAATTTTTAATTT
1 TTTAATTTAAAATTTAATTT
2780210 TTTAATTTAAAATTTAAT
1 TTTAATTTAAAATTTAAT
2780228 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAATTTAAAATTTAATTT
Found at i:2788060 original size:18 final size:17
Alignment explanation
Indices: 2788034--2788067 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2788024 GAAGAAGTTT
*
2788034 TTGATAATTCTGATGGTA
1 TTGAAAATTCT-ATGGTA
2788052 TTGAAAATTCTATGGT
1 TTGAAAATTCTATGGT
2788068 CCCAAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (17 bp):
TTGAAAATTCTATGGTA
Found at i:2789347 original size:22 final size:22
Alignment explanation
Indices: 2789313--2789370 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
2789303 AAAATATAAA
2789313 ATATATATTTTTATT-AAATTTAT
1 ATATA-ATTTTTATTAAAATTT-T
*
2789336 TTATAATTTTTATTAAAATTTT
1 ATATAATTTTTATTAAAATTTT
*
2789358 ATATTATTTTTAT
1 ATATAATTTTTAT
2789371 ATCATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATAATTTTTATTAAAATTTT
Found at i:2789391 original size:13 final size:13
Alignment explanation
Indices: 2789314--2789372 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 13
2789304 AAATATAAAA
2789314 TATATATTTT-TAT
1 TATA-ATTTTATAT
2789327 TA-AA-TTTAT-T
1 TATAATTTTATAT
2789337 TATAATTTT-TAT
1 TATAATTTTATAT
*
2789349 TAAAATTTTATAT
1 TATAATTTTATAT
2789362 TAT--TTTTATAT
1 TATAATTTTATAT
2789373 CATATTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
10 6 0.15
11 13 0.33
12 13 0.33
13 7 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATAATTTTATAT
Found at i:2789853 original size:32 final size:31
Alignment explanation
Indices: 2789794--2789853 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
2789784 CTCTATCCCA
* *
2789794 TTTTTTATATTTTAAAATTATATTTTATGAT
1 TTTTTTATATTTTAAAATTAAAATTTATGAT
* *
2789825 TTTTTTAATTTTTTAACATTAAAATTTAT
1 TTTTTT-ATATTTTAAAATTAAAATTTAT
2789854 AAACCTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 6 0.25
32 18 0.75
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTTTATATTTTAAAATTAAAATTTATGAT
Found at i:2793365 original size:15 final size:16
Alignment explanation
Indices: 2793339--2793387 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 16
2793329 TTAAAAAATT
2793339 TTAATAAAATATTTAAA
1 TTAAT-AAATATTTAAA
2793356 TT-ATAAATATATT-AA
1 TTAATAAATAT-TTAAA
2793371 TTAATATAATATTTAAA
1 TTAATA-AATATTTAAA
2793388 AAATTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.36
16 9 0.32
17 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATAAATATTTAAA
Found at i:2793382 original size:32 final size:29
Alignment explanation
Indices: 2793294--2793387 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
2793284 ATATGTCATG
*
2793294 AATTATAGAAAAATATTTAACATAATATTTA
1 AATTATA-AAAAAT-TTTAATATAATATTTA
* * *
2793325 ATTTTTAAAAAATTTTAATAAAATATTTA
1 AATTATAAAAAATTTTAATATAATATTTA
*
2793354 AATTATAAATATATTAATTAATATAATATTTA
1 AATTATAAA-AAATT--TTAATATAATATTTA
2793386 AA
1 AA
2793388 AAATTATTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 21 0.40
30 10 0.19
31 5 0.10
32 16 0.31
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
AATTATAAAAAATTTTAATATAATATTTA
Found at i:2793481 original size:15 final size:16
Alignment explanation
Indices: 2793457--2793490 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2793447 ATTCAAGCAA
2793457 AATCACATT-AAAATT
1 AATCACATTAAAAATT
*
2793472 AATCATATTAAAAATT
1 AATCACATTAAAAATT
2793488 AAT
1 AAT
2793491 ATCAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
AATCACATTAAAAATT
Found at i:2793537 original size:28 final size:28
Alignment explanation
Indices: 2793500--2793561 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2793490 TATCAAATTA
*
2793500 ATTAATAAA-TTTATAAGTTAAATATCAT
1 ATTAAAAAATTTTA-AAGTTAAATATCAT
* *
2793528 ATTAAAAAATTTTAAATTTAAATATTAT
1 ATTAAAAAATTTTAAAGTTAAATATCAT
2793556 ATTAAA
1 ATTAAA
2793562 TACTTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
ATTAAAAAATTTTAAAGTTAAATATCAT
Found at i:2794003 original size:8 final size:8
Alignment explanation
Indices: 2793982--2794022 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
2793972 TATTATTTTT
2793982 TAAATATA
1 TAAATATA
2793990 -AAATATA
1 TAAATATA
2793997 TAAATATA
1 TAAATATA
*
2794005 TAATTATA
1 TAAATATA
2794013 TAAATATA
1 TAAATATA
2794021 TA
1 TA
2794023 TAAATAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAAATATA
Found at i:2794014 original size:16 final size:16
Alignment explanation
Indices: 2793961--2794022 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 16
2793951 TTCGACTCGA
2793961 AATTA-ATAAAT-TAT
1 AATTATATAAATATAT
* * *
2793975 TATTTTTTAAATATA-
1 AATTATATAAATATAT
*
2793990 AAATATATAAATATAT
1 AATTATATAAATATAT
2794006 AATTATATAAATATAT
1 AATTATATAAATATAT
2794022 A
1 A
2794023 TAAATAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
14 3 0.08
15 16 0.43
16 18 0.49
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATATAAATATAT
Found at i:2794026 original size:10 final size:10
Alignment explanation
Indices: 2793985--2794028 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 10
2793975 TATTTTTTAA
2793985 ATATAAA-AT
1 ATATAAATAT
2793994 ATAT-AA-AT
1 ATATAAATAT
2794002 ATAT-AAT-T
1 ATATAAATAT
2794010 ATATAAATAT
1 ATATAAATAT
2794020 ATATAAATA
1 ATATAAATA
2794029 AAATTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.47
9 7 0.22
10 10 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATAAATAT
Found at i:2794726 original size:40 final size:40
Alignment explanation
Indices: 2794671--2794750 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
2794661 AAAGAAAGAA
2794671 AGAATTTATAGACAGAGGGTCTTCTTATATGTGATAAGGC
1 AGAATTTATAGACAGAGGGTCTTCTTATATGTGATAAGGC
2794711 AGAATTTATAGACAGAGGGTCTTCTTATATGTGATAAGGC
1 AGAATTTATAGACAGAGGGTCTTCTTATATGTGATAAGGC
2794751 TCACCTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (40 bp):
AGAATTTATAGACAGAGGGTCTTCTTATATGTGATAAGGC
Found at i:2799209 original size:83 final size:83
Alignment explanation
Indices: 2799070--2799234 Score: 217
Period size: 83 Copynumber: 2.0 Consensus size: 83
2799060 AGAAAATAAT
* * * *
2799070 TAAGAAATTACTGTCTCTCAATACCAATTATTCATTTGCTTCCTTATTTTATCCTATTTTTAGAA
1 TAAGAAATTACCGTCTCTCAATACCAATTATTCATTGGCATCCTTATTTTATCCTATTTTGAGAA
2799135 TATGGAGTC-GTTGAGAAA
66 TATGGAG-CAGTTGAGAAA
* ** * *
2799153 TAAGAAATTACCGTCTCTCAGTGTCAATTGTTC-TCTGGCATCCTTATTTTATCCTATTTTGGGA
1 TAAGAAATTACCGTCTCTCAATACCAATTATTCAT-TGGCATCCTTATTTTATCCTATTTTGAGA
2799217 ATATGGAGCAGTTGAGAA
65 ATATGGAGCAGTTGAGAA
2799235 CACTTCTGGA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
82 2 0.03
83 69 0.97
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (83 bp):
TAAGAAATTACCGTCTCTCAATACCAATTATTCATTGGCATCCTTATTTTATCCTATTTTGAGAA
TATGGAGCAGTTGAGAAA
Found at i:2801245 original size:17 final size:17
Alignment explanation
Indices: 2801220--2801260 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 17
2801210 ATTTCCTAAT
2801220 TATTATATATTTATTTTTA
1 TATTATATATTTA--TTTA
2801239 TATTATATATTTATTTA
1 TATTATATATTTATTTA
2801256 TATTA
1 TATTA
2801261 ATAAATAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.41
19 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATATATTTATTTA
Found at i:2802316 original size:26 final size:25
Alignment explanation
Indices: 2802267--2802322 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
2802257 TTTTTTATCG
*
2802267 TAATTATAAAAATATCCTCTTATTA
1 TAATTATAAAAATATCCTCATATTA
*
2802292 TAATTATAAAAATACTTCTCATATTA
1 TAATTATAAAAATA-TCCTCATATTA
2802318 TAATT
1 TAATT
2802323 GGTTATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (25 bp):
TAATTATAAAAATATCCTCATATTA
Found at i:2803664 original size:61 final size:60
Alignment explanation
Indices: 2803525--2803702 Score: 169
Period size: 61 Copynumber: 2.9 Consensus size: 60
2803515 ATCTTTTTTA
* ** * *
2803525 AAAAATTAGACGGGATTATTGAATGTATTTTTGATCAAAAATACCTTTAATAATCTCCTCAT
1 AAAAATT-GAAGGGATTATTGAATGCGTTTTTGCT-AAAAACACCTTTAATAATCTCCTCAT
* * * **
2803587 CAAAATTGAAGTGATTATTGAATGCGTTTTTGCTAAAAACACCTTCAATAATC-CCTTGT
1 AAAAATTGAAGGGATTATTGAATGCGTTTTTGCTAAAAACACCTTTAATAATCTCCTCAT
* * * **
2803646 AAAAAATTTAAGAGGATTATTAAAGGCGTTTTTTGCTTGAAACACCTTTAATAATCT
1 -AAAAATTGAAG-GGATTATTGAATGCG-TTTTTGCTAAAAACACCTTTAATAATCT
2803703 TTTTTGCAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
59 4 0.04
60 26 0.28
61 34 0.36
62 30 0.32
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (60 bp):
AAAAATTGAAGGGATTATTGAATGCGTTTTTGCTAAAAACACCTTTAATAATCTCCTCAT
Found at i:2807249 original size:42 final size:41
Alignment explanation
Indices: 2807196--2807368 Score: 118
Period size: 42 Copynumber: 4.1 Consensus size: 41
2807186 TATGATGGCA
* * *
2807196 AAAATTTTATCAATGATTACTAAAATTATATGAAAAGTTATC
1 AAAATTATATCAATGATTA-TAAAATTATATTAAAAGTTACC
* * * * *
2807238 AAAATTATATCAAGAGATTACCAAAATT-TAATAAAAAATTATC
1 AAAATTATATCAA-TGATTA-TAAAATTAT-ATTAAAAGTTACC
* * * * *
2807281 -AAATATGTATCAATGGTTAAAAAAATATATTATAAGTTACC
1 AAAAT-TATATCAATGATTATAAAATTATATTAAAAGTTACC
* * *
2807322 AAACTAATAATTAA-GATTATCAAAATTATATTAAAAGTTACC
1 AAAATTAT-ATCAATGATTAT-AAAATTATATTAAAAGTTACC
2807364 AAAAT
1 AAAAT
2807369 GTTTTCAAAG
Statistics
Matches: 101, Mismatches: 23, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
41 19 0.19
42 52 0.51
43 30 0.30
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (41 bp):
AAAATTATATCAATGATTATAAAATTATATTAAAAGTTACC
Found at i:2807293 original size:43 final size:43
Alignment explanation
Indices: 2807196--2807283 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
2807186 TATGATGGCA
* * * * *
2807196 AAAATTTTATCAA-TGATTACTAAAATTATATGAAAAGTTATC
1 AAAATTATATCAAGAGATTACCAAAATTATATAAAAAATTATC
2807238 AAAATTATATCAAGAGATTACCAAAATT-TAATAAAAAATTATC
1 AAAATTATATCAAGAGATTACCAAAATTAT-ATAAAAAATTATC
2807281 AAA
1 AAA
2807284 TATGTATCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 13 0.33
43 26 0.67
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (43 bp):
AAAATTATATCAAGAGATTACCAAAATTATATAAAAAATTATC
Found at i:2807367 original size:21 final size:21
Alignment explanation
Indices: 2807212--2807368 Score: 79
Period size: 21 Copynumber: 7.5 Consensus size: 21
2807202 TTATCAATGA
* *
2807212 TTACTAAAATTATATGAAAAG
1 TTACCAAAATTATATTAAAAG
* * *
2807233 TTATCAAAATTATATCAAGAG
1 TTACCAAAATTATATTAAAAG
* *
2807254 ATTACCAAAATT-TAATAAAAAA
1 -TTACCAAAATTAT-ATTAAAAG
* * * **
2807276 TTATC-AAATATGTATCAATGG
1 TTACCAAAAT-TATATTAAAAG
* * *
2807297 TTA-AAAAAATATATTATAAG
1 TTACCAAAATTATATTAAAAG
* * *
2807317 TTACCAAACTAATAATTAAGA-
1 TTACCAAAATTAT-ATTAAAAG
*
2807338 TTATCAAAATTATATTAAAAG
1 TTACCAAAATTATATTAAAAG
2807359 TTACCAAAAT
1 TTACCAAAAT
2807369 GTTTTCAAAG
Statistics
Matches: 97, Mismatches: 31, Indels: 16
0.67 0.22 0.11
Matches are distributed among these distances:
20 19 0.20
21 57 0.59
22 21 0.22
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.33
Consensus pattern (21 bp):
TTACCAAAATTATATTAAAAG
Found at i:2813077 original size:12 final size:12
Alignment explanation
Indices: 2813045--2813091 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
2813035 TCTGTTAATT
2813045 AAAAT-AAATAA
1 AAAATAAAATAA
2813056 ATAAATAAAATAA
1 A-AAATAAAATAA
*
2813069 AAAATAAAACGAA
1 AAAATAAAA-TAA
*
2813082 AAAAGAAAAT
1 AAAATAAAAT
2813092 CAATAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 1 0.03
12 12 0.40
13 17 0.57
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:2820104 original size:18 final size:17
Alignment explanation
Indices: 2820090--2820164 Score: 91
Period size: 16 Copynumber: 4.4 Consensus size: 17
2820080 ATGAAAATGA
*
2820090 AAAAAATGAAAAAAATAA
1 AAAAAAT-AAAAAAATAT
2820108 AAAAAATATAAAAAATAT
1 AAAAAATA-AAAAAATAT
*
2820126 AAAAAAT-ATAAAATAT
1 AAAAAATAAAAAAATAT
*
2820142 AAAATAT-AAAAAATAT
1 AAAAAATAAAAAAATAT
2820158 AAAAAAT
1 AAAAAAT
2820165 GTAAAAAGAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
16 28 0.55
17 1 0.02
18 22 0.43
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.20
Consensus pattern (17 bp):
AAAAAATAAAAAAATAT
Found at i:2820109 original size:7 final size:7
Alignment explanation
Indices: 2820099--2820162 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
2820089 AAAAAAATGA
2820099 AAAAAAT
1 AAAAAAT
2820106 AAAAAA-
1 AAAAAAT
*
2820112 AATATAA-
1 AA-AAAAT
*
2820119 AAAATAT
1 AAAAAAT
2820126 AAAAAAT
1 AAAAAAT
2820133 ATAAAATAT
1 A-AAAA-AT
*
2820142 AAAATAT
1 AAAAAAT
2820149 AAAAAAT
1 AAAAAAT
2820156 ATAAAAA
1 A-AAAAA
2820163 ATGTAAAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
6 4 0.09
7 27 0.59
8 12 0.26
9 3 0.07
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAAAAAT
Found at i:2820109 original size:15 final size:15
Alignment explanation
Indices: 2820075--2820155 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 15
2820065 ATAATGGGTG
*
2820075 AAAAAATGAAAATGA
1 AAAAAATGAAAATAA
2820090 AAAAAATGAAAA-AA
1 AAAAAATGAAAATAA
2820104 ATAAAAA--AAATATAA
1 A-AAAAATGAAA-ATAA
* * *
2820119 AAAATATAAAAAATAT
1 AAAAAAT-GAAAATAA
* *
2820135 AAAATAT-AAAATAT
1 AAAAAATGAAAATAA
2820149 AAAAAAT
1 AAAAAAT
2820156 ATAAAAAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
13 3 0.05
14 20 0.36
15 20 0.36
16 10 0.18
17 3 0.05
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
AAAAAATGAAAATAA
Found at i:2820151 original size:32 final size:32
Alignment explanation
Indices: 2820110--2820170 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
2820100 AAAAATAAAA
2820110 AAAATATAAAAAATATAAAAAATATAAAATAT
1 AAAATATAAAAAATATAAAAAATATAAAATAT
*
2820142 AAAATATAAAAAATATAAAAAATGTAAAA
1 AAAATATAAAAAATATAAAAAATATAAAA
2820171 AGAGAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (32 bp):
AAAATATAAAAAATATAAAAAATATAAAATAT
Found at i:2820164 original size:9 final size:9
Alignment explanation
Indices: 2820090--2820171 Score: 102
Period size: 9 Copynumber: 9.6 Consensus size: 9
2820080 ATGAAAATGA
2820090 AAAAAATGA-
1 AAAAAAT-AT
*
2820099 AAAAAATAA
1 AAAAAATAT
2820108 AAAAAATAT
1 AAAAAATAT
2820117 AAAAAATAT
1 AAAAAATAT
2820126 AAAAAATAT
1 AAAAAATAT
2820135 --AAAATAT
1 AAAAAATAT
2820142 --AAAATAT
1 AAAAAATAT
2820149 AAAAAATAT
1 AAAAAATAT
*
2820158 AAAAAATGT
1 AAAAAATAT
2820167 AAAAA
1 AAAAA
2820172 GAGAGAAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
7 14 0.21
8 1 0.01
9 53 0.78
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (9 bp):
AAAAAATAT
Found at i:2821123 original size:33 final size:33
Alignment explanation
Indices: 2821081--2821148 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
2821071 TGACATTTGC
***
2821081 ATAGCATGCATTACATTTTTTAATGTTTAGTGT
1 ATAGCATGCATTACATTTAAGAATGTTTAGTGT
*
2821114 ATAGCATGCATTGCATTTAAGAATGTTTAGTGT
1 ATAGCATGCATTACATTTAAGAATGTTTAGTGT
2821147 AT
1 AT
2821149 GAATTTAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (33 bp):
ATAGCATGCATTACATTTAAGAATGTTTAGTGT
Found at i:2821590 original size:44 final size:44
Alignment explanation
Indices: 2821454--2821728 Score: 220
Period size: 44 Copynumber: 6.3 Consensus size: 44
2821444 AAGCCGTAAA
* * *
2821454 CCTC-ATTTAGAAGG-GCCTTATTTA-TTTTTCAAAGTCA-TGAG
1 CCTCTATTTAG-AGGAGCTTTATTTATTTTTTAAAAGTTATTGAG
* * * * * * ** *
2821495 CCTTTGTTTAAAGCAACTTTATTTA-TTTTTCAAAGTCGTTGAA
1 CCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAG
2821538 CCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAG
1 CCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAG
* * * * *
2821582 CCTTTATTTAAAGAAGCTTTATTTATTTTTCAAAAATTATTGAG
1 CCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAG
* * *
2821626 CCTCTGTTTAGAAGAGCCTTTATTTATTTTTT-AAAGTTATTGAA
1 CCTCTATTTAGAGGAG-CTTTATTTATTTTTTAAAAGTTATTGAG
* ** * * * * *
2821670 CCTCTACTTAGAAAAGATTTATTTATTTCTCAAAAGTTGTGGAG
1 CCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAG
* *
2821714 TCTCTATTTGGAGGA
1 CCTCTATTTAGAGGA
2821729 ATTTTATATT
Statistics
Matches: 184, Mismatches: 44, Indels: 9
0.78 0.19 0.04
Matches are distributed among these distances:
41 5 0.03
42 24 0.13
43 35 0.19
44 106 0.58
45 14 0.08
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (44 bp):
CCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAG
Found at i:2821592 original size:87 final size:86
Alignment explanation
Indices: 2821426--2821703 Score: 307
Period size: 88 Copynumber: 3.2 Consensus size: 86
2821416 ATTATTGAAG
* * * *
2821426 AGCTTTATTTATTTTTCAAAGCCG-TAAACCTC-ATTTAGAAGG-GCCTTATTTATTTTTCAAAG
1 AGCTTTATTTATTTTTCAAAGTCGTTGAACCTCTATTTAG-AGGAGCTTTATTTATTTTTTAAAG
* *
2821488 TCA-TGAGCCTTTGTTTAAAGCA
65 TTATTGAGCCTTTATTTAAAG-A
2821510 A-CTTTATTTATTTTTCAAAGTCGTTGAACCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAAG
1 AGCTTTATTTATTTTTCAAAGTCGTTGAACCTCTATTTAGAGGAGCTTTATTTATTTTTT-AAAG
2821574 TTATTGAGCCTTTATTTAAAGA
65 TTATTGAGCCTTTATTTAAAGA
* ** * * *
2821596 AGCTTTATTTATTTTTCAAAAATTATTGAGCCTCTGTTTAGAAGAGCCTTTATTTATTTTTTAAA
1 AGCTTTATTTATTTTTC-AAAGTCGTTGAACCTCTATTTAGAGGAG-CTTTATTTATTTTTTAAA
* * *
2821661 GTTATTGAACCTCTACTTAGAA-A
64 GTTATTGAGCCTTTATTTA-AAGA
* *
2821684 AGATTTATTTATTTCTCAAA
1 AGCTTTATTTATTTTTCAAA
2821704 AGTTGTGGAG
Statistics
Matches: 168, Mismatches: 17, Indels: 15
0.84 0.09 0.08
Matches are distributed among these distances:
83 21 0.12
84 11 0.07
85 20 0.12
86 8 0.05
87 34 0.20
88 57 0.34
89 17 0.10
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (86 bp):
AGCTTTATTTATTTTTCAAAGTCGTTGAACCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAGT
TATTGAGCCTTTATTTAAAGA
Found at i:2821669 original size:132 final size:129
Alignment explanation
Indices: 2821471--2821707 Score: 314
Period size: 132 Copynumber: 1.8 Consensus size: 129
2821461 TAGAAGGGCC
* * *
2821471 TTATTTATTTTTCAAAGTCATGAGCCTTTGTTTAAAGCAACTTTATTTATTTTTCAAAGTCGTTG
1 TTATTTATTTTTCAAAATCATGAGCCTCTGTTTAAAGCAACTTTATTTATTTTTCAAAGTCATTG
* ** * * *
2821536 AACCTCTATTTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAGCCTTTATTTAAAGAAGCT
66 AACCTCTACTTAGAAAAGATTTATTTATTTCTCAAAAGTTATTGAGCCTTTATTTAAAGAAGCT
* * * *
2821600 TTATTTATTTTTCAAAAATTATTGAGCCTCTGTTTAGAAG-AGCCTTTATTTATTTTTTAAAGTT
1 TTATTTATTTTTC-AAAATCA-TGAGCCTCTGTTTA-AAGCA-ACTTTATTTATTTTTCAAAGTC
2821664 ATTGAACCTCTACTTAGAAAAGATTTATTTATTTCTCAAAAGTT
62 ATTGAACCTCTACTTAGAAAAGATTTATTTATTTCTCAAAAGTT
2821708 GTGGAGTCTC
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
129 13 0.14
130 5 0.05
131 14 0.15
132 59 0.65
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (129 bp):
TTATTTATTTTTCAAAATCATGAGCCTCTGTTTAAAGCAACTTTATTTATTTTTCAAAGTCATTG
AACCTCTACTTAGAAAAGATTTATTTATTTCTCAAAAGTTATTGAGCCTTTATTTAAAGAAGCT
Found at i:2822808 original size:20 final size:18
Alignment explanation
Indices: 2822773--2822814 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
2822763 TTAAATTTTA
*
2822773 AAAAAATTACAAAAAAAT
1 AAAAAATTAAAAAAAAAT
2822791 AAAAAATATAAAACAAAAAT
1 AAAAAAT-TAAAA-AAAAAT
2822811 AAAA
1 AAAA
2822815 TATTTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 4 0.19
20 10 0.48
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAATTAAAAAAAAAT
Found at i:2822889 original size:25 final size:25
Alignment explanation
Indices: 2822844--2822892 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2822834 ATAATTATCC
*
2822844 AATGATGAAATTTTGAGAAATTTCA
1 AATGATGAAATTTTGAAAAATTTCA
*
2822869 AATGAT-AAATTTTTATAAAATTTC
1 AATGATGAAATTTTGA-AAAATTTC
2822893 TAGGTGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (25 bp):
AATGATGAAATTTTGAAAAATTTCA
Found at i:2823248 original size:40 final size:40
Alignment explanation
Indices: 2823203--2823286 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
2823193 CCAAAGAATA
*
2823203 AAAAAAAAATTATAAATAGACCCAAATGGTGAAAAATTTAG
1 AAAAAAAAA-TATAAATAGACCCAAATGATGAAAAATTTAG
* * * *
2823244 AAAAAAAAATCTAAATTGACCCAAATTATGGAAAATTTAG
1 AAAAAAAAATATAAATAGACCCAAATGATGAAAAATTTAG
2823284 AAA
1 AAA
2823287 TAGAAATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 29 0.76
41 9 0.24
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23
Consensus pattern (40 bp):
AAAAAAAAATATAAATAGACCCAAATGATGAAAAATTTAG
Found at i:2828702 original size:42 final size:42
Alignment explanation
Indices: 2828527--2828936 Score: 213
Period size: 43 Copynumber: 9.3 Consensus size: 42
2828517 CTCCACGACT
* * * * * *
2828527 TTTAAAAAATAAATAAAGTTCCTATAAACATATGCTCAACAAC
1 TTTAAAAAATAAATAAGGCTCCTCTAATCA-AAGCTCTACAAC
** *
2828570 TTTGGAAAATAAATAAGGCTCCTCTAAGCAAAAGCT-TA-ATGAC
1 TTTAAAAAATAAATAAGGCTCCTCTAATC-AAAGCTCTACA--AC
* * *
2828613 TTTTGAAAAAATAAATAAGGCACCTCTAAAT-AGAGGCT-TAACGAC
1 -TTT-AAAAAATAAATAAGGCTCCTCT-AATCA-AAGCTCT-ACAAC
*
2828658 TTT-AAAAATAAATAAGGCTCCTCTAATCAGAACCTCTACAAC
1 TTTAAAAAATAAATAAGGCTCCTCTAATCA-AAGCTCTACAAC
* * *
2828700 TTTGGAAAACAAATCCAAATAAATAAGGCTCTTCTAATCAAAGGTTCAACAAC
1 TTT-------AAA---AAATAAATAAGGCTCCTCTAATCAAA-GCTCTACAAC
* * *
2828753 TTTGAAAAATAAATAAAGCTCATCTAAT-AAGATGCTCTACAAC
1 TTTAAAAAATAAATAAGGCTCCTCTAATCAA-A-GCTCTACAAC
** * * * * *
2828796 TTTGGAAAATAAATAAAGCCCCTCTAAACAAAGGCTCAAAAAC
1 TTTAAAAAATAAATAAGGCTCCTCTAATCAAA-GCTCTACAAC
* * * * * *
2828839 TTTAAAAAATAAATAAGACTCTTCTAAACATAGGCTCAACGAC
1 TTTAAAAAATAAATAAGGCTCCTCTAATCA-AAGCTCTACAAC
* * * *
2828882 TTT-AAAAATAAATAATGCTTCTCTAATTAAAGACTCTACGAC
1 TTTAAAAAATAAATAAGGCTCCTCTAATCAAAG-CTCTACAAC
2828924 TTTAAAAAATAAA
1 TTTAAAAAATAAA
2828937 AAAAGCTCAT
Statistics
Matches: 287, Mismatches: 52, Indels: 56
0.73 0.13 0.14
Matches are distributed among these distances:
41 6 0.02
42 66 0.23
43 136 0.47
44 11 0.04
45 26 0.09
46 5 0.02
50 2 0.01
52 2 0.01
53 33 0.11
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (42 bp):
TTTAAAAAATAAATAAGGCTCCTCTAATCAAAGCTCTACAAC
Found at i:2828752 original size:53 final size:53
Alignment explanation
Indices: 2828663--2828766 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
2828653 ACGACTTTAA
* *
2828663 AAATAAATAAGGCTCCTCTAATCAGAACCTCTACAACTTTGGAAAACAAATCC
1 AAATAAATAAGGCTCCTCTAATCAGAACCTCAACAACTTTGAAAAACAAATCC
* ** *
2828716 AAATAAATAAGGCTCTTCTAATCA-AAGGTTCAACAACTTTGAAAAATAAAT
1 AAATAAATAAGGCTCCTCTAATCAGAA-CCTCAACAACTTTGAAAAACAAAT
2828767 AAAGCTCATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
52 2 0.05
53 42 0.95
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (53 bp):
AAATAAATAAGGCTCCTCTAATCAGAACCTCAACAACTTTGAAAAACAAATCC
Found at i:2828765 original size:43 final size:43
Alignment explanation
Indices: 2828716--2828944 Score: 214
Period size: 43 Copynumber: 5.3 Consensus size: 43
2828706 AAACAAATCC
* * *
2828716 AAATAAATAAGGCTCTTCTAATCAAAGGTTCAACAACTTTGAA
1 AAATAAATAAAGCTCTTCTAATCAAAGGCTCAACAACTTTAAA
* * * **
2828759 AAATAAATAAAGCTCATCTAAT-AAGATGCTCTACAACTTTGGA
1 AAATAAATAAAGCTCTTCTAATCAA-AGGCTCAACAACTTTAAA
* * * *
2828802 AAATAAATAAAGCCCCTCTAAACAAAGGCTCAAAAACTTTAAA
1 AAATAAATAAAGCTCTTCTAATCAAAGGCTCAACAACTTTAAA
* * *
2828845 AAATAAAT-AAGACTCTTCTAAACATAGGCTCAACGACTTT-AA
1 AAATAAATAAAG-CTCTTCTAATCAAAGGCTCAACAACTTTAAA
* * * * *
2828887 AAATAAATAATGCT-TCTCTAATTAAAGACTCTACGACTTTAAA
1 AAATAAATAAAGCTCT-TCTAATCAAAGGCTCAACAACTTTAAA
*
2828930 AAATAAAAAAAGCTC
1 AAATAAATAAAGCTC
2828945 ATCGAGAACA
Statistics
Matches: 152, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.01
42 36 0.24
43 113 0.74
44 2 0.01
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (43 bp):
AAATAAATAAAGCTCTTCTAATCAAAGGCTCAACAACTTTAAA
Found at i:2828791 original size:96 final size:95
Alignment explanation
Indices: 2828621--2828809 Score: 247
Period size: 96 Copynumber: 2.0 Consensus size: 95
2828611 ACTTTTGAAA
* * * * *
2828621 AAATAAATAAGGCACCTCTAAATAGAGGCTTAACGACTTTAAAAATAAATAAGGCTCCTCTAATC
1 AAATAAATAAGGCACCTCTAAATAAAGGCTTAACAACTTTAAAAATAAATAAAGCTCATCTAATA
2828686 AGAACCTCTACAACTTTGGAAAACAAATCC
66 AGAACCTCTACAACTTTGGAAAACAAATCC
* *
2828716 AAATAAATAAGGCTCTTCT-AATCAAAGG-TTCAACAACTTTGAAAAATAAATAAAGCTCATCTA
1 AAATAAATAAGGCACCTCTAAAT-AAAGGCTT-AACAACTTT-AAAAATAAATAAAGCTCATCTA
** *
2828779 ATAAGATGCTCTACAACTTTGGAAAATAAAT
63 ATAAGAACCTCTACAACTTTGGAAAACAAAT
2828810 AAAGCCCCTC
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
94 5 0.06
95 29 0.36
96 47 0.58
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (95 bp):
AAATAAATAAGGCACCTCTAAATAAAGGCTTAACAACTTTAAAAATAAATAAAGCTCATCTAATA
AGAACCTCTACAACTTTGGAAAACAAATCC
Found at i:2828840 original size:139 final size:140
Alignment explanation
Indices: 2828576--2828841 Score: 292
Period size: 139 Copynumber: 1.9 Consensus size: 140
2828566 CAACTTTGGA
** * *
2828576 AAATAAATAAGGCTCCTCTAAGCAAAAGCTTAATGACTTTTGAAAAAATAAATAAGGCACCTCTA
1 AAATAAATAAGGCTCCTCTAAGCAAAAGCTTAACAACTTTTGAAAAAATAAATAAAGCACATCTA
* * * * * *
2828641 AATAGAGGCTTAACGACTTTAAAAATAAATAAGGCTCCTCTAATCAGAACCTCTACAACTTTGGA
66 AATAGAGGCTTAACAACTTTAAAAATAAATAAAGCCCCTCTAAACAGAACCTCAAAAACTTTGGA
2828706 AAACAAATCC
131 AAACAAATCC
* * * *
2828716 AAATAAATAAGGCTCTTCTAATC-AAAGGTTCAACAAC-TTTG-AAAAATAAATAAAGCTCATCT
1 AAATAAATAAGGCTCCTCTAAGCAAAAGCTT-AACAACTTTTGAAAAAATAAATAAAGCACATCT
* * *
2828778 -AATAAGATGCTCT-ACAACTTTGGAAAATAAATAAAGCCCCTCTAAACA-AAGGCTCAAAAACT
65 AAAT-AGAGGCT-TAACAACTTT-AAAAATAAATAAAGCCCCTCTAAACAGAA-CCTCAAAAACT
2828840 TT
126 TT
2828842 AAAAAATAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
137 3 0.03
138 33 0.32
139 43 0.41
140 25 0.24
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (140 bp):
AAATAAATAAGGCTCCTCTAAGCAAAAGCTTAACAACTTTTGAAAAAATAAATAAAGCACATCTA
AATAGAGGCTTAACAACTTTAAAAATAAATAAAGCCCCTCTAAACAGAACCTCAAAAACTTTGGA
AAACAAATCC
Found at i:2830493 original size:25 final size:24
Alignment explanation
Indices: 2830465--2830535 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
2830455 TCTTTCGTTC
2830465 TCTTTTTTTTTTTCTTTTTTATTTA
1 TCTTTTTTTTTTT-TTTTTTATTTA
* *
2830490 TCTTTTTTTTTCATTTTTTTCATTTT
1 TCTTTTTTTTT--TTTTTTTTATTTA
*
2830516 TCATTTTTTTATTTTTTTTT
1 TC-TTTTTTTTTTTTTTTTT
2830536 GTTTTTTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 18 0.46
26 11 0.28
27 10 0.26
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (24 bp):
TCTTTTTTTTTTTTTTTTTATTTA
Found at i:2830523 original size:16 final size:15
Alignment explanation
Indices: 2830471--2830531 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
2830461 GTTCTCTTTT
* *
2830471 TTTTTTTCTTTTTTA
1 TTTTTTTATTTTTCA
*
2830486 TTTATCTTTTTTTTTCA
1 TTT-T-TTTATTTTTCA
2830503 TTTTTTTCATTTTTCA
1 TTTTTTT-ATTTTTCA
2830519 TTTTTTTATTTTT
1 TTTTTTTATTTTT
2830532 TTTTGTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.30
16 16 0.40
17 12 0.30
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTATTTTTCA
Found at i:2830540 original size:25 final size:23
Alignment explanation
Indices: 2830468--2830541 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 23
2830458 TTCGTTCTCT
*
2830468 TTTTTTTTTTCTTTTTTATTTATC
1 TTTTTTTTTT-TTTTTTATTTTTC
2830492 TTTTTTTTTCATTTTTTTCATTTTTC
1 TTTTTTTTT--TTTTTTT-ATTTTTC
*
2830518 ATTTTTTTATTTTTTTTTGTTTTT
1 -TTTTTTT-TTTTTTTTTATTTTT
2830542 TCATCCATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
24 9 0.21
25 11 0.26
26 14 0.33
27 7 0.16
28 2 0.05
ACGTcount: A:0.08, C:0.07, G:0.01, T:0.84
Consensus pattern (23 bp):
TTTTTTTTTTTTTTTTATTTTTC
Found at i:2830742 original size:71 final size:73
Alignment explanation
Indices: 2830619--2830756 Score: 199
Period size: 71 Copynumber: 1.9 Consensus size: 73
2830609 ACAAGCATGC
* * * *
2830619 TTTCTGTCAATAAAGAAAGTTTTTTTTTTCTGGTGATAATGATTTAAGTGTATCTATTGTCTGTT
1 TTTCTATCAATAAAAAAAG-TTTTTTTTTCTGGTGATAATGATTTAAGTGTATCTATTATCTATT
2830684 CATCCTCTG
65 CATCCTCTG
* *
2830693 TTTCTATCAATAAAAAAAG-TTTTTTTT-TGTTGATAATGATTTGAGTGTATCTATTATCTATTC
1 TTTCTATCAATAAAAAAAGTTTTTTTTTCTGGTGATAATGATTTAAGTGTATCTATTATCTATTC
2830756 A
66 A
2830757 AATTCGTAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 33 0.57
72 8 0.14
74 17 0.29
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (73 bp):
TTTCTATCAATAAAAAAAGTTTTTTTTTCTGGTGATAATGATTTAAGTGTATCTATTATCTATTC
ATCCTCTG
Found at i:2830935 original size:18 final size:18
Alignment explanation
Indices: 2830914--2831019 Score: 167
Period size: 18 Copynumber: 5.9 Consensus size: 18
2830904 AAGTATTTTA
2830914 TTTTAGTTTCATTATTTC
1 TTTTAGTTTCATTATTTC
2830932 TTTTAGTTTCATTATTTC
1 TTTTAGTTTCATTATTTC
* * *
2830950 TTTTAATTTTATCATTTC
1 TTTTAGTTTCATTATTTC
2830968 TTTTAGTTTCATTATTTC
1 TTTTAGTTTCATTATTTC
*
2830986 TTTTAATTTCATTATTTC
1 TTTTAGTTTCATTATTTC
*
2831004 TTTTACTTTCATTATT
1 TTTTAGTTTCATTATT
2831020 AATTTCATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 80 1.00
ACGTcount: A:0.19, C:0.11, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTAGTTTCATTATTTC
Found at i:2831045 original size:12 final size:12
Alignment explanation
Indices: 2831010--2831045 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2831000 TTTCTTTTAC
*
2831010 TTTCATTATTAA
1 TTTCATTATTAG
2831022 TTTCATTATTAG
1 TTTCATTATTAG
2831034 TTTCATTATTAG
1 TTTCATTATTAG
2831046 AGAATCGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (12 bp):
TTTCATTATTAG
Found at i:2837654 original size:22 final size:21
Alignment explanation
Indices: 2837622--2837664 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2837612 TTTTATTTTT
*
2837622 TTAAGTTACATCAATCTAATTA
1 TTAAGTAACATCAATC-AATTA
*
2837644 TTAAGTAACATTAATCAATTA
1 TTAAGTAACATCAATCAATTA
2837665 ATTTTTTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (21 bp):
TTAAGTAACATCAATCAATTA
Found at i:2838467 original size:13 final size:13
Alignment explanation
Indices: 2838444--2838490 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
2838434 GAATTTTATT
2838444 TAAAGAAAATAAAA
1 TAAA-AAAATAAAA
2838458 TAAAAAAATAAAA
1 TAAAAAAATAAAA
*
2838471 -ATAAAAATAGAAA
1 TAAAAAAATA-AAA
2838484 TAAAAAA
1 TAAAAAA
2838491 TATTAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 12 0.41
14 9 0.31
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:2838470 original size:6 final size:6
Alignment explanation
Indices: 2838449--2838489 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
2838439 TTATTTAAAG
* *
2838449 AAAATA AAATAAA AAAATA AAAATA AAAATA GAAATA AAAA
1 AAAATA AAA-ATA AAAATA AAAATA AAAATA AAAATA AAAA
2838490 ATATTAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:2838471 original size:14 final size:14
Alignment explanation
Indices: 2838444--2838490 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2838434 GAATTTTATT
2838444 TAAAGAAAAT-AAAA
1 TAAA-AAAATAAAAA
2838458 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
*
2838472 T--AAAAATAGAAA
1 TAAAAAAATAAAAA
2838484 TAAAAAA
1 TAAAAAA
2838491 TATTAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 11 0.38
13 5 0.17
14 13 0.45
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:2838512 original size:3 final size:3
Alignment explanation
Indices: 2838504--2838535 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2838494 TAAACAATCC
2838504 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2838536 AAACCTGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2839383 original size:22 final size:23
Alignment explanation
Indices: 2839332--2839396 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
2839322 TAGATAGACC
*
2839332 ATAAAAA-AAATAAAAATGATAAAT
1 ATAAAAATAAA-AAAAAT-CTAAAT
*
2839356 ACAAAAATAAAAAAAATCTAAA-
1 ATAAAAATAAAAAAAATCTAAAT
*
2839378 ATAAAAATGAATAAAAATC
1 ATAAAAAT-AAAAAAAATC
2839397 CCTACACCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 7 0.20
23 13 0.37
24 12 0.34
25 3 0.09
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (23 bp):
ATAAAAATAAAAAAAATCTAAAT
Found at i:2839665 original size:45 final size:44
Alignment explanation
Indices: 2839610--2839774 Score: 208
Period size: 44 Copynumber: 3.7 Consensus size: 44
2839600 GCTCAACGAT
* * *
2839610 AGAGACTCAACAACTTGAAAAAAATAAACAAAGGCTCCTCTAAAT
1 AGAGGCTCAACAACTTG-AAAAAATAAATAAAGGCTCCTCTAAAC
* *
2839655 AGAGGTTCAACGACTTTGAAAAAATAAATAAA-GCTCCTCTAAAC
1 AGAGGCTCAACAAC-TTGAAAAAATAAATAAAGGCTCCTCTAAAC
*
2839699 AGAGGCTCAACAACTTCGAAAAAATAAATAAAGGCTCCTCTAAGC
1 AGAGGCTCAACAACTT-GAAAAAATAAATAAAGGCTCCTCTAAAC
* *
2839744 AGAGGCTC-ACGACTTTGGAAAAATAAATAAA
1 AGAGGCTCAACAAC-TTGAAAAAATAAATAAA
2839775 TTCTCTAAGC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
43 2 0.02
44 56 0.53
45 45 0.42
46 3 0.03
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (44 bp):
AGAGGCTCAACAACTTGAAAAAATAAATAAAGGCTCCTCTAAAC
Found at i:2839765 original size:89 final size:88
Alignment explanation
Indices: 2839610--2839774 Score: 244
Period size: 89 Copynumber: 1.9 Consensus size: 88
2839600 GCTCAACGAT
* *
2839610 AGAGACTCAACAACTTGAAAAAAATAAACAAAGGCTCCTCTAAATAGAGGTTCAACGACTTTGAA
1 AGAGACTCAACAACTTGAAAAAAATAAACAAAGGCTCCTCTAAACAGAGGCTCAACGACTTTG-A
2839675 AAAATAAATAAAGCTCCTCTAAAC
65 AAAATAAATAAAGCTCCTCTAAAC
* * *
2839699 AGAGGCTCAACAACTTCG-AAAAAATAAATAAAGGCTCCTCTAAGCAGAGGCTC-ACGACTTTGG
1 AGAGACTCAACAACTT-GAAAAAAATAAACAAAGGCTCCTCTAAACAGAGGCTCAACGACTTT-G
2839762 AAAAATAAATAAA
64 AAAAATAAATAAA
2839775 TTCTCTAAGC
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
88 21 0.30
89 47 0.68
90 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (88 bp):
AGAGACTCAACAACTTGAAAAAAATAAACAAAGGCTCCTCTAAACAGAGGCTCAACGACTTTGAA
AAATAAATAAAGCTCCTCTAAAC
Found at i:2839837 original size:125 final size:124
Alignment explanation
Indices: 2839664--2839972 Score: 309
Period size: 125 Copynumber: 2.4 Consensus size: 124
2839654 TAGAGGTTCA
* * *
2839664 ACGACTTTGAAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTCGAAAAAATAAATA
1 ACGACTTTG-AAAAATAAAT---GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAATAAAT-
* * * * *
2839729 AAGGCTCCTCTAAGCAGAGGC-TCACGACTTTGGAAAAATAAATAAATTCTCTAAGCAGAAGCAC
61 --GGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATAAATCCTCTAAACAGAAGCAC
2839793 C
124 C
* * * * *
2839794 ATGAC-TTGAAAAATAAATGCTCCTCTAAACGGATGCACCACAACTTTG-AAAAGTAAATTGCTC
1 ACGACTTTGAAAAATAAATGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAATAAATGGCTC
* * *** *
2839857 TTCTAAATAGAGGCAACCACGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACC
66 CTCTAAACAGAGGC-ACCACGACTTTGAAAAAATAAATAAATCCTCTAAACAGAAGCACC
* * * *
2839917 ACGACTTTGAAAAGTAAATCACTCCTCTAAACAGAGGCAACAAAACTTTGAAAAAA
1 ACGACTTTGAAAAATAAAT-GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAA
2839973 AATAAATTGC
Statistics
Matches: 147, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
121 15 0.10
123 40 0.27
124 21 0.14
125 50 0.34
126 4 0.03
128 10 0.07
129 3 0.02
130 4 0.03
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (124 bp):
ACGACTTTGAAAAATAAATGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAATAAATGGCTC
CTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATAAATCCTCTAAACAGAAGCACC
Found at i:2839916 original size:84 final size:84
Alignment explanation
Indices: 2839643--2839984 Score: 259
Period size: 84 Copynumber: 4.0 Consensus size: 84
2839633 ATAAACAAAG
* ** * * * * *
2839643 GCTCCTCTAAATAGAGGTTCAACGACTTTGAAAAAATAAATAAAGCTCCTCTAAACAGAGGC-TC
1 GCTCCTCTAAACAGAGGCACCACAACTTTG-AAAAGTAAAT-CA-CTCCTCTAAACAGAGGCAAC
* *
2839707 AACAACTTCG-AAAAAATAAATAAAG
63 AA-AACTTTGAAAAAAATAAAT---T
* * * * * * * * * * *
2839732 GCTCCTCTAAGCAGAGGC-TCACGACTTTGGAAAAATAAATAAATTCTCTAAGCAGAAGCACCAT
1 GCTCCTCTAAACAGAGGCACCACAACTTT-GAAAAGTAAATCACTCCTCTAAACAGAGGCAACAA
*
2839796 GAC-TTG--AAAAATAAA-T
65 AACTTTGAAAAAAATAAATT
* * ** * * *
2839812 GCTCCTCTAAACGGATGCACCACAACTTTGAAAAGTAAATTGCTCTTCTAAATAGAGGCAACCAC
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAGTAAATCACTCCTCTAAACAGAGGCAA-CAA
*
2839877 GACTTTG-AAAAAATAAATT
65 AACTTTGAAAAAAATAAATT
*
2839896 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATCACTCCTCTAAACAGAGGCAACAAA
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAGTAAATCACTCCTCTAAACAGAGGCAACAAA
2839961 ACTTTGAAAAAAAATAAATT
66 ACTTTG-AAAAAAATAAATT
2839981 GCTC
1 GCTC
2839985 TTTAACCATC
Statistics
Matches: 205, Mismatches: 39, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
80 37 0.18
81 13 0.06
82 3 0.01
83 17 0.08
84 64 0.31
85 18 0.09
86 15 0.07
87 4 0.02
88 18 0.09
89 16 0.08
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.22
Consensus pattern (84 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAGTAAATCACTCCTCTAAACAGAGGCAACAAA
ACTTTGAAAAAAATAAATT
Found at i:2839947 original size:41 final size:41
Alignment explanation
Indices: 2839644--2839977 Score: 271
Period size: 41 Copynumber: 8.0 Consensus size: 41
2839634 TAAACAAAGG
* ** *
2839644 CTCCTCTAAATAGAGGTTCAACGACTTTGAAAAAATAAATAAA
1 CTCCTCTAAACAGAGGCACCACGACTTTG-AAAAATAAAT-AA
* * * *
2839687 GCTCCTCTAAACAGAGGCTCAACAACTTCGAAAAAATAAATAAA
1 -CTCCTCTAAACAGAGGCACCACGACTTTG-AAAAATAAAT-AA
* *
2839731 GGCTCCTCTAAGCAGAGGC-TCACGACTTTGGAAAAATAAATAA
1 --CTCCTCTAAACAGAGGCACCACGACTTT-GAAAAATAAATAA
* * * * * *
2839774 ATTCTCTAAGCAGAAGCACCATGAC-TTGAAAAATAAAT-G
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATAA
* * * * **
2839813 CTCCTCTAAACGGATGCACCACAACTTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATAA
* * **
2839854 CTCTTCTAAATAGAGGCAACCACGACTTTGAAAAAATAAATTG
1 CTCCTCTAAACAGAGGC-ACCACGACTTTG-AAAAATAAATAA
* *
2839897 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATCA
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATAA
* **
2839938 CTCCTCTAAACAGAGGCAACAAAACTTTGAAAAA-AAATAA
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATAA
2839978 ATTGCTCTTT
Statistics
Matches: 244, Mismatches: 39, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
39 18 0.07
40 28 0.11
41 69 0.28
42 28 0.11
43 28 0.11
44 55 0.23
45 18 0.07
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (41 bp):
CTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATAA
Found at i:2840331 original size:44 final size:43
Alignment explanation
Indices: 2840270--2840373 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
2840260 TTCAAGGCTT
* *
2840270 TTCAAAGGTTCTCATTTGGCAAACTTGGA-ATTCATATCCAAAAA
1 TTCAAAGCTTCTCATTT-G-AAACTTGGAGATTCACATCCAAAAA
* **
2840314 -TCTAAAGCTTTTCATTTGAATTTTGGAGATTCACATCCAAAAA
1 TTC-AAAGCTTCTCATTTGAAACTTGGAGATTCACATCCAAAAA
2840357 TTCAAAGCTTCTCATTT
1 TTCAAAGCTTCTCATTT
2840374 AAGTTCAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 7 0.14
43 30 0.59
44 14 0.27
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (43 bp):
TTCAAAGCTTCTCATTTGAAACTTGGAGATTCACATCCAAAAA
Found at i:2840606 original size:22 final size:21
Alignment explanation
Indices: 2840559--2840617 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
2840549 GGTTTCACTC
2840559 CTCAAAGATTCTCATTTTGAAA
1 CTCAAAGATTCTCA-TTTGAAA
**
2840581 CTCAAAGATTCTCATTTGAGTT
1 CTCAAAGATTCTCATTTGA-AA
*
2840603 CTCAAAAATTCTCAT
1 CTCAAAGATTCTCAT
2840618 CAAAATATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAA
Found at i:2841745 original size:20 final size:19
Alignment explanation
Indices: 2841722--2841759 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
2841712 ATTTGAGTTT
2841722 TCCTTTTTTTTCCTTTCATG
1 TCCTTTTTTTT-CTTTCATG
2841742 TCCTTTTTTTTCTTTCAT
1 TCCTTTTTTTTCTTTCAT
2841760 CATTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (19 bp):
TCCTTTTTTTTCTTTCATG
Found at i:2841762 original size:22 final size:21
Alignment explanation
Indices: 2841722--2841784 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
2841712 ATTTGAGTTT
*
2841722 TCCTTTTTTTTCCTT-TCATG
1 TCCTTTTTTTTCTTTCTCATG
*
2841742 TCCTTTTTTTTCTTTCATCATT
1 TCCTTTTTTTTCTTTC-TCATG
* *
2841764 TTCTTTTCTTTTTTTTCTCAT
1 TCCTTTT-TTTTCTTTCTCAT
2841785 CTTTCATCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.39
22 14 0.39
23 8 0.22
ACGTcount: A:0.06, C:0.22, G:0.02, T:0.70
Consensus pattern (21 bp):
TCCTTTTTTTTCTTTCTCATG
Found at i:2846014 original size:59 final size:59
Alignment explanation
Indices: 2845767--2846046 Score: 363
Period size: 61 Copynumber: 4.7 Consensus size: 59
2845757 TTTTGTATAG
* * * *
2845767 GAAAAATTGATACTTTCAACTTTTTC-CCAAAATA-TCTTTTAGAAA-CTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAGC-TTATTTTCAA
* * * * *
2845824 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTATTTTTTTTGAAAACTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAA--TATTTTTTTAGAAAGCTTATTTTCAA
2845885 -AGAAAATTGATACTTTCAAC-TTTTCTCCAAAAATATTTTTTTTTAGAAAGCTTATTTTCAA
1 GA-AAAATTGATACTTTCAACTTTTTCT-CAAAAATA--TTTTTTTAGAAAGCTTATTTTCAA
*
2845946 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAGCTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAGCTTATTTTCAA
*
2846005 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTT
2846047 TGAATTTTAT
Statistics
Matches: 196, Mismatches: 16, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
57 24 0.12
58 5 0.03
59 66 0.34
60 7 0.04
61 87 0.44
62 7 0.04
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.44
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAGCTTATTTTCAA
Found at i:2846039 original size:120 final size:121
Alignment explanation
Indices: 2845767--2846047 Score: 391
Period size: 120 Copynumber: 2.4 Consensus size: 121
2845757 TTTTGTATAG
* *
2845767 GAAAAATTGATACTTTCAACTTTTTCC-C-AAAATA---TCTTTTAGAAACTTTAATTTCGAGGA
1 GAAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTTTAGAAACTTTAATTTCAAGGA
* *
2845827 AAATTGATACTTTCAACTTTTCCTCAAAAATCTATTTTTTTTGAAAACTTATTTTTAA
65 AAATTGATACTTTCAACTTTTCCTCAAAAA-CTATTTTTTTAGAAAACTTATTTTCAA
*
2845885 -AGAAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTTTTAGAAAGC-TTATTTTCAAG
1 GA-AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTTTAGAAA-CTTTAATTTCAAG
* *
2845947 GAAAATTGATACTTTCAACTTTTTCTCAAAAA-TATTTTTTTAGAAAGCTTATTTTCAA
63 GAAAATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTTTAGAAAACTTATTTTCAA
2846005 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTT
2846048 GAATTTTATT
Statistics
Matches: 146, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
116 1 0.01
117 5 0.03
118 19 0.13
119 6 0.04
120 61 0.42
121 3 0.02
122 50 0.34
123 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.44
Consensus pattern (121 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAGAAACTTTAATTTCAAGGAA
AATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTTTAGAAAACTTATTTTCAA
Found at i:2846071 original size:5 final size:5
Alignment explanation
Indices: 2846063--2846138 Score: 68
Period size: 5 Copynumber: 14.8 Consensus size: 5
2846053 TTATTTAAAG
*
2846063 AAAAT AAAAT --AAT AAAAT AAAAT AAAAAT AAAA- ATAAAT AAATT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT A-AAAT AAAAT AAAAT
*
2846112 AAATT AAAAAT AAAAAT AGAAAT AAAA
1 AAAAT -AAAAT -AAAAT A-AAAT AAAA
2846139 AATATTAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
3 3 0.05
4 1 0.02
5 35 0.58
6 21 0.35
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:2846092 original size:6 final size:6
Alignment explanation
Indices: 2846063--2846139 Score: 70
Period size: 6 Copynumber: 12.7 Consensus size: 6
2846053 TTATTTAAAG
*
2846063 AAAAT- AAAATA ATAAA-A TAAAATA AAAATA AAAATAA ATAAATT AAAAT-
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAAT-A A-AAATA AAAATA
* *
2846112 AAATTA AAAATA AAAATA GAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
2846140 ATATTAAACA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
5 9 0.15
6 39 0.65
7 8 0.13
8 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:2846113 original size:31 final size:30
Alignment explanation
Indices: 2846063--2846142 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 30
2846053 TTATTTAAAG
2846063 AAAATAAAATAATAAAATAAAATAAAAATA
1 AAAATAAAATAATAAAATAAAATAAAAATA
*
2846093 AAAAT-AAATAAATTAAAATAAATTAAAAATA
1 AAAATAAAAT-AA-TAAAATAAAATAAAAATA
2846124 AAAATAGAAATAA-AAAATA
1 AAAATA-AAATAATAAAATA
2846143 TTAAACAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
29 4 0.09
30 13 0.29
31 22 0.49
32 2 0.04
33 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (30 bp):
AAAATAAAATAATAAAATAAAATAAAAATA
Found at i:2846128 original size:37 final size:37
Alignment explanation
Indices: 2846073--2846147 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
2846063 AAAATAAAAT
*
2846073 AATAAAATAAAATAAAAATAAAAATAAATAA-ATTAA
1 AATAAAATAAAATAAAAATAAAAATAAAAAATATTAA
* *
2846109 AATAAATTAAAAATAAAAATAGAAATAAAAAATATTAA
1 AATAAAAT-AAAATAAAAATAAAAATAAAAAATATTAA
2846147 A
1 A
2846148 CAATCCTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 7 0.21
37 21 0.62
38 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (37 bp):
AATAAAATAAAATAAAAATAAAAATAAAAAATATTAA
Found at i:2846171 original size:3 final size:3
Alignment explanation
Indices: 2846163--2846205 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
2846153 CTAATCTAAT
*
2846163 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
2846206 AAAAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2846770 original size:13 final size:13
Alignment explanation
Indices: 2846731--2846771 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2846721 AAAATTTTTC
2846731 AAAAATT-TCTAGA
1 AAAAATTCTCTA-A
*
2846744 AAAAATTCAC-AA
1 AAAAATTCTCTAA
2846756 AAAAATTCTCTAA
1 AAAAATTCTCTAA
2846769 AAA
1 AAA
2846772 TTTCCACCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 10 0.42
13 13 0.54
14 1 0.04
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.24
Consensus pattern (13 bp):
AAAAATTCTCTAA
Done.