Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 63 of 163
Found at i:20754373 original size:42 final size:41
Alignment explanation
Indices: 20754322--20754407 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 41
20754312 GTGCTAAACT
* * * *
20754322 GAAACCCATAAGGGTTGAATGGAAGCTCATAGGAGTTGAACA
1 GAAACCCATAAGGGTTAAACGAAAACTCATAGGAGTT-AACA
* *
20754364 GAAAGCCATAAGGGTTAAACGAAAACTCATATGAGTTAACA
1 GAAACCCATAAGGGTTAAACGAAAACTCATAGGAGTTAACA
20754405 GAA
1 GAA
20754408 GCTCGTGAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 7 0.18
42 31 0.82
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (41 bp):
GAAACCCATAAGGGTTAAACGAAAACTCATAGGAGTTAACA
Found at i:20759368 original size:67 final size:67
Alignment explanation
Indices: 20759257--20759391 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 67
20759247 GTAATTGTCG
*
20759257 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGTTGTAAAAAATGAGGTTCGCAGGAGTGTGCTC
1 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAAAATGAGGTTCGCAGGAGTGTGCTC
20759322 TC
66 TC
** **
20759324 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAGGAAATGAGGTTCGTGGGAGTGTGCTC
1 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAAAATGAGGTTCGCAGGAGTGTGCTC
20759389 TC
66 TC
20759391 T
1 T
20759392 GAATTGGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (67 bp):
TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAAAATGAGGTTCGCAGGAGTGTGCTC
TC
Found at i:20774213 original size:13 final size:13
Alignment explanation
Indices: 20774195--20774219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20774185 TGATTTATAT
20774195 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20774208 GTGTGAAAATTT
1 GTGTGAAAATTT
20774220 TATCATTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20776370 original size:13 final size:13
Alignment explanation
Indices: 20776352--20776381 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20776342 TCTATGAGGT
*
20776352 TTTTGGTTGATTG
1 TTTTGGTTGATTA
20776365 TTTTGGTTGATTA
1 TTTTGGTTGATTA
20776378 TTTT
1 TTTT
20776382 TGGAGGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.67
Consensus pattern (13 bp):
TTTTGGTTGATTA
Found at i:20776382 original size:14 final size:13
Alignment explanation
Indices: 20776351--20776384 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
20776341 TTCTATGAGG
20776351 TTTTTGGTTGATT
1 TTTTTGGTTGATT
*
20776364 GTTTTGGTTGATT
1 TTTTTGGTTGATT
20776377 ATTTTTGG
1 -TTTTTGG
20776385 AGGTTGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.09, C:0.00, G:0.26, T:0.65
Consensus pattern (13 bp):
TTTTTGGTTGATT
Found at i:20778561 original size:21 final size:20
Alignment explanation
Indices: 20778537--20778580 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
20778527 GAGCTGAATG
*
20778537 GAAACCCATAAGGGTTAAACA
1 GAAACCCATAAGAGTT-AACA
* *
20778558 GAAACTCATATGAGTTAACA
1 GAAACCCATAAGAGTTAACA
20778578 GAA
1 GAA
20778581 GCTTGTGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (20 bp):
GAAACCCATAAGAGTTAACA
Found at i:20780103 original size:24 final size:23
Alignment explanation
Indices: 20780076--20780121 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
20780066 CTATTTTATT
*
20780076 TTCCCCAAAATAAATAAATAAAAA
1 TTCCACAAAATAAAT-AATAAAAA
* *
20780100 TTCCATAAATTAAATAATAAAA
1 TTCCACAAAATAAATAATAAAA
20780122 CCACCTCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (23 bp):
TTCCACAAAATAAATAATAAAAA
Found at i:20780375 original size:5 final size:5
Alignment explanation
Indices: 20780367--20780392 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20780357 GAGATGAAAT
20780367 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
20780393 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:20781198 original size:9 final size:9
Alignment explanation
Indices: 20781184--20781211 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20781174 AGTTGATTCA
20781184 AATAACTCG
1 AATAACTCG
20781193 AATAACTCG
1 AATAACTCG
20781202 AATAACTCG
1 AATAACTCG
20781211 A
1 A
20781212 TTCGTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (9 bp):
AATAACTCG
Found at i:20786998 original size:16 final size:16
Alignment explanation
Indices: 20786964--20787001 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
20786954 TTAAAATCTA
20786964 TAAAAA-AAGATAATT
1 TAAAAATAAGATAATT
20786979 TAAAAATAA-ATAATT
1 TAAAAATAAGATAATT
20786994 GTAAAAAT
1 -TAAAAAT
20787002 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (16 bp):
TAAAAATAAGATAATT
Found at i:20787022 original size:22 final size:24
Alignment explanation
Indices: 20786975--20787028 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
20786965 AAAAAAAGAT
20786975 AATT-TAAAAATAAATAATTGTAAA
1 AATTATAAAAATAAATAA-TGTAAA
20786999 AATTATAAAAATAAAT-A-GTAAA
1 AATTATAAAAATAAATAATGTAAA
*
20787021 AATAATAA
1 AATTATAA
20787029 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 12 0.43
24 5 0.18
25 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AATTATAAAAATAAATAATGTAAA
Found at i:20787132 original size:29 final size:27
Alignment explanation
Indices: 20787088--20787149 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
20787078 ATTTGTTTAC
* * *
20787088 ATTTTTTTACATTTATACAAAATTTTAA
1 ATTTTTTAACAGTTATA-AAAATTGTAA
20787116 TATTTTTTAACAGTTATAAAAATTGTAA
1 -ATTTTTTAACAGTTATAAAAATTGTAA
20787144 ATTTTT
1 ATTTTT
20787150 AAAATGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 6 0.20
28 9 0.30
29 15 0.50
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTTTTTAACAGTTATAAAAATTGTAA
Found at i:20787573 original size:18 final size:17
Alignment explanation
Indices: 20787552--20787600 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
20787542 AAAAAAAATA
20787552 TAATTTTTAAAATTTTAT
1 TAATTTTTAAAATTTT-T
20787570 TAATTTTTACAAA-TTTT
1 TAATTTTTA-AAATTTTT
20787587 TAATATTTTAAAAT
1 TAAT-TTTTAAAAT
20787601 AAATTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.29
18 17 0.61
19 3 0.11
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTTTTAAAATTTTT
Found at i:20804615 original size:21 final size:21
Alignment explanation
Indices: 20804591--20804640 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
20804581 TGCTCATCAA
20804591 ACTTATTTATCAAATATATAT
1 ACTTATTTATCAAATATATAT
*
20804612 ACTTGATCT-TCAAATATATAT
1 ACTT-ATTTATCAAATATATAT
20804633 A-TTATTTA
1 ACTTATTTA
20804641 CATATCACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 17 0.68
22 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (21 bp):
ACTTATTTATCAAATATATAT
Found at i:20804816 original size:41 final size:40
Alignment explanation
Indices: 20804726--20804845 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 40
20804716 TGATTTAATA
* * * * * *
20804726 CACCGGCTTTTAGCCTGCTAGACTTATAGTCCGAATAATTT
1 CACCGGCATTAAGCCTGCTAGAC-AATAGTCTGAATTATAT
*
20804767 CACTGGCATTAAGCCTGCTAGACAATGAGTCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGACAAT-AGTCTGAATTATAT
* *
20804808 CACCGGCATCAAGCCTGCTAGATAATAAGTCTGAATTA
1 CACCGGCATTAAGCCTGCTAGACAAT-AGTCTGAATTA
20804846 CATTCGATCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
40 2 0.03
41 65 0.97
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACAATAGTCTGAATTATAT
Found at i:20805032 original size:2 final size:2
Alignment explanation
Indices: 20805025--20805061 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
20805015 AGCCAAAGTG
*
20805025 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20805062 TCAGACCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:20812759 original size:50 final size:50
Alignment explanation
Indices: 20812650--20812884 Score: 272
Period size: 50 Copynumber: 4.6 Consensus size: 50
20812640 GGTAAAGAGA
* * *
20812650 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGATATCATGAGAGG
1 TCCCATATAAGACCATGTCTGGGACATGGCATGGGCA-CC--G--A-CATGAGAAG
* * * *
20812706 TCCCCTATAAGACCATGTCTGGAACATGGCATGGGCATCGAGATGAGAAG
1 TCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAG
* * *
20812756 TCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAG
*** *
20812806 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAAA
1 TCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAG-AAG
*
20812857 TCCCATGTAAGACCATGTCTGGGACATG
1 TCCCATATAAGACCATGTCTGGGACATG
20812885 ACTTTGGCAT
Statistics
Matches: 157, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
50 94 0.60
51 28 0.18
53 1 0.01
55 1 0.01
56 33 0.21
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (50 bp):
TCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAG
Found at i:20812833 original size:100 final size:105
Alignment explanation
Indices: 20812649--20812894 Score: 349
Period size: 100 Copynumber: 2.4 Consensus size: 105
20812639 GGGTAAAGAG
*
20812649 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGATATCATGAGAGGTCCCCTAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGA-ATCATGAGAGGTCCCCCAT
* *
20812714 AAGACCATGTCTGGAACATGGCATGGGCATCGAGATGAG-AA
64 AAGACCATGTCTGGAACATGGCATGGGCACCGACATGAGAAA
* * * *
20812755 GTCCCATATAAGACCATGTCTGGGACATGGCATTGGCA-CC-G-A-GATGAGAGGTCCCCCGTAA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAATCATGAGAGGTCCCCCATAA
*
20812816 GACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAA
66 GACCATGTCTGGAACATGGCATGGGCACCGACATGAGAAA
* *
20812856 ATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
20812895 GTTTTTACCA
Statistics
Matches: 126, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
100 50 0.40
101 37 0.29
103 1 0.01
105 2 0.02
106 36 0.29
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (105 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAATCATGAGAGGTCCCCCATAA
GACCATGTCTGGAACATGGCATGGGCACCGACATGAGAAA
Found at i:20814595 original size:21 final size:21
Alignment explanation
Indices: 20814569--20814631 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
20814559 TACACCATCC
*
20814569 CAGGGAACACCGTAGTGAT-AA
1 CAGGGAACACCGAAGTG-TGAA
*
20814590 CAGGGAA-ACCAAAGTGTGAA
1 CAGGGAACACCGAAGTGTGAA
*
20814610 CAGGG-ACACCGAAGTGTAAA
1 CAGGGAACACCGAAGTGTGAA
20814630 CA
1 CA
20814632 TATAGGCATC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.06
20 27 0.75
21 7 0.19
ACGTcount: A:0.41, C:0.19, G:0.29, T:0.11
Consensus pattern (21 bp):
CAGGGAACACCGAAGTGTGAA
Found at i:20820692 original size:21 final size:21
Alignment explanation
Indices: 20820668--20820727 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 21
20820658 CCCTTCCCTC
20820668 TTTT-TATTTATTTATTTATTCT
1 TTTTATATTTA-TTA-TTATTCT
20820690 TTTTATATTTATTATTATTCT
1 TTTTATATTTATTATTATTCT
* *
20820711 TGTT-T-GTTATTATTATT
1 TTTTATATTTATTATTATT
20820728 TGTTTTAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 11 0.31
20 1 0.03
21 10 0.29
22 7 0.20
23 6 0.17
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (21 bp):
TTTTATATTTATTATTATTCT
Found at i:20820859 original size:14 final size:14
Alignment explanation
Indices: 20820840--20820878 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20820830 TTGTTTCATT
*
20820840 GAAAATGGCTTCTG
1 GAAAATGACTTCTG
*
20820854 GAAAATGATTTCTG
1 GAAAATGACTTCTG
20820868 GAAAATGACTT
1 GAAAATGACTT
20820879 ACTTTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (14 bp):
GAAAATGACTTCTG
Found at i:20825501 original size:25 final size:26
Alignment explanation
Indices: 20825473--20825544 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 26
20825463 ATTTTCACCA
*
20825473 CTCGTGTGAGTGC-TT-TGATTCATAG
1 CTCGTGTGAG-GCATTCTGATTCACAG
20825498 CTCGTGTGA-GCATTCTGATTCACAG
1 CTCGTGTGAGGCATTCTGATTCACAG
*
20825523 GTCGTGTGA-GCATTCTGATTCA
1 CTCGTGTGAGGCATTCTGATTCA
20825545 GGAATTGACG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 39 0.91
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.36
Consensus pattern (26 bp):
CTCGTGTGAGGCATTCTGATTCACAG
Found at i:20825884 original size:188 final size:188
Alignment explanation
Indices: 20825562--20825945 Score: 651
Period size: 188 Copynumber: 2.0 Consensus size: 188
20825552 ACGGATTACA
* * * *
20825562 GTTATATGAGCTAGCACACTATGTGTGAGTTATCCCGGGTATCCAACGGTATTCTAAATGGTTTA
1 GTTACATGAGCTAGCACACAATGTGTGAGCTATCCCGGGTATCCAACGGTATTCTAAATGGTTCA
* * * * *
20825627 TTGGACATGATTTGAAAGGAAATGGTAAGAGTTAGATATGAACTAAGATATGTTCATATATGAAT
66 ATGGACAAGATTTGAAAGAAAATGGTAAGAGTTAGATAAGAACTAAGATATGTTCACATATGAAT
*
20825692 TGCATTGGATGGGTGATATATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
131 TGCATTGGATGGGTGATACATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
20825750 GTTACATGAGCTAGCACACAATGTGTGAGCTATCCCGGGTATCCAACGGTATTCTAAATGGTTCA
1 GTTACATGAGCTAGCACACAATGTGTGAGCTATCCCGGGTATCCAACGGTATTCTAAATGGTTCA
* *
20825815 ATGGGCAAGATTTGAAAGAAAATGGTAAGAGTTCGATAAGAACTAAGATATGTTCACATATGAAT
66 ATGGACAAGATTTGAAAGAAAATGGTAAGAGTTAGATAAGAACTAAGATATGTTCACATATGAAT
*
20825880 TGCATTGGATTGGTGATACATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
131 TGCATTGGATGGGTGATACATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
20825938 GTTACATG
1 GTTACATG
20825946 CTTAAATGTT
Statistics
Matches: 183, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
188 183 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (188 bp):
GTTACATGAGCTAGCACACAATGTGTGAGCTATCCCGGGTATCCAACGGTATTCTAAATGGTTCA
ATGGACAAGATTTGAAAGAAAATGGTAAGAGTTAGATAAGAACTAAGATATGTTCACATATGAAT
TGCATTGGATGGGTGATACATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
Found at i:20826090 original size:15 final size:15
Alignment explanation
Indices: 20826070--20826099 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20826060 CTTACTTATA
20826070 TAAGTGCCCAAATGG
1 TAAGTGCCCAAATGG
20826085 TAAGTGCCCAAATGG
1 TAAGTGCCCAAATGG
20826100 AAATATGTTT
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:0.27, T:0.20
Consensus pattern (15 bp):
TAAGTGCCCAAATGG
Found at i:20826389 original size:20 final size:19
Alignment explanation
Indices: 20826366--20826407 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
20826356 TAAAGAAAGT
20826366 AAATAC-AATGGAAAGTAATG
1 AAATACAAAT-GAAAGTAA-G
*
20826386 AAATGCAAATGAAAGTAAG
1 AAATACAAATGAAAGTAAG
20826405 AAA
1 AAA
20826408 ATTTGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.17
Consensus pattern (19 bp):
AAATACAAATGAAAGTAAG
Found at i:20831258 original size:23 final size:23
Alignment explanation
Indices: 20831232--20831351 Score: 127
Period size: 23 Copynumber: 5.3 Consensus size: 23
20831222 ATAAGTGCCA
*
20831232 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
20831255 CACT--TACGTAACCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20831276 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* ** *
20831299 CACTGATATATAGCCTTATCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
20831322 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20831345 CACTGAT
1 CACTGAT
20831352 CAATAACACT
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
21 17 0.23
23 58 0.77
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:20831334 original size:46 final size:46
Alignment explanation
Indices: 20831232--20831351 Score: 154
Period size: 46 Copynumber: 2.7 Consensus size: 46
20831222 ATAAGTGCCA
* * *
20831232 CACTGATATGTAGCCAAAGCTACCACT--TACGTAACCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACATAACCGTAGCTAC
* * * *
20831276 CACTGAAATGTAGCCGAAGCTACCACTGATATATAGCCTTATCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACATAACCGTAGCTAC
*
20831322 CACTGAAATGTAGTCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
20831352 CAATAACACT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
44 25 0.38
46 41 0.62
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACATAACCGTAGCTAC
Found at i:20831597 original size:17 final size:18
Alignment explanation
Indices: 20831575--20831615 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
20831565 TAAATTTTCC
20831575 TTCACAT-TC-AATATTAA
1 TTCACATATCAAATA-TAA
20831592 TTCACATATCAAATATAA
1 TTCACATATCAAATATAA
20831610 TTCACA
1 TTCACA
20831616 ATTTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
TTCACATATCAAATATAA
Found at i:20848713 original size:17 final size:16
Alignment explanation
Indices: 20848691--20848724 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20848681 GAGGATGGCG
20848691 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
20848708 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
20848724 T
1 T
20848725 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:20856209 original size:29 final size:29
Alignment explanation
Indices: 20856136--20856347 Score: 201
Period size: 29 Copynumber: 7.2 Consensus size: 29
20856126 GTGTGTTAAA
* * *
20856136 CGATGGTCGAAATCATCCCTTTTCTTTAAT
1 CGATGGTCGAAACCATCCCTTTTC-ATATT
*
20856166 CGATGGTC-ATCACCATCCCTTTTCATATT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
**
20856195 CGATGGTCGAAACCATCCCTTTTCATTAAA
1 CGATGGTCGAAACCATCCCTTTTCA-TATT
** ***
20856225 CGATGACCTTCACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * *
20856254 CGATAGTTGAAACTATCTCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
** *
20856283 CGATGGTCGTCACCATCCCTTTTCATAGT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* *
20856312 CGATAGTCGAAACTATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
20856341 CAATGGT
1 CGATGGT
20856348 TGTCGATTCG
Statistics
Matches: 142, Mismatches: 37, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
29 99 0.70
30 43 0.30
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.37
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:20856315 original size:58 final size:58
Alignment explanation
Indices: 20856136--20856347 Score: 255
Period size: 59 Copynumber: 3.6 Consensus size: 58
20856126 GTGTGTTAAA
* * *
20856136 CGATGGTCGAAA-TCATCCCTTTTCTTTAATCGATGGTCATCACCATCCCTTTTCATATT
1 CGATAGTCGAAACT-ATCCCTTTTC-ATATTCGATGGTCATCACCATCCCTTTTCATATT
* * ** ** *
20856195 CGATGGTCGAAACCATCCCTTTTCATTAAACGATGACCTTCACCATCCCTTTTCATATT
1 CGATAGTCGAAACTATCCCTTTTCA-TATTCGATGGTCATCACCATCCCTTTTCATATT
* * * *
20856254 CGATAGTTGAAACTATCTCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGT
1 CGATAGTCGAAACTATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATATT
*
20856312 CGATAGTCGAAACTATCCCTTTTCATATTCAATGGT
1 CGATAGTCGAAACTATCCCTTTTCATATTCGATGGT
20856348 TGTCGATTCG
Statistics
Matches: 132, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
58 60 0.45
59 72 0.55
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.37
Consensus pattern (58 bp):
CGATAGTCGAAACTATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATATT
Found at i:20862228 original size:111 final size:111
Alignment explanation
Indices: 20862034--20862252 Score: 429
Period size: 111 Copynumber: 2.0 Consensus size: 111
20862024 CATTTACAAC
20862034 ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
1 ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
20862099 CCTTAGAAACAATTCGGGACTAAATCAAAAACATTTAAAACTTAAG
66 CCTTAGAAACAATTCGGGACTAAATCAAAAACATTTAAAACTTAAG
20862145 ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
1 ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
*
20862210 CCTTAGAAACAATTCGGGACTAAATTAAAAACATTTAAAACTT
66 CCTTAGAAACAATTCGGGACTAAATCAAAAACATTTAAAACTT
20862253 TATGGAAAAA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.29
Consensus pattern (111 bp):
ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
CCTTAGAAACAATTCGGGACTAAATCAAAAACATTTAAAACTTAAG
Found at i:20864072 original size:32 final size:32
Alignment explanation
Indices: 20864036--20864100 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
20864026 CATCAACAAC
20864036 ACATGTTACTTCATTTAAACATGATTCATATG
1 ACATGTTACTTCATTTAAACATGATTCATATG
* *
20864068 ACATGTTAGTTCATTTAAACATGATTTATATG
1 ACATGTTACTTCATTTAAACATGATTCATATG
20864100 A
1 A
20864101 ATTTGACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (32 bp):
ACATGTTACTTCATTTAAACATGATTCATATG
Found at i:20864664 original size:28 final size:29
Alignment explanation
Indices: 20864487--20864771 Score: 252
Period size: 29 Copynumber: 9.8 Consensus size: 29
20864477 TGGTCGAAAT
* *
20864487 CATCCCTTTTCTTTAATTGATGGTTGTCAC
1 CATCCCTTTTC-ATAGTTGATGGTTGTCAC
* * * * **
20864517 CATCCCATTTCATATTTGATGATCGAAAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
* *
20864546 CATCCCTTTTCATTAATTGAT-GTCCGTCAC
1 CATCCCTTTTCA-TAGTTGATGGT-TGTCAC
* * * * **
20864576 CATCCATTTTCTTATTTGATGGTCGAAAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
**
20864605 CATCCCTTTTCATTAGTCAATGGTTGTCAC
1 CATCCCTTTTCA-TAGTTGATGGTTGTCAC
*
20864635 CATCCCTTTTCA-AGTTCATGGTTGTCAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
* * **
20864663 CAT-CCTTTTCATAGCTGATAGTTGAAAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
* * * **
20864691 TATCCATTTTCATATTTGATGGTCATCAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
*
20864720 CATCCCTTTTCATAGTTGATGGTCGTCAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
20864749 CATCCCTTTTCATAGTTGATGGT
1 CATCCCTTTTCATAGTTGATGGT
20864772 CAAAACTACC
Statistics
Matches: 204, Mismatches: 45, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
27 8 0.04
28 30 0.15
29 110 0.54
30 56 0.27
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (29 bp):
CATCCCTTTTCATAGTTGATGGTTGTCAC
Found at i:20864701 original size:86 final size:86
Alignment explanation
Indices: 20864544--20864801 Score: 252
Period size: 87 Copynumber: 3.0 Consensus size: 86
20864534 GATGATCGAA
* * * * *
20864544 ACCATCCCTTTTCATTAATTGAT-GTCCGTCACCATCCATTTTCTTATTTGATGGTCGAAACCAT
1 ACCATCCCTTTTCA-TAGTTCATGGT-CGTCACCATCC-TTTTCATAGTTGATAGTCGAAACCAT
* **
20864608 CCCTTTTCATTAGTCAATGGTTGTC
63 CCATTTTCA-TAGTCAATGGTCATC
* * * *
20864633 ACCATCCCTTTTCA-AGTTCATGGTTGTCACCATCCTTTTCATAGCTGATAGTTGAAACTATCCA
1 ACCATCCCTTTTCATAGTTCATGGTCGTCACCATCCTTTTCATAGTTGATAGTCGAAACCATCCA
* **
20864697 TTTTCATATTTGATGGTCATC
66 TTTTCATAGTCAATGGTCATC
* * * *
20864718 ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCAAAACTA-CC
1 ACCATCCCTTTTCATAGTTCATGGTCGTCACCAT-CCTTTTCATAGTTGATAGTCGAAACCATCC
* *
20864782 TTTTTTCATATTCAATGGTC
65 -ATTTTCATAGTCAATGGTC
20864802 GTCGATTCGT
Statistics
Matches: 141, Mismatches: 24, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
85 24 0.17
86 47 0.33
87 54 0.38
88 2 0.01
89 14 0.10
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (86 bp):
ACCATCCCTTTTCATAGTTCATGGTCGTCACCATCCTTTTCATAGTTGATAGTCGAAACCATCCA
TTTTCATAGTCAATGGTCATC
Found at i:20864791 original size:58 final size:58
Alignment explanation
Indices: 20864475--20864777 Score: 290
Period size: 59 Copynumber: 5.2 Consensus size: 58
20864465 TGTGCTAAAC
* * * * *
20864475 GATGGTCGAAATCATCCCTTTTCTTTAATTGATGGTTGTCACCATCCCATTTCATATTT
1 GATGGTCGAAACCATCCCTTTTC-ATAGTTGATGGTCGTCACCATCCCTTTTCATATTT
* * * *
20864534 GATGATCGAAACCATCCCTTTTCATTAATTGAT-GTCCGTCACCATCCATTTTCTTATTT
1 GATGGTCGAAACCATCCCTTTTCA-TAGTTGATGGT-CGTCACCATCCCTTTTCATATTT
** * *
20864593 GATGGTCGAAACCATCCCTTTTCATTAGTCAATGGTTGTCACCATCCCTTTTCA-AGTT
1 GATGGTCGAAACCATCCCTTTTCA-TAGTTGATGGTCGTCACCATCCCTTTTCATATTT
* * ** * * * ** * *
20864651 CATGGTTGTCACCAT-CCTTTTCATAGCTGATAGTTGAAACTATCCATTTTCATATTT
1 GATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATATTT
* *
20864708 GATGGTC-ATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTT
1 GATGGTCGA-AACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATATTT
*
20864766 GATGGTCAAAAC
1 GATGGTCGAAAC
20864778 TACCTTTTTT
Statistics
Matches: 197, Mismatches: 40, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
56 21 0.11
57 22 0.11
58 59 0.30
59 93 0.47
60 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (58 bp):
GATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATATTT
Found at i:20868837 original size:42 final size:43
Alignment explanation
Indices: 20868718--20868884 Score: 196
Period size: 43 Copynumber: 3.9 Consensus size: 43
20868708 CGTTTATGTG
* * *
20868718 AAAAACGCTGCTAAAGAACATGACCTTTGGCGACACTTTACCG
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTACCC
* * *
20868761 AAAAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCC
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTACCC
* * *
20868804 AAAAACGCTGCTAAAG-ACATGATCTTTAGCGGCGCTTGTA-TC
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTT-TACCC
* *
20868846 ACAAAC-CTTGCTAAAGATCATGACCTTTAGCGGCACTTT
1 AAAAACGC-TGCTAAAGAACATGACCTTTAGCGGCACTTT
20868885 TACAAACGCC
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 35 0.33
43 71 0.66
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTACCC
Found at i:20868872 original size:85 final size:86
Alignment explanation
Indices: 20868718--20868884 Score: 214
Period size: 85 Copynumber: 2.0 Consensus size: 86
20868708 CGTTTATGTG
*
20868718 AAAAACGCTGCTAAAGAACATGACCTTTGGCGACACTTTACCGAAAAACACCGCTAAAGAACATG
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGACACTTTACCGAAAAACACCGCTAAAGAACATG
*
20868783 ACCTTTAGCGGCGCTTTACCC
66 ACCTTTAGCGGCACTTTACCC
* * * * * * *
20868804 AAAAACGCTGCTAAAG-ACATGATCTTTAGCGGCGCTTGTATC-ACAAAC-CTTGCTAAAGATCA
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGACACTT-TACCGAAAAACAC-CGCTAAAGAACA
20868866 TGACCTTTAGCGGCACTTT
64 TGACCTTTAGCGGCACTTT
20868885 TACAAACGCC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 1 0.01
85 50 0.71
86 19 0.27
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (86 bp):
AAAAACGCTGCTAAAGAACATGACCTTTAGCGACACTTTACCGAAAAACACCGCTAAAGAACATG
ACCTTTAGCGGCACTTTACCC
Found at i:20868942 original size:83 final size:81
Alignment explanation
Indices: 20868767--20868943 Score: 196
Period size: 83 Copynumber: 2.1 Consensus size: 81
20868757 ACCGAAAAAC
* ***
20868767 ACCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAAAAACGCTGCTAAAGACATGATCTTTA
1 ACCGCTAAAGAACATGACCTTTAGCGGCACTTTA-CC-AAAACGCCAATAAAGACATGATCTTTA
20868832 GCGGCGCTTGTATCACAA
64 GCGGCGCTTGTATCACAA
* *
20868850 ACCTTGCTAAAGATCATGACCTTTAGCGGCACTTTTA-C-AAACGCCAATATAGAACATGATCTT
1 ACC--GCTAAAGAACATGACCTTTAGCGGCAC-TTTACCAAAACGCCAATAAAG-ACATGATCTT
* *
20868913 TAGCGGCGTTTTTATCACAA
62 TAGCGGCGCTTGTATCACAA
20868933 ATGCCGCTAAA
1 A--CCGCTAAA
20868944 AGTACCATTC
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
82 10 0.12
83 38 0.47
84 1 0.01
85 27 0.34
86 4 0.05
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (81 bp):
ACCGCTAAAGAACATGACCTTTAGCGGCACTTTACCAAAACGCCAATAAAGACATGATCTTTAGC
GGCGCTTGTATCACAA
Found at i:20872931 original size:14 final size:14
Alignment explanation
Indices: 20872914--20872960 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
20872904 AAATCTGAGT
20872914 AATGAACACAACAA
1 AATGAACACAACAA
20872928 AATGAAACACACACACA
1 AATG-AACACA-ACA-A
*
20872945 AATAAACA-AACAA
1 AATGAACACAACAA
20872958 AAT
1 AAT
20872961 AATAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 4 0.14
14 7 0.24
15 7 0.24
16 7 0.24
17 4 0.14
ACGTcount: A:0.66, C:0.21, G:0.04, T:0.09
Consensus pattern (14 bp):
AATGAACACAACAA
Found at i:20873667 original size:14 final size:14
Alignment explanation
Indices: 20873650--20873693 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
20873640 ATAAACCCTA
20873650 AACCCCTAACACTT
1 AACCCCTAACACTT
* *
20873664 AACCCCTAACTCCT
1 AACCCCTAACACTT
*
20873678 AACCCCTAACCCTT
1 AACCCCTAACACTT
20873692 AA
1 AA
20873694 ACCATAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCCCTAACACTT
Found at i:20873667 original size:21 final size:21
Alignment explanation
Indices: 20873643--20873696 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
20873633 ATAAATAATA
*
20873643 AACCCTAAACCCCTAACACTT
1 AACCCTAAACCCCTAACACCT
* *
20873664 AACCCCT-AACTCCTAACCCCT
1 AA-CCCTAAACCCCTAACACCT
20873685 AACCCTTAAACC
1 AACCC-TAAACC
20873697 ATAAATCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 3 0.12
21 16 0.62
22 7 0.27
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCTAAACCCCTAACACCT
Found at i:20873779 original size:14 final size:14
Alignment explanation
Indices: 20873747--20873799 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
20873737 AATGGTAACA
*
20873747 CCTAAACTTTAAAC
1 CCTAAACTATAAAC
* *
20873761 TCTAAACTATATAC
1 CCTAAACTATAAAC
* *
20873775 CCTAAACCAAAAAC
1 CCTAAACTATAAAC
*
20873789 CCTAAATTATA
1 CCTAAACTATA
20873800 GTGATAATTA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (14 bp):
CCTAAACTATAAAC
Found at i:20874193 original size:41 final size:41
Alignment explanation
Indices: 20874120--20874200 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
20874110 AAAAATAGAG
*
20874120 CATTAGCGGCGCTTTTTCAAAAACGCCCCTAAAGTCCCGAC
1 CATTAGCGGCGCTTTTTCAAAAACGCCCCTAAAGCCCCGAC
* * * *
20874161 CATTAGCGGCGCTTTTTTAAAAATGTCGCTAAAGCCCCGA
1 CATTAGCGGCGCTTTTTCAAAAACGCCCCTAAAGCCCCGA
20874201 AAGCTCAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (41 bp):
CATTAGCGGCGCTTTTTCAAAAACGCCCCTAAAGCCCCGAC
Found at i:20874898 original size:20 final size:19
Alignment explanation
Indices: 20874834--20874899 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
20874824 CAGAAGCACT
*
20874834 GAAGTGAAA-ATGAAGGCGTC
1 GAAGTGAAATA-G-AGGCATC
* *
20874854 GAAGTGAAATCAAAGGCACC
1 GAAGTGAAAT-AGAGGCATC
*
20874874 AAAGTGAAAGTAGAGGCATC
1 GAAGTGAAA-TAGAGGCATC
20874894 GAAGTG
1 GAAGTG
20874900 CAAACTCGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 34 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.32, T:0.14
Consensus pattern (19 bp):
GAAGTGAAATAGAGGCATC
Found at i:20881785 original size:25 final size:25
Alignment explanation
Indices: 20881752--20881813 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
20881742 ACGAGCTGTA
20881752 AACGGTAAGCTCCTCCAAGCTGAAT
1 AACGGTAAGCTCCTCCAAGCTGAAT
**
20881777 AACGGTAAGCTCCTCTGAGCTGAAT
1 AACGGTAAGCTCCTCCAAGCTGAAT
**
20881802 AATTGTAAGCTC
1 AACGGTAAGCTC
20881814 ATGCAAGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (25 bp):
AACGGTAAGCTCCTCCAAGCTGAAT
Found at i:20881821 original size:50 final size:49
Alignment explanation
Indices: 20881736--20881858 Score: 122
Period size: 50 Copynumber: 2.5 Consensus size: 49
20881726 GTACAAGTAT
* * ** * *
20881736 GCTCATACGAGCTGTAAACGGTAAGCTCCTCCAAGCTGA-ATAACGGTAA
1 GCTCATATGAGCTGAAAATTGTAAGCTCATCCAAGCAGAGA-AACGGTAA
* * * *
20881785 GCTCCTCTGAGCTGAATAATTGTAAGCTCATGCAAGCAGAGAACCGGTAA
1 GCTCATATGAGCTGAA-AATTGTAAGCTCATCCAAGCAGAGAAACGGTAA
*
20881835 GCTCATATGAGCTGAAATTTGTAA
1 GCTCATATGAGCTGAAAATTGTAA
20881859 CCCTAATGAC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
49 19 0.32
50 39 0.66
51 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (49 bp):
GCTCATATGAGCTGAAAATTGTAAGCTCATCCAAGCAGAGAAACGGTAA
Found at i:20892287 original size:22 final size:24
Alignment explanation
Indices: 20892242--20892288 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
20892232 ATGAACTTAA
*
20892242 GACATATTTAAAATGCTCAGATTAT
1 GACATATTTAAAA-GCTCAAATTAT
20892267 GACATATTT-AAA-CTCAAATTAT
1 GACATATTTAAAAGCTCAAATTAT
20892289 TGATGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
24 3 0.14
25 9 0.43
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (24 bp):
GACATATTTAAAAGCTCAAATTAT
Found at i:20897208 original size:13 final size:13
Alignment explanation
Indices: 20897190--20897234 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
20897180 CTATAAACTC
20897190 TGTTTTCAAGTTA
1 TGTTTTCAAGTTA
*
20897203 TGTTTTCAAGTCA
1 TGTTTTCAAGTTA
20897216 TGTTTTCAAGTTA
1 TGTTTTCAAGTTA
20897229 TGTTTT
1 TGTTTT
20897235 ACATGAGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.56
Consensus pattern (13 bp):
TGTTTTCAAGTTA
Found at i:20898472 original size:17 final size:18
Alignment explanation
Indices: 20898439--20898474 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20898429 AGTCATGTCT
20898439 TATGTTGTTATGCGAACC
1 TATGTTGTTATGCGAACC
*
20898457 TATGTTG-TATGTGAACC
1 TATGTTGTTATGCGAACC
20898474 T
1 T
20898475 TTATAACACA
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:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (18 bp):
TATGTTGTTATGCGAACC
Found at i:20900862 original size:16 final size:16
Alignment explanation
Indices: 20900841--20900875 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20900831 TGAAAAGGTA
20900841 TGAGTTGATGATGATT
1 TGAGTTGATGATGATT
*
20900857 TGAGTTGATGATGTTT
1 TGAGTTGATGATGATT
20900873 TGA
1 TGA
20900876 ATATGTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (16 bp):
TGAGTTGATGATGATT
Found at i:20906783 original size:37 final size:37
Alignment explanation
Indices: 20906742--20906815 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
20906732 TTTAATAAAA
20906742 TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
1 TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
20906779 TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
1 TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
20906816 ACATCTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (37 bp):
TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
Found at i:20913804 original size:14 final size:13
Alignment explanation
Indices: 20913786--20913819 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
20913776 TAAATAATTA
20913786 ATTTTTTAATATT
1 ATTTTTTAATATT
20913799 ATTTTTTAATATT
1 ATTTTTTAATATT
20913812 ATTTTTTA
1 ATTTTTTA
20913820 TAAAAACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTTAATATT
Found at i:20914061 original size:20 final size:20
Alignment explanation
Indices: 20914007--20914061 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
20913997 TCTAATGTTT
20914007 TTTTTAGT-AATTTTTTATA
1 TTTTTAGTAAATTTTTTATA
* * *
20914026 TTTTTCTGCAATTTTTTTATA
1 TTTTT-AGTAAATTTTTTATA
20914047 TTTTTAGTAAATTTT
1 TTTTTAGTAAATTTT
20914062 ATAATGATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.18
20 8 0.29
21 15 0.54
ACGTcount: A:0.24, C:0.04, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTAGTAAATTTTTTATA
Found at i:20914983 original size:33 final size:33
Alignment explanation
Indices: 20914938--20915004 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
20914928 TAATTATTTT
20914938 AATTAATTAAATTTTATTAAAAT-TATATTTAAA
1 AATTAATTAAATTTT-TTAAAATATATATTTAAA
*
20914971 AATT-ATTGAAATTTTTTATAATATATATTTAAA
1 AATTAATT-AAATTTTTTAAAATATATATTTAAA
20915004 A
1 A
20915005 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
AATTAATTAAATTTTTTAAAATATATATTTAAA
Found at i:20918003 original size:13 final size:13
Alignment explanation
Indices: 20917970--20917995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20917960 GGGTTCTTAG
20917970 GCCTAATTTTCAA
1 GCCTAATTTTCAA
20917983 GCCTAATTTTCAA
1 GCCTAATTTTCAA
20917996 TCTCAATTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
GCCTAATTTTCAA
Found at i:20932895 original size:2 final size:2
Alignment explanation
Indices: 20932885--20932923 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
20932875 TAAATTGGTG
* *
20932885 AT AT A- AT AT AT AT AC AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20932924 TCCATTGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:20937219 original size:59 final size:59
Alignment explanation
Indices: 20937148--20937325 Score: 347
Period size: 59 Copynumber: 3.0 Consensus size: 59
20937138 TGTAATTAAG
*
20937148 TAAATTAGAAAATTAATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
1 TAAATTAGAAAATTCATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
20937207 TAAATTAGAAAATTCATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
1 TAAATTAGAAAATTCATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
20937266 TAAATTAGAAAATTCATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
1 TAAATTAGAAAATTCATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
20937325 T
1 T
20937326 TTATTGAAAA
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 118 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (59 bp):
TAAATTAGAAAATTCATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
Found at i:20939526 original size:39 final size:42
Alignment explanation
Indices: 20939481--20939561 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 42
20939471 TATTTAAGTA
*
20939481 TTGATACCTTTTG-TT-AAA-ACAATAGTATAGTATTTTGTT
1 TTGATACCTTTTGTTTGAAAGAAAATAGTATAGTATTTTGTT
20939520 TTGATACCTTTTGTTTTGAAATGAAAATAGTATAGTATTTTG
1 TTGATACCTTTTG-TTTGAAA-GAAAATAGTATAGTATTTTG
20939562 GTATTGATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 13 0.36
41 2 0.06
42 3 0.08
44 18 0.50
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (42 bp):
TTGATACCTTTTGTTTGAAAGAAAATAGTATAGTATTTTGTT
Found at i:20941786 original size:41 final size:41
Alignment explanation
Indices: 20941729--20941809 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
20941719 TTGCGGCTAG
20941729 GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTTT
1 GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTTT
20941770 GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTT
1 GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTT
20941810 GAACAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (41 bp):
GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTTT
Found at i:20944401 original size:74 final size:73
Alignment explanation
Indices: 20944222--20944413 Score: 188
Period size: 74 Copynumber: 2.6 Consensus size: 73
20944212 CAGGTGAAAA
* * * *
20944222 AATAGTGTTTAGTTGCCCTTTTTAGGTTAAACCTACACGATAAACATCAATTGCTCATCCAAGCT
1 AATAGTGTTT-GTTG-CCTGTTTGGGTTAAACCTACACAACAAACATCAATTGCTCATCCAAGCT
*
20944287 AATCATGAAC
64 AATCATAAAC
* * * ** * **
20944297 AATAGTGTTTGGTTACCCAG-TCGGGTTAAACCTACACAACAAGTATCAATTGCTTATCTGAGCT
1 AATAGTGTTT-GTT-GCCTGTTTGGGTTAAACCTACACAACAAACATCAATTGCTCATCCAAGCT
*
20944361 TATCATAAAC
64 AATCATAAAC
* *
20944371 AATAGTGTTTGCTTGCCTGTTTGGGATAAACCTACACAGCAAA
1 AATAGTGTTTG-TTGCCTGTTTGGGTTAAACCTACACAACAAA
20944414 TGTAACAACT
Statistics
Matches: 93, Mismatches: 21, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
73 4 0.04
74 74 0.80
75 15 0.16
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (73 bp):
AATAGTGTTTGTTGCCTGTTTGGGTTAAACCTACACAACAAACATCAATTGCTCATCCAAGCTAA
TCATAAAC
Found at i:20944556 original size:84 final size:84
Alignment explanation
Indices: 20944445--20944665 Score: 361
Period size: 84 Copynumber: 2.6 Consensus size: 84
20944435 GTCTTCATAA
* * * ** * **
20944445 TTGGTTATTGTTTGGCATATAAATGGTAAATTAAACATAGATTTGAGTAAGTATGTAACAGTCCG
1 TTGGTTACTGTTTAGCGTATAGTTGGTAAAATAAGGATAGATTTGAGTAAGTATGTAACAGTCCG
20944510 CCTAGCGAAGTCTCTGTAT
66 CCTAGCGAAGTCTCTGTAT
20944529 TTGGTTACTGTTTAGCGTATAGTTGGTAAAATAAGGATAGATTTGAGTAAGTATGTAACAGTCCG
1 TTGGTTACTGTTTAGCGTATAGTTGGTAAAATAAGGATAGATTTGAGTAAGTATGTAACAGTCCG
20944594 CCTAGCGAAGTCTCTGTAT
66 CCTAGCGAAGTCTCTGTAT
*
20944613 TTGGTTACTGTTTAGCGTATAGTTGGTAAAATAAGGATAGATATGAGTAAGTA
1 TTGGTTACTGTTTAGCGTATAGTTGGTAAAATAAGGATAGATTTGAGTAAGTA
20944666 AAATTTTTGT
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 128 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (84 bp):
TTGGTTACTGTTTAGCGTATAGTTGGTAAAATAAGGATAGATTTGAGTAAGTATGTAACAGTCCG
CCTAGCGAAGTCTCTGTAT
Found at i:20946030 original size:16 final size:16
Alignment explanation
Indices: 20945992--20946031 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
20945982 TTTTTTGTGT
*
20945992 TTAAATCGGTTAATTC
1 TTAAATTGGTTAATTC
20946008 TTAAATTGGTTAATTC
1 TTAAATTGGTTAATTC
20946024 TTAAATTG
1 TTAAATTG
20946032 ATCCCTGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (16 bp):
TTAAATTGGTTAATTC
Found at i:20954556 original size:18 final size:19
Alignment explanation
Indices: 20954512--20954560 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
20954502 CCAAAATGAA
20954512 ATTGAGAAAAGAAAAAAATG
1 ATTGA-AAAAGAAAAAAATG
** *
20954532 AGAGAAAAAGAAAAAGA-G
1 ATTGAAAAAGAAAAAAATG
20954550 ATTGAAAAAGA
1 ATTGAAAAAGA
20954561 GCAAAAAGCG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 10 0.42
19 11 0.46
20 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.10
Consensus pattern (19 bp):
ATTGAAAAAGAAAAAAATG
Found at i:20979749 original size:22 final size:23
Alignment explanation
Indices: 20979721--20979773 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
20979711 ACACATTAGC
20979721 AAACAAATATATAAATAT-AAAT
1 AAACAAATATATAAATATAAAAT
* *
20979743 AAACAAATATTTATATATAAAAT
1 AAACAAATATATAAATATAAAAT
*
20979766 AAATAAAT
1 AAACAAAT
20979774 TGAATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
AAACAAATATATAAATATAAAAT
Found at i:20979779 original size:28 final size:29
Alignment explanation
Indices: 20979727--20979792 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
20979717 TAGCAAACAA
20979727 ATATATAAATATAAATAAACAAAT-ATTT
1 ATATATAAATATAAATAAACAAATAATTT
**
20979755 ATATATAAA-ATAAATAAATTGAATAATTT
1 ATATATAAATATAAATAAA-CAAATAATTT
*
20979784 ATATTTAAA
1 ATATATAAA
20979793 CTATCAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.27
28 12 0.36
29 12 0.36
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
ATATATAAATATAAATAAACAAATAATTT
Found at i:20993701 original size:87 final size:88
Alignment explanation
Indices: 20993595--20993806 Score: 306
Period size: 87 Copynumber: 2.4 Consensus size: 88
20993585 TATTAAACAC
*
20993595 CAGGAATAAATCCCAAAACAGATTTTATTTAATTTTAAAT-TCTCGTTTGGAAACAAAAT-AAAA
1 CAGGAATAAATCCCTAAACAGATTTTATTTAATTTTAAATAT-TCGTTTGGAAACAAAATCAAAA
* *
20993658 AATGGAATAAAATATGTTGAATGA
65 AATGAAATAAAATATGTTGAACGA
* * *
20993682 CGGGAATAAATCCCTAAACAGATTTTATTTAATTTT-AATATTCGTTTTGAAACAAAGTCAAAAA
1 CAGGAATAAATCCCTAAACAGATTTTATTTAATTTTAAATATTCGTTTGGAAACAAAATCAAAAA
20993746 ATGAAATAAAATATGTTGAACGA
66 ATGAAATAAAATATGTTGAACGA
*
20993769 CAGGAATAAAT-CCTAAAACAGATTTTATTCAATATTTA
1 CAGGAATAAATCCCT-AAACAGATTTTATTTAAT-TTTA
20993807 TTTTTATTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
86 21 0.19
87 88 0.79
88 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (88 bp):
CAGGAATAAATCCCTAAACAGATTTTATTTAATTTTAAATATTCGTTTGGAAACAAAATCAAAAA
ATGAAATAAAATATGTTGAACGA
Found at i:20994200 original size:14 final size:14
Alignment explanation
Indices: 20994181--20994211 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20994171 GATGATCAAA
20994181 GCAGTAACACCTCT
1 GCAGTAACACCTCT
20994195 GCAGTAACACCTCT
1 GCAGTAACACCTCT
20994209 GCA
1 GCA
20994212 ACAAACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.19
Consensus pattern (14 bp):
GCAGTAACACCTCT
Found at i:20994260 original size:285 final size:286
Alignment explanation
Indices: 20993925--20994496 Score: 1137
Period size: 285 Copynumber: 2.0 Consensus size: 286
20993915 CACGTTAGTG
20993925 AACAAACATATAAATATAAATAAACAAATATTTATATATAAAATAAAATAAATTGAATAAATTAT
1 AACAAACATATAAATATAAATAAACAAATATTTATATATAAAATAAAATAAATTGAATAAATTAT
20993990 ATTTAAATTATCATATAAGAAAAACTAACAAATAACATAACGAAAACCAGAAATCAAAAAGAAGA
66 ATTTAAATTATCATATAAGAAAAACTAACAAATAACATAACGAAAACCAGAAATCAAAAAGAAGA
20994055 ATCGAGTTTTACAATATGTTGATGCATGTTTTACACAGTTTCCTTAAGACAGATTCGGCCGCTCC
131 ATCGAGTTTTACAATATGTTGATGCATGTTTTACACAGTTTCCTTAAGACAGATTCGGCCGCTCC
20994120 TACGATACTTGGAGAAACGTTGGGCGACTGTCTTCCAGGATACAACAATACGATGATCAAAGCAG
196 TACGATACTTGGAGAAACGTTGGGCGACTGTCTTCCAGGATACAACAATACGATGATCAAAGCAG
20994185 TAACACCTCTGCAGTAACACCTCTGC
261 TAACACCTCTGCAGTAACACCTCTGC
20994211 AACAAACATA-AAATATAAATAAACAAATATTTATATATAAAATAAAATAAATTGAATAAATTAT
1 AACAAACATATAAATATAAATAAACAAATATTTATATATAAAATAAAATAAATTGAATAAATTAT
20994275 ATTTAAATTATCATATAAGAAAAACTAACAAATAACATAACGAAAACCAGAAATCAAAAAGAAGA
66 ATTTAAATTATCATATAAGAAAAACTAACAAATAACATAACGAAAACCAGAAATCAAAAAGAAGA
20994340 ATCGAGTTTTACAATATGTTGATGCATGTTTTACACAGTTTCCTTAAGACAGATTCGGCCGCTCC
131 ATCGAGTTTTACAATATGTTGATGCATGTTTTACACAGTTTCCTTAAGACAGATTCGGCCGCTCC
20994405 TACGATACTTGGAGAAACGTTGGGCGACTGTCTTCCAGGATACAACAATACGATGATCAAAGCAG
196 TACGATACTTGGAGAAACGTTGGGCGACTGTCTTCCAGGATACAACAATACGATGATCAAAGCAG
20994470 TAACACCTCTGCAGTAACACCTCTGC
261 TAACACCTCTGCAGTAACACCTCTGC
20994496 A
1 A
20994497 GCAATCAACG
Statistics
Matches: 286, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
285 276 0.97
286 10 0.03
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (286 bp):
AACAAACATATAAATATAAATAAACAAATATTTATATATAAAATAAAATAAATTGAATAAATTAT
ATTTAAATTATCATATAAGAAAAACTAACAAATAACATAACGAAAACCAGAAATCAAAAAGAAGA
ATCGAGTTTTACAATATGTTGATGCATGTTTTACACAGTTTCCTTAAGACAGATTCGGCCGCTCC
TACGATACTTGGAGAAACGTTGGGCGACTGTCTTCCAGGATACAACAATACGATGATCAAAGCAG
TAACACCTCTGCAGTAACACCTCTGC
Found at i:20994485 original size:14 final size:14
Alignment explanation
Indices: 20994466--20994497 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
20994456 GATGATCAAA
20994466 GCAGTAACACCTCT
1 GCAGTAACACCTCT
20994480 GCAGTAACACCTCT
1 GCAGTAACACCTCT
20994494 GCAG
1 GCAG
20994498 CAATCAACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (14 bp):
GCAGTAACACCTCT
Found at i:20995539 original size:20 final size:20
Alignment explanation
Indices: 20995514--20995552 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
20995504 GTTAATGTGA
20995514 AAATTTGTCACTATATTTTG
1 AAATTTGTCACTATATTTTG
20995534 AAATTTGTCACTATATTTT
1 AAATTTGTCACTATATTTT
20995553 ACTTTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (20 bp):
AAATTTGTCACTATATTTTG
Found at i:20995597 original size:29 final size:29
Alignment explanation
Indices: 20995531--20995597 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
20995521 TCACTATATT
* *
20995531 TTGAAATTTGTCACTATATTTTACTTTAA
1 TTGAAATTTGCCACTATATTTTACTCTAA
* *
20995560 TTGATATTTGCCATTATATTTTACTCTATA
1 TTGAAATTTGCCACTATATTTTACTCTA-A
20995590 TT-AAATTT
1 TTGAAATTT
20995598 TACATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (29 bp):
TTGAAATTTGCCACTATATTTTACTCTAA
Found at i:20998090 original size:19 final size:18
Alignment explanation
Indices: 20998063--20998114 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
20998053 GTAAGGGTTA
*
20998063 ATTTCATTTTTTTAATATT
1 ATTTAATTTTTTTAAT-TT
*
20998082 ATTTAATTTTTATAATTT
1 ATTTAATTTTTTTAATTT
*
20998100 AATTAATATTTTTTA
1 ATTTAAT-TTTTTTA
20998115 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTAATTTTTTTAATTT
Found at i:21000147 original size:59 final size:59
Alignment explanation
Indices: 21000055--21000248 Score: 307
Period size: 59 Copynumber: 3.3 Consensus size: 59
21000045 ATTGATTTAT
* * *
21000055 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTAAATAAAATGGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
* *
21000114 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTTATTTAATAAAATAAAAGTTA
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
* * * *
21000173 TTTTGAATATTTTTATACAACTTATTTTTATATTATTTCATTTAATAAAATAGAAGTTT
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
21000232 TTTTGAATATTTTTGTA
1 TTTTGAATATTTTTGTA
21000249 AATATATTAT
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 123 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
Found at i:21000346 original size:29 final size:28
Alignment explanation
Indices: 21000305--21000378 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
21000295 AAATTCATCT
* *
21000305 TTGTCAAAATATTTTTTCAGAACACATCA
1 TTGTCAAATTATTTTTTCAAAACACAT-A
*
21000334 -TGTCAAATTTATTTTTTCAAAATACATA
1 TTGTCAAA-TTATTTTTTCAAAACACATA
21000362 TTGTCAAAATTATTTTT
1 TTGTC-AAATTATTTTT
21000379 CCCATAACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 8 0.21
29 28 0.72
30 3 0.08
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.46
Consensus pattern (28 bp):
TTGTCAAATTATTTTTTCAAAACACATA
Found at i:21000441 original size:24 final size:23
Alignment explanation
Indices: 21000406--21000450 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
21000396 CAATTAAAAA
*
21000406 AATTAAACCCTAAAACCCTAAAC
1 AATTAAAACCTAAAACCCTAAAC
*
21000429 AATTAAAAACCTAATACCCTAA
1 AATT-AAAACCTAAAACCCTAA
21000451 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (23 bp):
AATTAAAACCTAAAACCCTAAAC
Found at i:21001103 original size:22 final size:20
Alignment explanation
Indices: 21001072--21001112 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
21001062 AAATTTAAAA
21001072 ATTTTAAAAATATATAAAAATT
1 ATTTTAAAAA-A-ATAAAAATT
*
21001094 ATTTTTAAAAAATAAAAAT
1 ATTTTAAAAAAATAAAAAT
21001113 CATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTTAAAAAAATAAAAATT
Found at i:21001177 original size:162 final size:163
Alignment explanation
Indices: 21000965--21001289 Score: 643
Period size: 162 Copynumber: 2.0 Consensus size: 163
21000955 TACGTTTTAT
21000965 GTCAAATCATCCCAAAATGAATGGAAAAACTAATGTTTTTTAAATTTTGCTGATGTGGCATACAC
1 GTCAAATCATCCCAAAATGAATGGAAAAACTAATGTTTTTTAAATTTTGCTGATGTGGCATACAC
21001030 GTGGATGGCATGCAAGCATTTAATTATTTTTTAAATTTAAAAATTTTAAAAATATATAAAAATTA
66 GTGGATGGCATGCAAGCATTTAATTATTTTTTAAATTTAAAAATTTTAAAAATATATAAAAATTA
21001095 TTTTTAAAAAATAAAAATCATTAAATTTATTAA
131 TTTTTAAAAAATAAAAATCATTAAATTTATTAA
21001128 GTCAAATCATCCC-AAATGAATGGAAAAACTAATGTTTTTTAAATTTTGCTGATGTGGCATACAC
1 GTCAAATCATCCCAAAATGAATGGAAAAACTAATGTTTTTTAAATTTTGCTGATGTGGCATACAC
21001192 GTGGATGGCATGCAAGCATTTAATTATTTTTTAAATTTAAAAATTTTAAAAATATATAAAAATTA
66 GTGGATGGCATGCAAGCATTTAATTATTTTTTAAATTTAAAAATTTTAAAAATATATAAAAATTA
21001257 TTTTTAAAAAATAAAAATCATTAAATTTATTAA
131 TTTTTAAAAAATAAAAATCATTAAATTTATTAA
21001290 AAAGTATAAT
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 149 0.92
163 13 0.08
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (163 bp):
GTCAAATCATCCCAAAATGAATGGAAAAACTAATGTTTTTTAAATTTTGCTGATGTGGCATACAC
GTGGATGGCATGCAAGCATTTAATTATTTTTTAAATTTAAAAATTTTAAAAATATATAAAAATTA
TTTTTAAAAAATAAAAATCATTAAATTTATTAA
Found at i:21001265 original size:22 final size:20
Alignment explanation
Indices: 21001234--21001274 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
21001224 AAATTTAAAA
21001234 ATTTTAAAAATATATAAAAATT
1 ATTTTAAAAA-A-ATAAAAATT
*
21001256 ATTTTTAAAAAATAAAAAT
1 ATTTTAAAAAAATAAAAAT
21001275 CATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTTAAAAAAATAAAAATT
Found at i:21002081 original size:31 final size:31
Alignment explanation
Indices: 21002024--21002085 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
21002014 ATTATTATTT
** *
21002024 TAGTTAAATTTGATGATCAATTTTTTAAAAA
1 TAGTTAAATTTGACAATCAATCTTTTAAAAA
21002055 TAGTTAAATTTGACAA-CTAATCTTTTAAAAA
1 TAGTTAAATTTGACAATC-AATCTTTTAAAAA
21002086 AAATTGAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (31 bp):
TAGTTAAATTTGACAATCAATCTTTTAAAAA
Found at i:21013741 original size:19 final size:18
Alignment explanation
Indices: 21013714--21013765 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
21013704 GTAAGGGTTA
*
21013714 ATTTCATTTTTTTAATATT
1 ATTTAATTTTTTTAAT-TT
*
21013733 ATTTAATTTTTATAATTT
1 ATTTAATTTTTTTAATTT
*
21013751 AATTAATATTTTTTA
1 ATTTAAT-TTTTTTA
21013766 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTAATTTTTTTAATTT
Found at i:21015812 original size:59 final size:59
Alignment explanation
Indices: 21015706--21015899 Score: 298
Period size: 59 Copynumber: 3.3 Consensus size: 59
21015696 ATTGATTTAT
* * *
21015706 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTAAATAAAATGGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
* * *
21015765 TTTTGAATATTTTTGTACAAATTATTTTTATATGGTTTTATTTAATAAAATAAAAGTTA
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
* * * *
21015824 TTTTGAATATTTTTATACAACTTATTTTTATATTATTTCATTTAATAAAATAGAAGTTT
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
21015883 TTTTGAATATTTTTGTA
1 TTTTGAATATTTTTGTA
21015900 AATATATTAT
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 121 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
Found at i:21015988 original size:29 final size:29
Alignment explanation
Indices: 21015951--21016029 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
21015941 AAAAAAAATT
* * *
21015951 CATCTTGTCAAAATAATTTTTTCAGAACA
1 CATCATGTCAAAATTATTTTTTCAAAACA
* *
21015980 CATCATGTCAAATTTATTTTTTCAAAATA
1 CATCATGTCAAAATTATTTTTTCAAAACA
21016009 CAT-ATTGTCAAAATTATTTTT
1 CATCA-TGTCAAAATTATTTTT
21016030 CCCATAACAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 1 0.02
29 42 0.98
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (29 bp):
CATCATGTCAAAATTATTTTTTCAAAACA
Found at i:21016092 original size:24 final size:23
Alignment explanation
Indices: 21016057--21016101 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
21016047 CAATTAAAAA
*
21016057 AATTAAACCCTAAAACCCTAAAC
1 AATTAAAACCTAAAACCCTAAAC
*
21016080 AATTAAAAACCTAATACCCTAA
1 AATT-AAAACCTAAAACCCTAA
21016102 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (23 bp):
AATTAAAACCTAAAACCCTAAAC
Found at i:21016754 original size:22 final size:20
Alignment explanation
Indices: 21016723--21016763 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
21016713 AAATTTAAAA
21016723 ATTTTAAAAATATATAAAAATT
1 ATTTTAAAAA-A-ATAAAAATT
*
21016745 ATTTTTAAAAAATAAAAAT
1 ATTTTAAAAAAATAAAAAT
21016764 CATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTTAAAAAAATAAAAATT
Found at i:21017570 original size:31 final size:31
Alignment explanation
Indices: 21017513--21017574 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
21017503 ATTATTATTT
** *
21017513 TAGTTAAATTTGATGATCAATTTTTTAAAAA
1 TAGTTAAATTTGACAATCAATCTTTTAAAAA
21017544 TAGTTAAATTTGACAA-CTAATCTTTTAAAAA
1 TAGTTAAATTTGACAATC-AATCTTTTAAAAA
21017575 AAATTGAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (31 bp):
TAGTTAAATTTGACAATCAATCTTTTAAAAA
Found at i:21025835 original size:9 final size:9
Alignment explanation
Indices: 21025821--21025851 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
21025811 GTTAAACGAA
21025821 TCGAGTTAT
1 TCGAGTTAT
*
21025830 TCGAGTTAA
1 TCGAGTTAT
21025839 TCGAGTTAT
1 TCGAGTTAT
21025848 TCGA
1 TCGA
21025852 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:21033608 original size:68 final size:70
Alignment explanation
Indices: 21033516--21033664 Score: 191
Period size: 69 Copynumber: 2.2 Consensus size: 70
21033506 GTCATAGCTG
* *
21033516 AGCCATGG-CTTATACCTCGAAATCCCTGT-TTTACTATC-CTGATGAACTAACCTAGTTGCCAT
1 AGCCATGGTCTTATACCTCAAAATCCCTATGTTTACTATCTC-GATGAACTAACCTAGTTGCCAT
21033578 AG-CCA
65 AGTCCA
* * **
21033583 AGCCATGGTCTTATACCTCAAAATCCCTATGTTTACTATCTCGGTGGACTAACCTAGTTTTCATA
1 AGCCATGGTCTTATACCTCAAAATCCCTATGTTTACTATCTCGATGAACTAACCTAGTTGCCATA
21033648 GTCCA
66 GTCCA
*
21033653 A-CCATGTTCTTA
1 AGCCATGGTCTTA
21033665 CATAGTATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
67 8 0.11
68 19 0.27
69 39 0.55
70 5 0.07
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (70 bp):
AGCCATGGTCTTATACCTCAAAATCCCTATGTTTACTATCTCGATGAACTAACCTAGTTGCCATA
GTCCA
Found at i:21033685 original size:69 final size:69
Alignment explanation
Indices: 21033545--21033963 Score: 180
Period size: 69 Copynumber: 6.1 Consensus size: 69
21033535 AAATCCCTGT
* * * * *
21033545 TTTACTATCCT-G-ATGAACTAACCTAGTTGCCATAG-CCAAGCCATGGTCTTATACCT-CAAAA
1 TTTACTATCCTGGCA-G-ACTAACCTAGTTGTCATAGTCCAA-CCATGGTCTTACA-CTGTATAT
21033606 T-CCCTATG
62 TCCCCT-TG
** * *
21033614 TTTACTAT-CTCGGTGGACTAACCTAGTTTTCATAGTCCAACCATGTTCTTACA-TAGTATATTC
1 TTTACTATCCT-GGCAGACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACT-GTATATTC
21033677 CCCTTG
64 CCCTTG
** * * * * *
21033683 TTTGTTGTCCTGGCAGACTATCCTGGTTGTCATAGTCTAACCATGGTCTTACACTGTATATTCCT
1 TTTACTATCCTGGCAGACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACTGTATATTCCC
*
21033748 CGTG
66 CTTG
* * * * * **
21033752 TTTACTGTCCTGG-TGAACTATCC-AGGTTG-CTATAATCCAACCATAGTCTTACACCATATATT
1 TTTACTATCCTGGCAG-ACTAACCTA-GTTGTC-ATAGTCCAACCATGGTCTTACACTGTATATT
**
21033814 -CATTATG
63 CCCCT-TG
* * * * * * * * * * **
21033821 TTTACTGTCCCGG-TGAACTATCCTGGTTGCCATTGTCCAACAATGGTATTATACTGTATATTTA
1 TTTACTATCCTGGCAG-ACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACTGTATATTCC
* **
21033885 TCGGG
65 CCTTG
* ** * * * * * *
21033890 TTTACTGTTATGGCAGACTATCTTGGTTGCCATAGTCCAACCATGGTCTTA-ACCGTATATTCCT
1 TTTACTATCCTGGCAGACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACTGTATATTCCC
*
21033954 CATG
66 CTTG
21033958 TTTACT
1 TTTACT
21033964 CAGAGCTTCG
Statistics
Matches: 273, Mismatches: 60, Indels: 35
0.74 0.16 0.10
Matches are distributed among these distances:
67 1 0.00
68 23 0.08
69 234 0.86
70 15 0.05
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (69 bp):
TTTACTATCCTGGCAGACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACTGTATATTCCC
CTTG
Found at i:21033823 original size:138 final size:137
Alignment explanation
Indices: 21033699--21033963 Score: 316
Period size: 138 Copynumber: 1.9 Consensus size: 137
21033689 GTCCTGGCAG
* * * * * * *
21033699 ACTATCCTGGTTGTCATAGTCTAACCATGGTCTTACACTGTATATTCCTCGTGTTTACTGTCCTG
1 ACTATCCTGGTTGCCATAGTCCAACAATGGTATTACACTGTATATTCATCGGGTTTACTGTCATG
* * *
21033764 G-TGAACTATCCAGGTTGCTATAATCCAACCATAGTCTTACACCATATATTCATTATGTTTACTG
66 GCAG-ACTATCCAGGTTGCCATAATCCAACCATAGTCTTA-ACCATATATTCATCATGTTTACTG
*
21033828 TCCCGGTGA
129 TCCCGGAGA
* * * *
21033837 ACTATCCTGGTTGCCATTGTCCAACAATGGTATTATACTGTATATTTATCGGGTTTACTGTTATG
1 ACTATCCTGGTTGCCATAGTCCAACAATGGTATTACACTGTATATTCATCGGGTTTACTGTCATG
** * * * *
21033902 GCAGACTATCTTGGTTGCCATAGTCCAACCATGGTCTTAACCGTATATTCCTCATGTTTACT
66 GCAGACTATCCAGGTTGCCATAATCCAACCATAGTCTTAACCATATATTCATCATGTTTACT
21033964 CAGAGCTTCG
Statistics
Matches: 106, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
137 20 0.19
138 85 0.80
139 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (137 bp):
ACTATCCTGGTTGCCATAGTCCAACAATGGTATTACACTGTATATTCATCGGGTTTACTGTCATG
GCAGACTATCCAGGTTGCCATAATCCAACCATAGTCTTAACCATATATTCATCATGTTTACTGTC
CCGGAGA
Found at i:21036418 original size:41 final size:39
Alignment explanation
Indices: 21036349--21036432 Score: 123
Period size: 41 Copynumber: 2.1 Consensus size: 39
21036339 ATAAACAGTA
* *
21036349 ATAAACATAACATATATAATATCCTACTAATATACATAC
1 ATAAACATAACATACAAAATATCCTACTAATATACATAC
*
21036388 ATAAACATTAATATACAAAATATCCATACTAATATACATAC
1 ATAAACA-TAACATACAAAATATCC-TACTAATATACATAC
21036429 ATAA
1 ATAA
21036433 TAGACATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.17
40 14 0.35
41 19 0.47
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.30
Consensus pattern (39 bp):
ATAAACATAACATACAAAATATCCTACTAATATACATAC
Found at i:21036422 original size:21 final size:22
Alignment explanation
Indices: 21036366--21036427 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
21036356 TAACATATAT
21036366 AATATCC-TACTAATATACATA
1 AATATCCATACTAATATACATA
* **
21036387 CATAAACAT--TAATATACA-A
1 AATATCCATACTAATATACATA
21036406 AATATCCATACTAATATACATA
1 AATATCCATACTAATATACATA
21036428 CATAATAGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 7 0.23
20 9 0.29
21 13 0.42
22 2 0.06
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.31
Consensus pattern (22 bp):
AATATCCATACTAATATACATA
Found at i:21036427 original size:12 final size:12
Alignment explanation
Indices: 21036373--21036450 Score: 62
Period size: 12 Copynumber: 7.0 Consensus size: 12
21036363 TATAATATCC
21036373 TACTAATATACA
1 TACTAATATACA
*
21036385 TAC--ATAAACA
1 TACTAATATACA
21036395 T--TAATATACA
1 TACTAATATACA
*
21036405 -A--AATATCCA
1 TACTAATATACA
21036414 TACTAATATACA
1 TACTAATATACA
*
21036426 TACATAATAGACA
1 TAC-TAATATACA
*
21036439 TAATAATATACA
1 TACTAATATACA
21036451 ATTGACTGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
9 7 0.13
10 14 0.27
12 21 0.40
13 10 0.19
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.29
Consensus pattern (12 bp):
TACTAATATACA
Found at i:21036428 original size:25 final size:25
Alignment explanation
Indices: 21036400--21036450 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
21036390 AAACATTAAT
** *
21036400 ATACAAAATATCCATACTAATATAC
1 ATACAAAATAGACATAATAATATAC
*
21036425 ATACATAATAGACATAATAATATAC
1 ATACAAAATAGACATAATAATATAC
21036450 A
1 A
21036451 ATTGACTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (25 bp):
ATACAAAATAGACATAATAATATAC
Found at i:21038975 original size:19 final size:20
Alignment explanation
Indices: 21038938--21038975 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21038928 GGAGTGAGTT
* *
21038938 AATATTTTTTTTAAGAAATA
1 AATAATTTTTATAAGAAATA
21038958 AATAATTTTTATAA-AAAT
1 AATAATTTTTATAAGAAAT
21038976 TCCAAGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATAATTTTTATAAGAAATA
Found at i:21041391 original size:19 final size:19
Alignment explanation
Indices: 21041359--21041402 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
21041349 ATGTTCTTAC
* * *
21041359 TAAAAATTAGAAAAGATTA
1 TAAAAATAAAAAAAAATTA
*
21041378 TAAAAATAAAAAAAAATTT
1 TAAAAATAAAAAAAAATTA
21041397 TAAAAA
1 TAAAAA
21041403 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
TAAAAATAAAAAAAAATTA
Found at i:21041431 original size:17 final size:17
Alignment explanation
Indices: 21041395--21041447 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
21041385 AAAAAAAAAT
* *
21041395 TTTAAAAAATTTA-AAT
1 TTTAAAAAAATTAGAAA
21041411 TTTAAAAAAATTAGAAA
1 TTTAAAAAAATTAGAAA
**
21041428 TTTATTAAAATTAGAAA
1 TTTAAAAAAATTAGAAA
21041445 TTT
1 TTT
21041448 TTTTATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (17 bp):
TTTAAAAAAATTAGAAA
Found at i:21041521 original size:19 final size:19
Alignment explanation
Indices: 21041491--21041535 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
21041481 AAAATTTTAT
21041491 TTTTTAT-A-TTTCTAT-A
1 TTTTTATAATTTTCTATGA
21041507 TATTTTATAATTTTCTATGA
1 T-TTTTATAATTTTCTATGA
21041527 TTTTTATAA
1 TTTTTATAA
21041536 AATTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.04
17 6 0.24
18 1 0.04
19 15 0.60
20 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTATAATTTTCTATGA
Found at i:21041557 original size:29 final size:29
Alignment explanation
Indices: 21041508--21041563 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
21041498 ATTTCTATAT
*
21041508 ATTTTATAATTTTCTATGATTTTTATAAA
1 ATTTTATAATTTTCTACGATTTTTATAAA
*
21041537 ATTTTA-AATATTTTTACGATTTTTATA
1 ATTTTATAAT-TTTCTACGATTTTTATA
21041564 TTTTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (29 bp):
ATTTTATAATTTTCTACGATTTTTATAAA
Found at i:21041566 original size:8 final size:8
Alignment explanation
Indices: 21041485--21041569 Score: 55
Period size: 9 Copynumber: 9.6 Consensus size: 8
21041475 AATTGTAAAA
21041485 TTTTAT-T
1 TTTTATAT
21041492 TTTTATAT
1 TTTTATAT
*
21041500 TTCTATAT
1 TTTTATAT
21041508 ATTTTATAAT
1 -TTTTAT-AT
21041518 TTTCTATGAT
1 TTT-TAT-AT
21041528 TTTTATAAAAT
1 TTTTAT---AT
*
21041539 TTTAAATAT
1 TTT-TATAT
*
21041548 TTTTACGAT
1 TTTTA-TAT
21041557 TTTTATAT
1 TTTTATAT
21041565 TTTTA
1 TTTTA
21041570 ATAACTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
7 6 0.10
8 16 0.26
9 23 0.37
10 10 0.16
11 5 0.08
12 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (8 bp):
TTTTATAT
Found at i:21041888 original size:90 final size:88
Alignment explanation
Indices: 21041659--21041888 Score: 336
Period size: 91 Copynumber: 2.6 Consensus size: 88
21041649 AATCTTTAAT
21041659 AAAAAAA-AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTGACACATTTTGAAAG
1 AAAAAAAGAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTGACACATTTTGAAAG
* * *
21041723 TTCAAGTACCCAATTGAGTGATA
66 TTCAAATACCCAATTGAGTCAAA
* * * * **
21041746 AAAAAAGGTAGGGGCTTAATTGCTTTTTTTTAAAAGGTTTGAGGGCTTTTTTGATGCATTTTGAA
1 AAAAAAAG-AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG-TCTTTTGACACATTTTGAA
21041811 AGTTCAAATACCCAATTGAGTACAAA
64 AGTTCAAATACCCAATTGAGT-CAAA
21041837 AAAAAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTG
1 AAAAAAAG-AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTG
21041889 CACCCTTAAG
Statistics
Matches: 125, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
87 6 0.05
89 34 0.27
90 42 0.34
91 43 0.34
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.36
Consensus pattern (88 bp):
AAAAAAAGAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTGACACATTTTGAAAG
TTCAAATACCCAATTGAGTCAAA
Found at i:21044101 original size:21 final size:21
Alignment explanation
Indices: 21044037--21044103 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
21044027 GCTCTGCTCC
* *
21044037 GCTTCTCTCGCTGCAGCCTCC
1 GCTTCCCTCGCTGCAGCCTCT
*
21044058 GCTTCCCTCGCTGCAGCCGCT
1 GCTTCCCTCGCTGCAGCCTCT
* *
21044079 GCTTCCCTCGCTTCCGCCTCT
1 GCTTCCCTCGCTGCAGCCTCT
21044100 GCTT
1 GCTT
21044104 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.48, G:0.19, T:0.30
Consensus pattern (21 bp):
GCTTCCCTCGCTGCAGCCTCT
Found at i:21044447 original size:16 final size:17
Alignment explanation
Indices: 21044426--21044576 Score: 75
Period size: 18 Copynumber: 8.7 Consensus size: 17
21044416 TGATATATGT
*
21044426 TTATGTA-TTAAGTAAA
1 TTATGTAGTTAAGTAAG
* *
21044442 TTATGTAAGTTATGTACG
1 TTATGT-AGTTAAGTAAG
*
21044460 TGTAT-AAGTTAAGTAAG
1 T-TATGTAGTTAAGTAAG
21044477 TTATGTA-TTAAGTAAG
1 TTATGTAGTTAAGTAAG
* *
21044493 TTATGTAAGTTATGAAAG
1 TTATGT-AGTTAAGTAAG
*
21044511 TAATGTA-TGTAATGTAAG
1 TTATGTAGT-TAA-GTAAG
21044529 -T-TGTAAGTTATTATGT-A-
1 TTATGT-AGTTA--A-GTAAG
*
21044546 TTATGTAAGTTATGTAAG
1 TTATGT-AGTTAAGTAAG
21044564 TTATGTAAGTTAA
1 TTATGT-AGTTAA
21044577 ATGTATTATG
Statistics
Matches: 104, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
16 30 0.29
17 20 0.19
18 38 0.37
19 16 0.15
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (17 bp):
TTATGTAGTTAAGTAAG
Found at i:21044456 original size:25 final size:25
Alignment explanation
Indices: 21044426--21044619 Score: 126
Period size: 25 Copynumber: 7.8 Consensus size: 25
21044416 TGATATATGT
*
21044426 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
*
21044451 TTATGTACGTGT-A-TAAGTTAAGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
21044477 TTATGTATTAAGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
21044502 TTATG-A--AAGTAA-TGTATGTAA-
1 TTATGTATTAAGTAAGT-TATGTAAG
* *
21044523 TGTAAGT-TGTAAGTTA-TTATGT-A-
1 T-TATGTAT-TAAGTAAGTTATGTAAG
*
21044546 TTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGT-A-TTAAGTAAGTTATGTAAG
*
21044573 TTAAATGTATTATGTAAG-T-TGTAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
21044598 TTAAATGTATTATGTAAGTTAT
1 TT--ATGTATTAAGTAAGTTAT
21044620 TATGTATTAT
Statistics
Matches: 140, Mismatches: 8, Indels: 40
0.74 0.04 0.21
Matches are distributed among these distances:
21 2 0.01
22 20 0.14
23 3 0.02
24 13 0.09
25 61 0.44
26 21 0.15
27 14 0.10
28 2 0.01
29 4 0.03
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.44
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:21044476 original size:9 final size:9
Alignment explanation
Indices: 21044433--21044576 Score: 56
Period size: 9 Copynumber: 16.4 Consensus size: 9
21044423 TGTTTATGTA
*
21044433 TTAAGTAAA
1 TTAAGTAAG
*
21044442 TTATGTAAG
1 TTAAGTAAG
* *
21044451 TTATGTACG
1 TTAAGTAAG
21044460 TGT-A-TAAG
1 T-TAAGTAAG
21044468 TTAAGTAAG
1 TTAAGTAAG
*
21044477 TTATGT-A-
1 TTAAGTAAG
21044484 TTAAGTAAG
1 TTAAGTAAG
*
21044493 TTATGTAAG
1 TTAAGTAAG
* *
21044502 TTATGAAAG
1 TTAAGTAAG
*
21044511 -TAATGTATG
1 TTAA-GTAAG
21044520 -TAATGTAAG
1 TTAA-GTAAG
21044529 TT--GTAAG
1 TTAAGTAAG
21044536 TTATTATGT-A-
1 TTA--A-GTAAG
*
21044546 TTATGTAAG
1 TTAAGTAAG
*
21044555 TTATGTAAG
1 TTAAGTAAG
*
21044564 TTATGTAAG
1 TTAAGTAAG
21044573 TTAA
1 TTAA
21044577 ATGTATTATG
Statistics
Matches: 106, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
7 15 0.14
8 10 0.09
9 73 0.69
10 5 0.05
11 1 0.01
12 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (9 bp):
TTAAGTAAG
Found at i:21044554 original size:62 final size:61
Alignment explanation
Indices: 21044477--21044811 Score: 278
Period size: 62 Copynumber: 5.3 Consensus size: 61
21044467 GTTAAGTAAG
* *
21044477 TTATGTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAGTTGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTATGTAAGT-ATGTATGTAATGTAAGTTGTAAGTTA
21044539 TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGTAT-T-ATGTAAGTTGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTATGTAAG-T--ATGTATGTAATGTAAGTTGTAAGTTA
* * * *
21044601 -AATGTATTATGTAAGTTAT-TATGTATTATGTAAGT-TGTAAGTTAAATGT-ATTATGTAAGTT
1 TTATGTATTATGTAAGTTATGTAAG--TTATGTAAGTATGTATG-T-AATGTAAGT-TGTAAGTT
21044662 A
61 A
*
21044663 TTATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTAT-TATGTATTATGTAAGTTGT
1 TTATGTATTATGTAAG-T-TATG-T-AA-G--TTATGTAAG-TATGTATGTA--ATGTAAGTTGT
21044727 AAGTTA
56 AAGTTA
* * * *
21044733 -AATGTATTATGTAAGTTAT-TATGTATTATGTAAGT-TGTAAGTTAAATGT-ATTATGTAAGTT
1 TTATGTATTATGTAAGTTATGTAAG--TTATGTAAGTATGTATG-T-AATGTAAGT-TGTAAGTT
21044794 A
61 A
21044795 TTATGTATTATGTAAGT
1 TTATGTATTATGTAAGT
21044812 CACCTGTTGT
Statistics
Matches: 230, Mismatches: 17, Indels: 51
0.77 0.06 0.17
Matches are distributed among these distances:
58 4 0.02
60 4 0.02
61 24 0.10
62 88 0.38
63 44 0.19
64 10 0.04
65 3 0.01
67 3 0.01
68 3 0.01
69 27 0.12
70 17 0.07
71 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.47
Consensus pattern (61 bp):
TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTATGTATGTAATGTAAGTTGTAAGTTA
Found at i:21044570 original size:44 final size:43
Alignment explanation
Indices: 21044472--21044811 Score: 452
Period size: 44 Copynumber: 8.0 Consensus size: 43
21044462 TATAAGTTAA
* * *
21044472 GTAAGTT-ATGTATTAAGTAAGTTATGTAAG--TTATGAAAGTAAT
1 GTAAGTTAATGTATTATGTAAGTTAT-TATGTATTATGTAAGT--T
* *
21044515 GTATG-TAATGTAAGT-TGTAAGTTATTATGTATTATGTAAG-T
1 GTAAGTTAATGT-ATTATGTAAGTTATTATGTATTATGTAAGTT
* *
21044556 -TATG-TAA-G--TTATGTAAGTTA-AATGTATTATGTAAGTT
1 GTAAGTTAATGTATTATGTAAGTTATTATGTATTATGTAAGTT
21044593 GTAAGTTAAATGTATTATGTAAGTTATTATGTATTATGTAAGTT
1 GTAAGTT-AATGTATTATGTAAGTTATTATGTATTATGTAAGTT
21044637 GTAAGTTAAATGTATTATGTAAGTTATTATGTATTATGTAAGTT
1 GTAAGTT-AATGTATTATGTAAGTTATTATGTATTATGTAAGTT
21044681 GTAAGTTAAATGTATTATGTAAGTTATTATGTATTATGTAAGTT
1 GTAAGTT-AATGTATTATGTAAGTTATTATGTATTATGTAAGTT
21044725 GTAAGTTAAATGTATTATGTAAGTTATTATGTATTATGTAAGTT
1 GTAAGTT-AATGTATTATGTAAGTTATTATGTATTATGTAAGTT
21044769 GTAAGTTAAATGTATTATGTAAGTTATTATGTATTATGTAAGT
1 GTAAGTT-AATGTATTATGTAAGTTATTATGTATTATGTAAGT
21044812 CACCTGTTGT
Statistics
Matches: 275, Mismatches: 9, Indels: 25
0.89 0.03 0.08
Matches are distributed among these distances:
36 15 0.05
37 10 0.04
38 3 0.01
39 2 0.01
40 9 0.03
41 2 0.01
42 4 0.01
43 29 0.11
44 201 0.73
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (43 bp):
GTAAGTTAATGTATTATGTAAGTTATTATGTATTATGTAAGTT
Found at i:21047102 original size:83 final size:83
Alignment explanation
Indices: 21047010--21047674 Score: 1312
Period size: 83 Copynumber: 8.0 Consensus size: 83
21047000 AAATCTATTA
*
21047010 AATTTCATTTCACGAAACGGCTACGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
21047075 CAAAAACGCCACTAAATT
66 CAAAAACGCCACTAAATT
21047093 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
21047158 CAAAAACGCCACTAAATT
66 CAAAAACGCCACTAAATT
21047176 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
21047241 CAAAAACGCCACTAAATT
66 CAAAAACGCCACTAAATT
21047259 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
21047324 CAAAAACGCCACTAAATT
66 CAAAAACGCCACTAAATT
21047342 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
21047407 CAAAAACGCCACTAAATT
66 CAAAAACGCCACTAAATT
21047425 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
21047490 CAAAAACGCCACTAAATT
66 CAAAAACGCCACTAAATT
21047508 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
21047573 CAAAAACGCCACTAAATT
66 CAAAAACGCCACTAAATT
21047591 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
*
21047656 AAAAAACGCCACTAAATT
66 CAAAAACGCCACTAAATT
21047674 A
1 A
21047675 TTTATATTTA
Statistics
Matches: 580, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 580 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.40
Consensus pattern (83 bp):
AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTTTTA
CAAAAACGCCACTAAATT
Found at i:21048122 original size:39 final size:40
Alignment explanation
Indices: 21048054--21048134 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
21048044 CCTAACCCAT
**
21048054 AACCCCTAAATCCCCCTTAACCTTTAAAGCATAAACCCTA
1 AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
* *
21048094 AACCCCTAAAT-CTCCTTAACCCCTAAAGCATAACCCCTA
1 AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
21048133 AA
1 AA
21048135 TAATTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.38, C:0.38, G:0.02, T:0.21
Consensus pattern (40 bp):
AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
Found at i:21048981 original size:111 final size:111
Alignment explanation
Indices: 21048621--21048954 Score: 632
Period size: 111 Copynumber: 3.0 Consensus size: 111
21048611 AAATTAGTCT
21048621 AAGTATGACCAAAAAAGTAAAAAAAAAAAATCAGATACGGAGATGAGAAAAACGTAGAGTTTAAG
1 AAGTATGACCAAAAAAGTAAAAAAAAAAAATCAGATACGGAGATGAGAAAAACGTAGAGTTTAAG
21048686 TTCCCTATGTGGATTAAGGAAAAAACAAAAGGAAAGGAAAAAAGAA
66 TTCCCTATGTGGATTAAGGAAAAAACAAAAGGAAAGGAAAAAAGAA
21048732 AAGTATGACCAAAAAAGTAAAAAAAAAAAATCAGATACGGAGATGAGAAAAACGTAGAGTTTAAG
1 AAGTATGACCAAAAAAGTAAAAAAAAAAAATCAGATACGGAGATGAGAAAAACGTAGAGTTTAAG
21048797 TTCCCTATGTGGATTAAGGAAAAAACAAAAGGAAAGGAAAAAAGAA
66 TTCCCTATGTGGATTAAGGAAAAAACAAAAGGAAAGGAAAAAAGAA
* *
21048843 AAGTATGACCAAAAAAGTAAAAAAAAAAAATCAGATACCGAGATGAGAATAACGTAGAGTTTAAG
1 AAGTATGACCAAAAAAGTAAAAAAAAAAAATCAGATACGGAGATGAGAAAAACGTAGAGTTTAAG
* *
21048908 TTCCCTATGTGGATTAAGGAAAAAACAGAAGGAAAGGAACAAAGAA
66 TTCCCTATGTGGATTAAGGAAAAAACAAAAGGAAAGGAAAAAAGAA
21048954 A
1 A
21048955 TTTACTAATA
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 219 1.00
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.16
Consensus pattern (111 bp):
AAGTATGACCAAAAAAGTAAAAAAAAAAAATCAGATACGGAGATGAGAAAAACGTAGAGTTTAAG
TTCCCTATGTGGATTAAGGAAAAAACAAAAGGAAAGGAAAAAAGAA
Found at i:21051291 original size:3 final size:3
Alignment explanation
Indices: 21051283--21051321 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
21051273 CTCCATTAGT
*
21051283 TTC TTC TTC TTC TTC TTC TTC CTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
21051322 GCCATTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:21057058 original size:11 final size:12
Alignment explanation
Indices: 21057042--21057074 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
21057032 ATTTCACTGA
21057042 AAAATTTCG-TG
1 AAAATTTCGTTG
21057053 AAAATTTCGTTTG
1 AAAATTTCG-TTG
21057066 AAAATTTCG
1 AAAATTTCG
21057075 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
13 11 0.55
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (12 bp):
AAAATTTCGTTG
Found at i:21058190 original size:42 final size:43
Alignment explanation
Indices: 21058139--21058379 Score: 221
Period size: 42 Copynumber: 5.7 Consensus size: 43
21058129 ATTGAATAAG
* *
21058139 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATTATTGACTTTA
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATTATTGAATTTA
21058180 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCT-TTG-ATTGTGA
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTAT-TATTGAATT-T-A
* * *
21058224 AAGG-GGTTGCTATGTGCTGATTCC-CCGTATTACTGAATATA
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATTATTGAATTTA
* * * * *
21058265 AAGGTGGTTGCTAAGTGTTCATTCCACTGTATCT-TTGACTGTGA
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTAT-TATTGAAT-TTA
* * * * *
21058309 AAGGGGGGTTGCTATGTGCTGATTCC-TCGTATCACTGAATTT-
1 AA-GGTGGTTGCTAAGTGCTGATTCCACCGTATTATTGAATTTA
*
21058351 AAGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGTGGTTGCTAAGTGCTGATTCCACCG
21058380 AGTAACGGAT
Statistics
Matches: 159, Mismatches: 27, Indels: 27
0.75 0.13 0.13
Matches are distributed among these distances:
41 30 0.19
42 52 0.33
43 40 0.25
44 18 0.11
45 19 0.12
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (43 bp):
AAGGTGGTTGCTAAGTGCTGATTCCACCGTATTATTGAATTTA
Found at i:21058289 original size:85 final size:84
Alignment explanation
Indices: 21058139--21058379 Score: 329
Period size: 85 Copynumber: 2.8 Consensus size: 84
21058129 ATTGAATAAG
* * * * *
21058139 AAGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGACTTTAAAGGTGGTTGCTAAGTGCTGATTC
1 AAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGA-ATTAAAGGTGGTTGCTAAGTGCTCATTC
*
21058204 CACCGTATCTTTGATTGTGA
65 CACCGTATCTTTGACTGTGA
*
21058224 AAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATATAAAGGTGGTTGCTAAGTGTTCATTC
1 AAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAAT-TAAAGGTGGTTGCTAAGTGCTCATTC
*
21058289 CACTGTATCTTTGACTGTGA
65 CACCGTATCTTTGACTGTGA
* * * * *
21058309 AAGGGGGGTTGCTATGTGCTGATTCCTCGTATCACTGAATTTAAGGTGGTTGCTAAGTGCTGAAT
1 AA--GGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCTCATT
21058374 CCACCG
64 CCACCG
21058380 AGTAACGGAT
Statistics
Matches: 138, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
84 1 0.01
85 77 0.56
86 26 0.19
87 34 0.25
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (84 bp):
AAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCTCATTCC
ACCGTATCTTTGACTGTGA
Found at i:21061170 original size:103 final size:104
Alignment explanation
Indices: 21061030--21061240 Score: 311
Period size: 103 Copynumber: 2.0 Consensus size: 104
21061020 GCCAAAATAA
* * *
21061030 TATCGATTTTCAATTGAGTATCGATACTTTTTGGTAAAATATCGATACCATCAACTAATTATTGA
1 TATCAATTTTCAATTGAGTATCAATACTTTTTGGTAAAATATCGATACCATCAACTAATTATCGA
*
21061095 TACCA-TTGTTTTACAAAGAAAACA-AAGTTGAATTTTTG
66 TACCATTTGTTTTACAAAGAAAACATAA-TTGAATTTTGG
*
21061133 TATCAATTTTCAATTGAGTATTAATACATTTTT-GTAAAATATCGATACCATCAACTAATTATCG
1 TATCAATTTTCAATTGAGTATCAATAC-TTTTTGGTAAAATATCGATACCATCAACTAATTATCG
* *
21061197 ATACCATTTTTTTTTACAAAGAAAATATAATTGAATTTTGG
65 ATACCA-TTTGTTTTACAAAGAAAACATAATTGAATTTTGG
21061238 TAT
1 TAT
21061241 TGATTTTTCT
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
103 60 0.62
104 5 0.05
105 30 0.31
106 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (104 bp):
TATCAATTTTCAATTGAGTATCAATACTTTTTGGTAAAATATCGATACCATCAACTAATTATCGA
TACCATTTGTTTTACAAAGAAAACATAATTGAATTTTGG
Found at i:21063561 original size:20 final size:20
Alignment explanation
Indices: 21063536--21063576 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
21063526 ATCAACAAGT
* *
21063536 TAGAGGACTAAAGAATTAAA
1 TAGAGGACCAAAGAATAAAA
21063556 TAGAGGACCAAAGAATAAAA
1 TAGAGGACCAAAGAATAAAA
21063576 T
1 T
21063577 TTATCCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (20 bp):
TAGAGGACCAAAGAATAAAA
Found at i:21079693 original size:30 final size:29
Alignment explanation
Indices: 21079657--21079819 Score: 134
Period size: 30 Copynumber: 5.4 Consensus size: 29
21079647 AGCTATCGAT
* *
21079657 TATGAAAAGGGATGGTGACGACCATGGAAC
1 TATGAAAAGGGATGATGACGACCAT-CAAC
* ** * *
21079687 TATGAAAAGGGATGGCT-TTGGCTATCAATC
1 TATGAAAAGGGAT-GATGACGACCATCAA-C
* *
21079717 TATGAAAAGGGATGACT-TC-AGCTATCAATC
1 TATGAAAAGGGATGA-TGACGA-CCATCAA-C
21079747 TATGAAAAGGGATGATGACGACCATCGAAC
1 TATGAAAAGGGATGATGACGACCATC-AAC
* *
21079777 TATGAAAAGGGATGATGACGACAATCAAAT
1 TATGAAAAGGGATGATGACGACCATC-AAC
21079807 TATGAAAAGGGAT
1 TATGAAAAGGGAT
21079820 AGCTTCAGTT
Statistics
Matches: 112, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.04
30 103 0.92
31 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGATGACGACCATCAAC
Found at i:21079804 original size:90 final size:90
Alignment explanation
Indices: 21079629--21079848 Score: 261
Period size: 90 Copynumber: 2.5 Consensus size: 90
21079619 TTATCAACGA
* * * * *
21079629 ATGAAAAGGAATAGCTTTAGCTATCGAT-TATGAAAAGGGATGGTGACGACCATGGAACTATGAA
1 ATGAAAAGGGATAGCTTCAGCTATCAATCTATGAAAAGGGATGATGACGACCATCGAACTATGAA
* ** * *
21079693 AAGGGATGGCTTTGGCTATC-AATCT
66 AAGGGATGGATACGACAATCAAAT-T
21079718 ATGAAAAGGGAT-GACTTCAGCTATCAATCTATGAAAAGGGATGATGACGACCATCGAACTATGA
1 ATGAAAAGGGATAG-CTTCAGCTATCAATCTATGAAAAGGGATGATGACGACCATCGAACTATGA
21079782 AAAGGGAT-GATGACGACAATCAAATT
65 AAAGGGATGGAT-ACGACAATCAAATT
* *
21079808 ATGAAAAGGGATAGCTTCAGTTGTCTAA-CTATGAAAAGGGA
1 ATGAAAAGGGATAGCTTCAGCTATC-AATCTATGAAAAGGGA
21079849 AAACTTCGGT
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
88 1 0.01
89 25 0.22
90 81 0.72
91 6 0.05
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (90 bp):
ATGAAAAGGGATAGCTTCAGCTATCAATCTATGAAAAGGGATGATGACGACCATCGAACTATGAA
AAGGGATGGATACGACAATCAAATT
Found at i:21086745 original size:29 final size:30
Alignment explanation
Indices: 21086651--21086868 Score: 180
Period size: 29 Copynumber: 7.4 Consensus size: 30
21086641 TCATTGACGA
*
21086651 ATGAAAAGGAATAGCTTCGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGGCTATCGAATT
* *
21086680 ACGGAAAGGGATAGCTTCGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGGCTATCGAATT
* * *
21086709 ACGGAAAGGGATAGCTTCAGCTATC-AATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATT
* * * * *
21086738 ATGAAAAGGGAT-GGTGACGACCATCGAACT
1 ATGAAAAGGGATAGCT-TCGGCTATCGAATT
* * ** * * *
21086768 ATGAAAAGGGAT-GGTGACAACCATCAAACT
1 ATGAAAAGGGATAGCT-TCGGCTATCGAATT
*
21086798 ATGAAAAGGGATGGCTTCGGCTATC-AATCT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT-T
*
21086828 ATGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATT
21086858 AT-AAAAGGGAT
1 ATGAAAAGGGAT
21086869 GGTGACAACC
Statistics
Matches: 162, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.02
29 77 0.48
30 76 0.47
31 5 0.03
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATT
Found at i:21086773 original size:30 final size:30
Alignment explanation
Indices: 21086737--21086928 Score: 183
Period size: 30 Copynumber: 6.4 Consensus size: 30
21086727 AGCTATCAAT
*
21086737 TATGAAAAGGGATGGTGACGACCATCGAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
*
21086767 TATGAAAAGGGATGGTGACAACCATCAAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
* * * *
21086797 TATGAAAAGGGATGGCT-TCGGCTATCAATC
1 TATGAAAAGGGATGG-TGACGACCATCAAAC
* * * * *
21086827 TATGAAAAGGGATAGCT-TCGGCTATCAAAT
1 TATGAAAAGGGAT-GGTGACGACCATCAAAC
* *
21086857 TAT-AAAAGGGATGGTGACAACCATCGAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
* * * *
21086886 TATGAAAAAGGATGGTAATGACCATCAAAT
1 TATGAAAAGGGATGGTGACGACCATCAAAC
*
21086916 TATAAAAAGGGAT
1 TATGAAAAGGGAT
21086929 AGCTTTGGCA
Statistics
Matches: 133, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
28 2 0.02
29 19 0.14
30 110 0.83
31 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCAAAC
Done.