Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 127 of 226
Found at i:42785752 original size:26 final size:26
Alignment explanation
Indices: 42785702--42785753 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
42785692 TTGCCACATA
*
42785702 TACTGTTACTGGCAGCCTTGCTGCGT
1 TACTGTTACTAGCAGCCTTGCTGCGT
* * *
42785728 TACTGTTACTAGTAGCTTTGTTGCGT
1 TACTGTTACTAGCAGCCTTGCTGCGT
42785754 CATTATTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.40
Consensus pattern (26 bp):
TACTGTTACTAGCAGCCTTGCTGCGT
Found at i:42792217 original size:13 final size:14
Alignment explanation
Indices: 42792199--42792229 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
42792189 TGTTGCCAAT
42792199 TTTTCCC-CTTCTC
1 TTTTCCCTCTTCTC
42792212 TTTTCCCTCTTCTC
1 TTTTCCCTCTTCTC
42792226 TTTT
1 TTTT
42792230 TTTCTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTCCCTCTTCTC
Found at i:42793139 original size:27 final size:27
Alignment explanation
Indices: 42793071--42793181 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
42793061 CACGATTCGT
*
42793071 GGTAAAATTACCGAACTACCCT--ACAA
1 GGTAAAATTACCGAAATACCCTCGA-AA
* *
42793097 GGTAAAATTACCGAAATACCCTCGTAG
1 GGTAAAATTACCGAAATACCCTCGAAA
* *
42793124 GGTAAAATTACTGAAATACCCTTGAAA
1 GGTAAAATTACCGAAATACCCTCGAAA
* * *
42793151 GGTGAAATTACCGAAATACCCCCGAAG
1 GGTAAAATTACCGAAATACCCTCGAAA
42793178 GGTA
1 GGTA
42793182 TAATAACTGT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
26 21 0.30
27 49 0.70
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.21
Consensus pattern (27 bp):
GGTAAAATTACCGAAATACCCTCGAAA
Found at i:42793166 original size:54 final size:53
Alignment explanation
Indices: 42793071--42793190 Score: 152
Period size: 54 Copynumber: 2.2 Consensus size: 53
42793061 CACGATTCGT
* * * *
42793071 GGTAAAATTACCGAACTACCCTACAAGGTAAAATTACCGAAATACCCTCGTAG
1 GGTAAAATTACTGAAATACCCTACAAGGTAAAATTACCGAAATACCCCCGAAG
*
42793124 GGTAAAATTACTGAAATACCCTTGA-AAGGTGAAATTACCGAAATACCCCCGAAG
1 GGTAAAATTACTGAAATACCC-T-ACAAGGTAAAATTACCGAAATACCCCCGAAG
* *
42793178 GGTATAATAACTG
1 GGTAAAATTACTG
42793191 TTATACCCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
53 19 0.33
54 38 0.66
55 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (53 bp):
GGTAAAATTACTGAAATACCCTACAAGGTAAAATTACCGAAATACCCCCGAAG
Found at i:42793397 original size:26 final size:26
Alignment explanation
Indices: 42793363--42793412 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
42793353 TTGCCACATA
42793363 TACTGTTACTGCCAGCCTTGCTGCGT
1 TACTGTTACTGCCAGCCTTGCTGCGT
* *
42793389 TACTGTTACTGGCAGCTTTGCTGC
1 TACTGTTACTGCCAGCCTTGCTGC
42793413 ATCATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.12, C:0.28, G:0.24, T:0.36
Consensus pattern (26 bp):
TACTGTTACTGCCAGCCTTGCTGCGT
Found at i:42793987 original size:20 final size:20
Alignment explanation
Indices: 42793962--42794004 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
42793952 ACACCGACTT
*
42793962 AAGAAATGAGTTTTATCAAC
1 AAGAAACGAGTTTTATCAAC
42793982 AAGAAACGAGTTTTATCAAC
1 AAGAAACGAGTTTTATCAAC
42794002 AAG
1 AAG
42794005 TCTAAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (20 bp):
AAGAAACGAGTTTTATCAAC
Found at i:42803143 original size:24 final size:24
Alignment explanation
Indices: 42803081--42803163 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 24
42803071 TACCGGAACT
* * *
42803081 CAGCTCGCATGAGCTTACTGTTATT
1 CAGCTCGTAAGAGCTTACTGTT-TA
* * *
42803106 TAGCTCGGAGGAGCTTACTGTTTA
1 CAGCTCGTAAGAGCTTACTGTTTA
* *
42803130 CAGCTCGTAAGAGCATACCGATTTA
1 CAGCTCGTAAGAGCTTACTG-TTTA
*
42803155 GAGCTCGTA
1 CAGCTCGTA
42803164 TAAGCATACA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 16 0.34
25 31 0.66
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (24 bp):
CAGCTCGTAAGAGCTTACTGTTTA
Found at i:42806211 original size:21 final size:21
Alignment explanation
Indices: 42806187--42806228 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42806177 CAACTTTTTC
42806187 TTTTT-CAGCAACAACTTCCT
1 TTTTTGCAGCAACAACTTCCT
**
42806207 TTTTTGCAGCAGTAACTTCCT
1 TTTTTGCAGCAACAACTTCCT
42806228 T
1 T
42806229 ATCAACAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (21 bp):
TTTTTGCAGCAACAACTTCCT
Found at i:42818743 original size:11 final size:11
Alignment explanation
Indices: 42818721--42818754 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
42818711 CCATAGACTG
*
42818721 AGAAATCGTCC
1 AGAAATCATCC
*
42818732 ATAAATCATCC
1 AGAAATCATCC
42818743 AGAAATCATCC
1 AGAAATCATCC
42818754 A
1 A
42818755 AAGAGTCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (11 bp):
AGAAATCATCC
Found at i:42824820 original size:81 final size:81
Alignment explanation
Indices: 42824685--42824839 Score: 283
Period size: 81 Copynumber: 1.9 Consensus size: 81
42824675 GATTACCTTT
*
42824685 GTTAATTCTGGGAAAACATTCATTCAATTAAATCAACCTTTATTAAGTTAGATTAGCAAAACTAG
1 GTTAATTCTGGGAAAACATTCATTCAATTAAATCAACCTTTATTAAGTCAGATTAGCAAAACTAG
42824750 TGTGATTTTGGAAAAA
66 TGTGATTTTGGAAAAA
*
42824766 GTTAATTCTGGGAAAACATTCATTTAATTAAATCAACCTTTATTAAGTCAGATTAGCAAAACTAG
1 GTTAATTCTGGGAAAACATTCATTCAATTAAATCAACCTTTATTAAGTCAGATTAGCAAAACTAG
*
42824831 TGTGGTTTT
66 TGTGATTTT
42824840 TAGAAAACAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (81 bp):
GTTAATTCTGGGAAAACATTCATTCAATTAAATCAACCTTTATTAAGTCAGATTAGCAAAACTAG
TGTGATTTTGGAAAAA
Found at i:42828600 original size:27 final size:27
Alignment explanation
Indices: 42828569--42828833 Score: 332
Period size: 27 Copynumber: 9.8 Consensus size: 27
42828559 GTTATGACTA
* *
42828569 AAATACCTCTATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
42828596 AAATACCCCCATAGGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
42828623 AAATACTCCCATAAGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
42828650 AAATACCCCCATAGGATAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
42828677 AAATACCCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
42828704 AAATACCCTCATAGGGTAAAATGAACG
1 AAATACCCCCATAGGGTAAAATGACCG
** * *
42828731 AAATACCCTTATAGGGTAGAATGACCA
1 AAATACCCCCATAGGGTAAAATGACCG
*** **
42828758 AAATACTGTCATAGGGTAAAATGGTCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
42828785 AAATACCCCCATAGGGAAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
42828812 AGATACCCCCATAGGGTAAAAT
1 AAATACCCCCATAGGGTAAAAT
42828834 AACTGTTATA
Statistics
Matches: 206, Mismatches: 32, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 206 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCG
Found at i:42831959 original size:13 final size:13
Alignment explanation
Indices: 42831941--42831966 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42831931 GGGAAGGGAT
42831941 TTGAACTTAGGAC
1 TTGAACTTAGGAC
42831954 TTGAACTTAGGAC
1 TTGAACTTAGGAC
42831967 CTCATTTAAT
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:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
TTGAACTTAGGAC
Found at i:42845524 original size:35 final size:33
Alignment explanation
Indices: 42845467--42845552 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 33
42845457 TGAATTGACG
* * *
42845467 GATAAGACCATGGTTGGACCATGGCAATGTTTAAAT
1 GATAAGACCATAGCTGGGCCATGGC-AT-TTT-AAT
42845503 G-TAAGACCATAGCTGGGCCATGGCATTTTAAT
1 GATAAGACCATAGCTGGGCCATGGCATTTTAAT
* *
42845535 GAAAAGACCATAACTGGG
1 GATAAGACCATAGCTGGG
42845553 TTATGGCACC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
32 4 0.09
33 17 0.39
34 2 0.05
35 20 0.45
36 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (33 bp):
GATAAGACCATAGCTGGGCCATGGCATTTTAAT
Found at i:42845654 original size:105 final size:101
Alignment explanation
Indices: 42845469--42845718 Score: 267
Period size: 105 Copynumber: 2.5 Consensus size: 101
42845459 AATTGACGGA
* *
42845469 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTGGGCCATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGCTGGGCCATGGCATTCTAA
*
42845534 TGAAAAGACCATAACTGGGTTATGGCACCTTGAACG
66 TGAAAAGACCATAACTAGGTTATGGCACCTTGAACG
* *
42845570 TAAGACCATGGTTGGACCATGGCAGTATAG-ATACATGTGTAAGACCATAGCTGGGCTATGGCAT
1 TAAGACCATGGTTGGACCATGGCA--AT-GTATA-A-ATGTAAGACCATAGCTGGGCCATGGCAT
* * * ** *
42845634 TCTGATGATAAA-AGCTTAACTAGGTTATGGCA-CTACAAATG
61 TCTAATGA-AAAGACCATAACTAGGTTATGGCACCT-TGAACG
** * *
42845675 TAAGACCATGGAAGGGCCATGGCAATG--CAAATGTAAGACCATAG
1 TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAG
42845719 TTGGACTATG
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
99 13 0.10
100 1 0.01
101 25 0.20
102 1 0.01
103 6 0.05
104 4 0.03
105 73 0.58
106 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGCTGGGCCATGGCATTCTAA
TGAAAAGACCATAACTAGGTTATGGCACCTTGAACG
Found at i:42845730 original size:33 final size:33
Alignment explanation
Indices: 42845659--42845731 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
42845649 TTAACTAGGT
* * *
42845659 TATGGCACTACAAATGTAAGACCATGGAAGGGC
1 TATGGCAATACAAATGTAAGACCATAGAAGGAC
* * **
42845692 CATGGCAATGCAAATGTAAGACCATAGTTGGAC
1 TATGGCAATACAAATGTAAGACCATAGAAGGAC
42845725 TATGGCA
1 TATGGCA
42845732 CAAAAAGAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (33 bp):
TATGGCAATACAAATGTAAGACCATAGAAGGAC
Found at i:42854367 original size:20 final size:21
Alignment explanation
Indices: 42854342--42854396 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
42854332 ATACACATCG
*
42854342 GTGCCCCTGTTTGCACTTC-A
1 GTGCCCCTGTTTGCACATCTA
*
42854362 GTGCCCCTGATTGCACATCTA
1 GTGCCCCTGTTTGCACATCTA
*
42854383 -TGCCCTTGTTTGCA
1 GTGCCCCTGTTTGCA
42854397 TCTATGATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.13, C:0.33, G:0.20, T:0.35
Consensus pattern (21 bp):
GTGCCCCTGTTTGCACATCTA
Found at i:42856880 original size:17 final size:16
Alignment explanation
Indices: 42856851--42856897 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
42856841 CACTTTTTCA
42856851 ATCATCC-CTCATCTC
1 ATCATCCTCTCATCTC
42856866 ATCATCCCTCTCATCTC
1 ATCAT-CCTCTCATCTC
42856883 -TCATCCTCTC-TCTC
1 ATCATCCTCTCATCTC
42856897 A
1 A
42856898 ACTCTCTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.14
15 11 0.38
16 6 0.21
17 8 0.28
ACGTcount: A:0.17, C:0.47, G:0.00, T:0.36
Consensus pattern (16 bp):
ATCATCCTCTCATCTC
Found at i:42856886 original size:19 final size:19
Alignment explanation
Indices: 42856862--42856903 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42856852 TCATCCCTCA
*
42856862 TCTCATCATCCCTCTCATC
1 TCTCATCATCCCTCTCAAC
* *
42856881 TCTCATCCTCTCTCTCAAC
1 TCTCATCATCCCTCTCAAC
42856900 TCTC
1 TCTC
42856904 TTAGCTCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.48, G:0.00, T:0.38
Consensus pattern (19 bp):
TCTCATCATCCCTCTCAAC
Found at i:42867721 original size:50 final size:49
Alignment explanation
Indices: 42867613--42867846 Score: 324
Period size: 50 Copynumber: 4.7 Consensus size: 49
42867603 ATGTCAAAGT
* * ** * *
42867613 CATGTCCTAGACATGGTCTTACATGGAATGTACTCATGTCGGTGCCCATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTC-GTGCCAATGC
** *
42867664 CATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTACGTGCCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGTGCCAATGC
*
42867714 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC-GTGCCAATGC
*
42867764 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATC-TCGTGCCAATGC
42867814 CATGTCCCAGACATGGTCTTACATGGGACCTCT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCT
42867847 TTACCCAAAT
Statistics
Matches: 165, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
49 1 0.01
50 137 0.83
51 27 0.16
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (49 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGTGCCAATGC
Found at i:42868233 original size:29 final size:31
Alignment explanation
Indices: 42868183--42868240 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
42868173 CCTCGACTCT
* *
42868183 AACTTTTTCAAAATTATGA-TTTTGCCCCTA
1 AACTTTTGCAAAATTATCATTTTTGCCCCTA
*
42868213 AACTTTTGCATAATTA-CATTTTTGCCCC
1 AACTTTTGCAAAATTATCATTTTTGCCCC
42868241 AAGGCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (31 bp):
AACTTTTGCAAAATTATCATTTTTGCCCCTA
Found at i:42871210 original size:18 final size:18
Alignment explanation
Indices: 42871186--42871229 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
42871176 CATAGTTTGG
42871186 CAAATTAATACAGT-TCAC
1 CAAATTAATACA-TATCAC
*
42871204 CATATTAATACATATCAC
1 CAAATTAATACATATCAC
42871222 CAAATTAA
1 CAAATTAA
42871230 CACACCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (18 bp):
CAAATTAATACATATCAC
Found at i:42871253 original size:31 final size:31
Alignment explanation
Indices: 42871201--42871262 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
42871191 TAATACAGTT
42871201 CACCATATTAATACATATCACCAAATTAACA
1 CACCATATTAATACATATCACCAAATTAACA
*
42871232 CACCATAATTATATA-AT-TCACCAAGTTAACA
1 CACCAT-ATTA-ATACATATCACCAAATTAACA
42871263 TGGTTCACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 19 0.68
32 6 0.21
33 3 0.11
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (31 bp):
CACCATATTAATACATATCACCAAATTAACA
Found at i:42874957 original size:13 final size:13
Alignment explanation
Indices: 42874939--42874965 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42874929 TTTCCAGCAA
42874939 TTATGAATTTATT
1 TTATGAATTTATT
42874952 TTATGAATTTATT
1 TTATGAATTTATT
42874965 T
1 T
42874966 AATGTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:42875140 original size:50 final size:50
Alignment explanation
Indices: 42875065--42875257 Score: 287
Period size: 50 Copynumber: 3.8 Consensus size: 50
42875055 ATTTGGGTAA
42875065 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
42875115 AGAGGTCCCATGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * * *
42875165 AGAGGTCCCCTGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
42875215 AGAAAATCCCACGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
42875258 TGTTATTATC
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
50 95 0.74
51 33 0.26
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:42878556 original size:2 final size:2
Alignment explanation
Indices: 42878544--42878582 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
42878534 TGATAAATAG
* * *
42878544 GT GT GT AT GT GT GT AT GT GT GT AT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
42878583 CACGTACGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.08, C:0.00, G:0.44, T:0.49
Consensus pattern (2 bp):
GT
Found at i:42878582 original size:8 final size:8
Alignment explanation
Indices: 42878544--42878581 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
42878534 TGATAAATAG
42878544 GTGTGTAT
1 GTGTGTAT
42878552 GTGTGTAT
1 GTGTGTAT
42878560 GTGTGTAT
1 GTGTGTAT
*
42878568 GTGTGTGT
1 GTGTGTAT
42878576 GTGTGT
1 GTGTGT
42878582 GCACGTACGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.08, C:0.00, G:0.42, T:0.50
Consensus pattern (8 bp):
GTGTGTAT
Found at i:42882624 original size:14 final size:15
Alignment explanation
Indices: 42882598--42882633 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
42882588 GGCCGTGTGT
42882598 CACACACGGCTGAGA
1 CACACACGGCTGAGA
42882613 CACACA-GGCTGAGA
1 CACACACGGCTGAGA
42882627 CACACAC
1 CACACAC
42882634 CAGTGTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.36, C:0.36, G:0.22, T:0.06
Consensus pattern (15 bp):
CACACACGGCTGAGA
Found at i:42884601 original size:13 final size:13
Alignment explanation
Indices: 42884583--42884607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42884573 TGATTTACTA
42884583 AATTAACCTTATT
1 AATTAACCTTATT
42884596 AATTAACCTTAT
1 AATTAACCTTAT
42884608 AATCACTTCA
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:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTAACCTTATT
Found at i:42886544 original size:23 final size:22
Alignment explanation
Indices: 42886518--42886572 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42886508 CTTGAATTTG
* * * *
42886518 TTCTTTTAATTGTTTTTTTTTC
1 TTCTTTTAAATATATTTGTTTC
42886540 TTTCTTTCTAAATATATTTGTTTC
1 -TTCTTT-TAAATATATTTGTTTC
42886564 TTCTTTTAA
1 TTCTTTTAA
42886573 GTTAAATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.11
23 12 0.44
24 12 0.44
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (22 bp):
TTCTTTTAAATATATTTGTTTC
Found at i:42888154 original size:14 final size:14
Alignment explanation
Indices: 42888118--42888151 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
42888108 CCATTATTTG
42888118 CCTATAACCAAAAC
1 CCTATAACCAAAAC
42888132 CCTATAACCAAAAC
1 CCTATAACCAAAAC
42888146 CC-ATAA
1 CCTATAA
42888152 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:42893411 original size:18 final size:19
Alignment explanation
Indices: 42893388--42893426 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
42893378 GATATAAAAA
42893388 AAGTACTTT-AAAAAAGTT
1 AAGTACTTTAAAAAAAGTT
42893406 AAGTACTTTAAAAAAAGTT
1 AAGTACTTTAAAAAAAGTT
42893425 AA
1 AA
42893427 CATTTGGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (19 bp):
AAGTACTTTAAAAAAAGTT
Found at i:42893490 original size:14 final size:14
Alignment explanation
Indices: 42893471--42893503 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
42893461 GCAGCTTGTG
42893471 TATTTCTTTTTAAA
1 TATTTCTTTTTAAA
*
42893485 TATTTCTTTTTTAA
1 TATTTCTTTTTAAA
42893499 TATTT
1 TATTT
42893504 TATTATAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTCTTTTTAAA
Found at i:42895638 original size:3 final size:3
Alignment explanation
Indices: 42895630--42895666 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
42895620 TAGAAGTGTG
42895630 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42895667 TAACGACCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42896258 original size:22 final size:22
Alignment explanation
Indices: 42896230--42896301 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
42896220 CCTCTTATCC
42896230 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
42896252 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
42896274 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
42896296 CTCATG
1 CTCATG
42896302 TTTGAACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:42900667 original size:63 final size:62
Alignment explanation
Indices: 42900568--42900695 Score: 202
Period size: 63 Copynumber: 2.0 Consensus size: 62
42900558 GTTGAACTTT
* * *
42900568 TTTATTGTTAATATTTTCTCTACCATGATTATCAAGGAGTGAAAATTATGGATTGAAGGCTAG
1 TTTATTGTTAATACTTTCTCTACCATGATTATCAAGGAGTGAAAACTATGGATAG-AGGCTAG
* *
42900631 TTTATTGTTAGTCCTTTCTCTACCATGATTATCAAGGAGTGAAAACTATGGATAGAGGCTAG
1 TTTATTGTTAATACTTTCTCTACCATGATTATCAAGGAGTGAAAACTATGGATAGAGGCTAG
42900693 TTT
1 TTT
42900696 GTTGCTATCA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
62 10 0.17
63 50 0.83
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.39
Consensus pattern (62 bp):
TTTATTGTTAATACTTTCTCTACCATGATTATCAAGGAGTGAAAACTATGGATAGAGGCTAG
Found at i:42901845 original size:17 final size:17
Alignment explanation
Indices: 42901823--42901856 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42901813 TTGGTAATGG
42901823 CTAAAGATTTGAACAAA
1 CTAAAGATTTGAACAAA
42901840 CTAAAGATTTGAACAAA
1 CTAAAGATTTGAACAAA
42901857 GAACATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
CTAAAGATTTGAACAAA
Found at i:42903763 original size:2 final size:2
Alignment explanation
Indices: 42903756--42903790 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
42903746 TTACCTTCTT
42903756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42903791 TTCATGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42904011 original size:14 final size:13
Alignment explanation
Indices: 42903992--42904037 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
42903982 TAAATTTGAG
42903992 ATTTAATCTATATA
1 ATTTAAT-TATATA
42904006 ATTTAATT-TATA
1 ATTTAATTATATA
*
42904018 ATATAATT-TATA
1 ATTTAATTATATA
*
42904030 ATATAATT
1 ATTTAATT
42904038 TAGTCCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 23 0.74
13 1 0.03
14 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAATTATATA
Found at i:42904019 original size:12 final size:12
Alignment explanation
Indices: 42904002--42904039 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
42903992 ATTTAATCTA
*
42904002 TATAATTTAATT
1 TATAATATAATT
42904014 TATAATATAATT
1 TATAATATAATT
42904026 TATAATATAATT
1 TATAATATAATT
42904038 TA
1 TA
42904040 GTCCTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATAATATAATT
Found at i:42905877 original size:9 final size:10
Alignment explanation
Indices: 42905854--42905878 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42905844 GTATTTTATT
42905854 TTTTTAAATA
1 TTTTTAAATA
42905864 TTTTTAAATA
1 TTTTTAAATA
42905874 TTTTT
1 TTTTT
42905879 TTGTTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:42924943 original size:50 final size:50
Alignment explanation
Indices: 42924720--42924956 Score: 305
Period size: 50 Copynumber: 4.7 Consensus size: 50
42924710 GGGAATGAGA
* * * * *
42924720 TCCCATGTAAGACCATGTCTGGGAAATTGCGTTGCCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
42924770 TCTCC-TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
42924820 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*** * * **
42924870 TCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * *
42924920 TCCCATGTAAGACCATATTTGGGATATGACATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42924957 GTACAGAAAA
Statistics
Matches: 163, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 2 0.01
50 159 0.98
51 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:42925222 original size:12 final size:12
Alignment explanation
Indices: 42925205--42925243 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42925195 ATGAGTTATT
42925205 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
42925217 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
42925229 TAAGTGAGTAAG
1 TAAGTAAGCAAG
42925241 TAA
1 TAA
42925244 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:42930072 original size:40 final size:40
Alignment explanation
Indices: 42930036--42930156 Score: 188
Period size: 40 Copynumber: 3.0 Consensus size: 40
42930026 ATGTGCATTG
* * * *
42930036 AGGGGTACCCAAGTACAAATAAGGACACGTAGGTGCAATC
1 AGGGGTACCGAAGTACAAATAGGGGCACGTAAGTGCAATC
* *
42930076 AGGGGTACCGAAGTACAGACAGGGGCACGTAAGTGCAATC
1 AGGGGTACCGAAGTACAAATAGGGGCACGTAAGTGCAATC
42930116 AGGGGTACCGAAGTACAAATAGGGGCACGTAAGTGCAATC
1 AGGGGTACCGAAGTACAAATAGGGGCACGTAAGTGCAATC
42930156 A
1 A
42930157 TTTAATAATT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.36, C:0.19, G:0.31, T:0.14
Consensus pattern (40 bp):
AGGGGTACCGAAGTACAAATAGGGGCACGTAAGTGCAATC
Found at i:42930089 original size:80 final size:80
Alignment explanation
Indices: 42929988--42930156 Score: 221
Period size: 80 Copynumber: 2.1 Consensus size: 80
42929978 AAGCACAAAT
* * * * * * *
42929988 GTGCGATCAGGGGCATCGAAGTGCAGACAGGGGTACATATGTGCATTGAGGGGTACCCAAGTACA
1 GTGCAATCAGGGGCACCGAAGTACAGACAGGGGCACATAAGTGCAATCAGGGGTACCCAAGTACA
*
42930053 AATAAGGACACGTAG
66 AATAAGGACACGTAA
* * *
42930068 GTGCAATCAGGGGTACCGAAGTACAGACAGGGGCACGTAAGTGCAATCAGGGGTACCGAAGTACA
1 GTGCAATCAGGGGCACCGAAGTACAGACAGGGGCACATAAGTGCAATCAGGGGTACCCAAGTACA
* *
42930133 AATAGGGGCACGTAA
66 AATAAGGACACGTAA
42930148 GTGCAATCA
1 GTGCAATCA
42930157 TTTAATAATT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.16
Consensus pattern (80 bp):
GTGCAATCAGGGGCACCGAAGTACAGACAGGGGCACATAAGTGCAATCAGGGGTACCCAAGTACA
AATAAGGACACGTAA
Found at i:42930100 original size:20 final size:20
Alignment explanation
Indices: 42930071--42930133 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
42930061 CACGTAGGTG
42930071 CAATCAGGGGTACCGAAGTA
1 CAATCAGGGGTACCGAAGTA
* *
42930091 CAGA-CAGGGGCA-CGTAAGTG
1 CA-ATCAGGGGTACCG-AAGTA
42930111 CAATCAGGGGTACCGAAGTA
1 CAATCAGGGGTACCGAAGTA
42930131 CAA
1 CAA
42930134 ATAGGGGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.35, C:0.21, G:0.32, T:0.13
Consensus pattern (20 bp):
CAATCAGGGGTACCGAAGTA
Found at i:42930149 original size:20 final size:20
Alignment explanation
Indices: 42930046--42930149 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
42930036 AGGGGTACCC
* *
42930046 AAGTACAAATAAGGACACGT
1 AAGTACAAATAGGGGCACGT
* * *
42930066 AGGTGC-AATCAGGGGTACCG-
1 AAGTACAAAT-AGGGGCA-CGT
* *
42930086 AAGTACAGACAGGGGCACGT
1 AAGTACAAATAGGGGCACGT
* *
42930106 AAGTGC-AATCAGGGGTACCG-
1 AAGTACAAAT-AGGGGCA-CGT
42930126 AAGTACAAATAGGGGCACGT
1 AAGTACAAATAGGGGCACGT
42930146 AAGT
1 AAGT
42930150 GCAATCATTT
Statistics
Matches: 60, Mismatches: 16, Indels: 16
0.65 0.17 0.17
Matches are distributed among these distances:
19 8 0.13
20 44 0.73
21 8 0.13
ACGTcount: A:0.37, C:0.17, G:0.32, T:0.14
Consensus pattern (20 bp):
AAGTACAAATAGGGGCACGT
Found at i:42940988 original size:50 final size:50
Alignment explanation
Indices: 42940934--42941107 Score: 206
Period size: 50 Copynumber: 3.5 Consensus size: 50
42940924 ATCCTAGATG
** * * *
42940934 TGGTCTTACATGGGAGTTCTCATATCGGTGCCTATGCCATGTCCTAGACA
1 TGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACA
* * *
42940984 TGGTCTTAC-GGAGGACCTCTCATCTTGGTGCCAACGCCATGTCCCAGACA
1 TGGTCTTACATG-GGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACA
* * * *
42941034 TAGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCCAAACA
1 TGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACA
* *
42941084 TGGTCTTAAATGGGATCTCTCATA
1 TGGTCTTACATGGGACCTCTCATA
42941108 ATCTCAATGA
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 1 0.01
50 102 0.98
51 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (50 bp):
TGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACA
Found at i:42947065 original size:22 final size:22
Alignment explanation
Indices: 42947040--42947082 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
42947030 ATTGCCTCTA
*
42947040 ATTTAGCA-ATAAACTGCCACTG
1 ATTT-GCAGATAAACTACCACTG
*
42947062 ATTTGTAGATAAACTACCACT
1 ATTTGCAGATAAACTACCACT
42947083 AATAACACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (22 bp):
ATTTGCAGATAAACTACCACTG
Found at i:42950668 original size:43 final size:43
Alignment explanation
Indices: 42950620--42950766 Score: 159
Period size: 43 Copynumber: 3.4 Consensus size: 43
42950610 TTTATACTTT
*
42950620 GGTTTGTCTGATGATGCATTATGTGTGCCAGTATATTTGCTTC
1 GGTTTGTCTGATGATGCATTATGTGTGCCAATATATTTGCTTC
* ** * * *
42950663 GGTTTGTCTGATGATGTACAATGTATGCCAATATGTTTGCTAC
1 GGTTTGTCTGATGATGCATTATGTGTGCCAATATATTTGCTTC
** * * * * *
42950706 GGTTTGTCCAATTATACATTGTGTGTGCAAATATATTTGTTTC
1 GGTTTGTCTGATGATGCATTATGTGTGCCAATATATTTGCTTC
*
42950749 GGTTTATCTGATGATGCA
1 GGTTTGTCTGATGATGCA
42950767 CTGAGGTGCT
Statistics
Matches: 79, Mismatches: 25, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (43 bp):
GGTTTGTCTGATGATGCATTATGTGTGCCAATATATTTGCTTC
Found at i:42966858 original size:2 final size:2
Alignment explanation
Indices: 42966853--42966877 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42966843 TATATATATA
42966853 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
42966878 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:42969114 original size:19 final size:20
Alignment explanation
Indices: 42969079--42969116 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42969069 GCAATTAATT
42969079 AAATTTTATACTTTTTTAAC
1 AAATTTTATACTTTTTTAAC
42969099 AAATTTTATA-TTTTTTAA
1 AAATTTTATACTTTTTTAA
42969117 ATTTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
AAATTTTATACTTTTTTAAC
Found at i:42975036 original size:34 final size:34
Alignment explanation
Indices: 42974998--42975070 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
42974988 CAGAAACTTA
42974998 ATAAGAATGACT-TTTGCTACTG-AGTTGAACTATT
1 ATAAGAAT-ACTATTTGCTACTGTA-TTGAACTATT
* * *
42975032 ATAAGCATATTATTTGCTACTGTATTGAACTGTT
1 ATAAGAATACTATTTGCTACTGTATTGAACTATT
42975066 ATAAG
1 ATAAG
42975071 CATATCGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 2 0.06
34 31 0.91
35 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (34 bp):
ATAAGAATACTATTTGCTACTGTATTGAACTATT
Found at i:42975071 original size:34 final size:34
Alignment explanation
Indices: 42975010--42975075 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
42975000 AAGAATGACT
42975010 TTTGCTACTGAGTTGAACTATTATAAGCATATTA
1 TTTGCTACTGAGTTGAACTATTATAAGCATATTA
*
42975044 TTTGCTACTGTA-TTGAACTGTTATAAGCATAT
1 TTTGCTACTG-AGTTGAACTATTATAAGCATAT
42975076 CGATTTTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTGCTACTGAGTTGAACTATTATAAGCATATTA
Found at i:42975091 original size:34 final size:34
Alignment explanation
Indices: 42975022--42975107 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
42975012 TGCTACTGAG
* * *
42975022 TTGAACTATTATAAGCATATTATTTGCTACTGTA
1 TTGAACTGTTATAAGCATATGATTTGCTACCGTA
*
42975056 TTGAACTGTTATAAGCATATCGATTT-TTACCGTA
1 TTGAACTGTTATAAGCATAT-GATTTGCTACCGTA
** *
42975090 TTGTTCTGTTAAAAGCAT
1 TTGAACTGTTATAAGCAT
42975108 GATAAATACT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 40 0.91
35 4 0.09
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (34 bp):
TTGAACTGTTATAAGCATATGATTTGCTACCGTA
Found at i:42975352 original size:25 final size:25
Alignment explanation
Indices: 42975265--42975348 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
42975255 CAGGTAACAC
* *
42975265 GCCATAAAGACTTTTCATAAGATTA
1 GCCACAAAGACTTTTCACAAGATTA
* *
42975290 GCCACAAAGAC--TTCCCAAGTAATA
1 GCCACAAAGACTTTTCACAAG-ATTA
* * *
42975314 CGCTACATAGGCTTTTCACAAGATTA
1 -GCCACAAAGACTTTTCACAAGATTA
42975340 GCCACAAAG
1 GCCACAAAG
42975349 GCTTCCCAAG
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
23 6 0.14
24 3 0.07
25 25 0.57
26 3 0.07
27 7 0.16
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (25 bp):
GCCACAAAGACTTTTCACAAGATTA
Found at i:42977376 original size:12 final size:12
Alignment explanation
Indices: 42977366--42977413 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
42977356 TATACTATAT
*
42977366 GTTATAATATAAA
1 GTTATAATA-ATA
42977379 GTTAATAATAATA
1 GTT-ATAATAATA
*
42977392 GTAATAATAATA
1 GTTATAATAATA
42977404 GTTATAATAA
1 GTTATAATAA
42977414 AAGAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 18 0.58
13 7 0.23
14 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
GTTATAATAATA
Found at i:42979110 original size:30 final size:30
Alignment explanation
Indices: 42979017--42979111 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
42979007 GTCTTAGCCA
* *
42979017 TGTGAGGCACACGGCCTGGCCACACAAGCA
1 TGTGAGGCACACGGCCTGGCCACACAGGCG
* * *
42979047 CGTGAGGCACACGACCTGGCCACA-TGTGCG
1 TGTGAGGCACACGGCCTGGCCACACAG-GCG
** *
42979077 TGTGAGGTGCACGGCCTGGCCACACAGGTG
1 TGTGAGGCACACGGCCTGGCCACACAGGCG
42979107 TGTGA
1 TGTGA
42979112 CCCTTGTAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 51 0.98
31 1 0.02
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.15
Consensus pattern (30 bp):
TGTGAGGCACACGGCCTGGCCACACAGGCG
Found at i:42981485 original size:26 final size:27
Alignment explanation
Indices: 42981455--42981507 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
42981445 TTTGTTTTTC
42981455 TATTTCTAA-AAATAAACATCTCAATA
1 TATTTCTAATAAATAAACATCTCAATA
* *
42981481 TATTTCTAATTAAATAATCTTCTCAAT
1 TATTTCTAA-TAAATAAACATCTCAAT
42981508 CCAATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
28 14 0.61
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (27 bp):
TATTTCTAATAAATAAACATCTCAATA
Found at i:42981746 original size:63 final size:62
Alignment explanation
Indices: 42981666--42981857 Score: 202
Period size: 57 Copynumber: 3.1 Consensus size: 62
42981656 ATTTCCAGGT
* *
42981666 CATTTTTATTTTTATTTTCATTTTGGAGAAAACCAAATTCATTTCCAAATGATTCATTTTTTC
1 CATTTTCA-TTTTATTTTCATTTTGGAGAAAACCAAATTCATTTCCAAATGATTCATTTTCTC
* * * *
42981729 CATTTTC-----GTTTTCATTTTGGAGAAAA-CAATAATCATATCCAAATGATTCCTTTTCTC
1 CATTTTCATTTTATTTTCATTTTGGAGAAAACCAA-ATTCATTTCCAAATGATTCATTTTCTC
* *
42981786 CATTTTCATTTTCATTTTCATTTTGGAGAAAACCATAATT-ATTTTCAAATGTTTC-TCATTTCT
1 CATTTTCATTTT-ATTTTCATTTTGGAGAAAACCA-AATTCATTTCCAAATGATTCAT--TTTCT
42981849 C
62 C
42981850 CATTTTCA
1 CATTTTCA
42981858 ACATTTCTAT
Statistics
Matches: 107, Mismatches: 11, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
56 3 0.03
57 48 0.45
62 1 0.01
63 36 0.34
64 18 0.17
65 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (62 bp):
CATTTTCATTTTATTTTCATTTTGGAGAAAACCAAATTCATTTCCAAATGATTCATTTTCTC
Found at i:42981841 original size:57 final size:57
Alignment explanation
Indices: 42981665--42981857 Score: 187
Period size: 63 Copynumber: 3.3 Consensus size: 57
42981655 CATTTCCAGG
* * *
42981665 TCATTTT-TATTTTTATTTTCATTTTGGAGAAAACCA-AATTCATTTCCAAATGATTC
1 TCATTTTCCATTTTCATTTTCATTTTGGAGAAAACCATAATT-ATTTCCAAATGTTTC
* * * * *
42981721 AT-TTTTTCCATTTTCGTTTTCATTTTGGAGAAAACAATAATCATATCCAAATGATTCCTTTTC
1 -TCATTTTCCATTTTCATTTTCATTTTGGAGAAAACCATAATTATTTCCAAATG------TTTC
*
42981784 TCCATTTT-CATTTTCATTTTCATTTTGGAGAAAACCATAATTATTTTCAAATGTTTC
1 T-CATTTTCCATTTTCATTTTCATTTTGGAGAAAACCATAATTATTTCCAAATGTTTC
42981841 TCATTTCTCCATTTTCA
1 TCATTT-TCCATTTTCA
42981858 ACATTTCTAT
Statistics
Matches: 110, Mismatches: 14, Indels: 23
0.75 0.10 0.16
Matches are distributed among these distances:
56 9 0.08
57 42 0.38
58 11 0.10
62 1 0.01
63 43 0.39
64 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (57 bp):
TCATTTTCCATTTTCATTTTCATTTTGGAGAAAACCATAATTATTTCCAAATGTTTC
Found at i:42987738 original size:21 final size:21
Alignment explanation
Indices: 42987721--42987760 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42987711 ACTAAAATTT
42987721 TATTTTAAAAATAAAAAAAAG
1 TATTTTAAAAATAAAAAAAAG
*
42987742 TATTTTAAAATTAAAAAAA
1 TATTTTAAAAATAAAAAAA
42987761 TAAAAGCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
TATTTTAAAAATAAAAAAAAG
Found at i:42995271 original size:29 final size:31
Alignment explanation
Indices: 42995238--42995295 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
42995228 CTGAATTTTG
42995238 AAATTCCTAAAAAT-AGAA-A-TATAAGGATT
1 AAATTCC-AAAAATGAGAAGAGTATAAGGATT
*
42995267 AAATTCCAAAACTGAGAAGAGTATAAGGA
1 AAATTCCAAAAATGAGAAGAGTATAAGGA
42995296 CCTATGCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 11 0.44
30 1 0.04
31 8 0.32
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (31 bp):
AAATTCCAAAAATGAGAAGAGTATAAGGATT
Found at i:42995719 original size:17 final size:19
Alignment explanation
Indices: 42995683--42995720 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
42995673 TTTAACCCCC
42995683 TAAAATTATGAAATTTTAAT
1 TAAAATTA-GAAATTTTAAT
42995703 TAAAATTA-AAA-TTTAAT
1 TAAAATTAGAAATTTTAAT
42995720 T
1 T
42995721 TCAACTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
20 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TAAAATTAGAAATTTTAAT
Found at i:42997977 original size:12 final size:13
Alignment explanation
Indices: 42997956--42997984 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42997946 TATTTTCATT
42997956 AAATTATTATTTA
1 AAATTATTATTTA
42997969 AAATT-TTATTTA
1 AAATTATTATTTA
42997981 AAAT
1 AAAT
42997985 AACAGTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTATTATTTA
Found at i:42998016 original size:2 final size:2
Alignment explanation
Indices: 42998001--42998041 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
42997991 AATTTATTAA
42998001 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42998041 A
1 A
42998042 AAGAGAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43012422 original size:16 final size:17
Alignment explanation
Indices: 43012389--43012422 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43012379 TATAAAGTTA
*
43012389 ATATTTACCTTATTACT
1 ATATTAACCTTATTACT
43012406 ATATTAACCTT-TTACT
1 ATATTAACCTTATTACT
43012422 A
1 A
43012423 ATAATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAACCTTATTACT
Found at i:43014922 original size:274 final size:274
Alignment explanation
Indices: 43014430--43014980 Score: 933
Period size: 274 Copynumber: 2.0 Consensus size: 274
43014420 TAAGGCCGCA
*
43014430 ACATAATGATAGAAGAAAAAATTTGTTTAGGGGAGTTATCAACATTCTGGTAGGAGGAAAACATA
1 ACATAATGATAGAAGAAAAAATTTGTTTAAGGGAGTTATCAACATTCTGGTAGGAGGAAAACATA
*
43014495 TAGAATTGGTTTCGTCAAACTCAAAGGAGAAGGCTCATATGAGAAGTGTCTTGTCGATTCCAGCC
66 TAGAATTGGTTTCGTCAAACTCAAAGGAGAAGGCTCATATGAGAAGTGTCTTGTCGATTCCAACC
* *
43014560 ACTATTAAAAAACCCAAACCTTCCCTATGGGTCCTTAGATTTTCAGAACAAGACAAAAGGGAGAT
131 ACTATTAAAAAACCCAAACCTTCCCTACGGGACCTTAGATTTTCAGAACAAGACAAAAGGGAGAT
* * *
43014625 TCTAAATGTGGAAGGCGAATACCCTCTAAAGGTCTCGAGTAATATCTCCTATTTCTAGGTTAGAA
196 TCTAAATATGGAAGGCAAATACCCTCTAAAGGTCTCGAGTAATATCTCCTATTTCTAGGTCAGAA
43014690 GGATTCTAGTCTAT
261 GGATTCTAGTCTAT
* *
43014704 ACATAATGATAGAGGAAAGAAA-TTGTTTAAGGGAGTTATCGACATTCTGGTAGGAGGAAAACAT
1 ACATAATGATAGAAGAAA-AAATTTGTTTAAGGGAGTTATCAACATTCTGGTAGGAGGAAAACAT
*
43014768 ATAGAATTGGTTTCGTCAAACTCAAAGGAGAAGGCTCATATGGGAAGTGTCTTGTCGATTCCAAC
65 ATAGAATTGGTTTCGTCAAACTCAAAGGAGAAGGCTCATATGAGAAGTGTCTTGTCGATTCCAAC
**
43014833 CACTATTAAAAAACCCAAACCTTTTCTACGGGACCTTAGATTTTCAGAACAAGACAAAAGGGAGA
130 CACTATTAAAAAACCCAAACCTTCCCTACGGGACCTTAGATTTTCAGAACAAGACAAAAGGGAGA
* * * *
43014898 TTCTAGATATGGAAGGTAAATACCCTCTAGAGGTCTCGAGTAATATCTCCTCTTTCTAGGTCAGA
195 TTCTAAATATGGAAGGCAAATACCCTCTAAAGGTCTCGAGTAATATCTCCTATTTCTAGGTCAGA
*
43014963 AGGATTTTAGTCTAT
260 AGGATTCTAGTCTAT
43014978 ACA
1 ACA
43014981 AGAAGTTTCG
Statistics
Matches: 259, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
274 256 0.99
275 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (274 bp):
ACATAATGATAGAAGAAAAAATTTGTTTAAGGGAGTTATCAACATTCTGGTAGGAGGAAAACATA
TAGAATTGGTTTCGTCAAACTCAAAGGAGAAGGCTCATATGAGAAGTGTCTTGTCGATTCCAACC
ACTATTAAAAAACCCAAACCTTCCCTACGGGACCTTAGATTTTCAGAACAAGACAAAAGGGAGAT
TCTAAATATGGAAGGCAAATACCCTCTAAAGGTCTCGAGTAATATCTCCTATTTCTAGGTCAGAA
GGATTCTAGTCTAT
Found at i:43021589 original size:28 final size:28
Alignment explanation
Indices: 43021549--43021650 Score: 177
Period size: 28 Copynumber: 3.6 Consensus size: 28
43021539 TGACTTTCGA
*
43021549 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
43021577 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
43021605 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
43021633 CACTAAGTGTGCGAGTTT
1 CACTAAGTGTGCGAGTTT
43021651 GATTATTGAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:43022450 original size:23 final size:23
Alignment explanation
Indices: 43022383--43022778 Score: 299
Period size: 23 Copynumber: 17.0 Consensus size: 23
43022373 TCTAAAATTG
* *
43022383 GTATATATATGCTGCCCAATTTT
1 GTATATACATGCTGTCCAATTTT
*
43022406 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
* *
43022430 GTATATACATGCCGTCAAATTTT
1 GTATATACATGCTGTCCAATTTT
* *
43022453 GTGTATA-AGTGCTGTCCAA-ATT
1 GTATATACA-TGCTGTCCAATTTT
* * *
43022475 GCTACATATATGCTGCCCAATTTT
1 G-TATATACATGCTGTCCAATTTT
* *
43022499 GGTGA-ATAAATGCTGCCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
43022523 GTATATACATGCTGTCCAATTTT
1 GTATATACATGCTGTCCAATTTT
* * *
43022546 GTGTATA-AGTGCTGTCCAAATTG
1 GTATATACA-TGCTGTCCAATTTT
* *
43022569 GTATATATATGCTGCCCAATTTT
1 GTATATACATGCTGTCCAATTTT
* *
43022592 GGTGA-ATAAATGCTATCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
*
43022616 GTATATACATGCTGTCAAATTTT
1 GTATATACATGCTGTCCAATTTT
* *
43022639 GTGTATA-AGTGCTGTCCAAATTGGT
1 GTATATACA-TGCTGTCC-AATT-TT
* * *
43022664 ATATATATATGCTGCCCAATTTT
1 GTATATACATGCTGTCCAATTTT
*
43022687 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
*
43022711 GTATATACATGCTGTCAAATTTT
1 GTATATACATGCTGTCCAATTTT
* * * *
43022734 GTGTATA-AGTGATGTCCAAATTG
1 GTATATACA-TGCTGTCCAATTTT
43022757 GTATATACATGCTG-CTCAATTT
1 GTATATACATGCTGTC-CAATTT
43022779 CTGATGTATA
Statistics
Matches: 299, Mismatches: 49, Indels: 49
0.75 0.12 0.12
Matches are distributed among these distances:
22 12 0.04
23 181 0.61
24 87 0.29
25 18 0.06
26 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (23 bp):
GTATATACATGCTGTCCAATTTT
Found at i:43022492 original size:93 final size:93
Alignment explanation
Indices: 43022377--43022800 Score: 706
Period size: 93 Copynumber: 4.5 Consensus size: 93
43022367 TAATGGTCTA
43022377 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
*
43022442 CGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* * *
43022470 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGCCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
*
43022535 TGTCCAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
*
43022563 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
43022628 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
43022656 AAATTGGTATATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACAT
1 AAATTGG--TATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACAT
*
43022721 GCTGTCAAATTTTGTGTATAAGTGATGTCC
64 GCTGTCAAATTTTGTGTATAAGTGCTGTCC
* * * *
43022751 AAATTGGTATATACATGCTGCTCAATTTCTGATGTATAAGA-GCTGTCCAA
1 AAATTGGTATATATATGCTGCCCAATTT-TGGTGAATAA-ATGCTGTCCAA
43022801 ATAGGGTAGA
Statistics
Matches: 311, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
93 202 0.65
94 17 0.05
95 92 0.30
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (93 bp):
AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
TGTCAAATTTTGTGTATAAGTGCTGTCC
Found at i:43022497 original size:46 final size:45
Alignment explanation
Indices: 43022377--43022802 Score: 429
Period size: 46 Copynumber: 9.1 Consensus size: 45
43022367 TAATGGTCTA
* * *
43022377 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCC
1 AAATT-GTATATACATGCTGCCCAATTTT-GTGTATAAGTGCTGTCC
* * * *
43022424 AATTTTGTATATACATGCCGTCAAATTTTGTGTATAAGTGCTGTCC
1 AA-ATTGTATATACATGCTGCCCAATTTTGTGTATAAGTGCTGTCC
* * * * *
43022470 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGCCC
1 AAATTG-TATATACATGCTGCCCAATTTT-GTGTATAAGTGCTGTCC
* *
43022517 AATTTTGTATATACATGCTGTCCAATTTTGTGTATAAGTGCTGTCC
1 AA-ATTGTATATACATGCTGCCCAATTTTGTGTATAAGTGCTGTCC
* * * *
43022563 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTATCC
1 AAATT-GTATATACATGCTGCCCAATTTT-GTGTATAAGTGCTGTCC
* * *
43022610 AATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCC
1 AA-ATTGTATATACATGCTGCCCAATTTTGTGTATAAGTGCTGTCC
* * *
43022656 AAATTGGTATATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCC
1 AAATT-G--TATATACATGCTGCCCAATTTT-GTGTATAAGTGCTGTCC
* * * *
43022705 AATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGATGTCC
1 AA-ATTGTATATACATGCTGCCCAATTTTGTGTATAAGTGCTGTCC
* *
43022751 AAATTGGTATATACATGCTGCTCAATTTCTGATGTATAAGAGCTGTCC
1 AAATT-GTATATACATGCTGCCCAATTT-TG-TGTATAAGTGCTGTCC
43022799 AAAT
1 AAAT
43022803 AGGGTAGATT
Statistics
Matches: 309, Mismatches: 55, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
45 9 0.03
46 123 0.40
47 113 0.37
48 44 0.14
49 18 0.06
50 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (45 bp):
AAATTGTATATACATGCTGCCCAATTTTGTGTATAAGTGCTGTCC
Found at i:43027065 original size:20 final size:20
Alignment explanation
Indices: 43027040--43027086 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
43027030 AAGATCACGG
43027040 TGAGGAAAGCTTGTGCTTAA
1 TGAGGAAAGCTTGTGCTTAA
43027060 TGAGGAAAGCTTGTGCTTAA
1 TGAGGAAAGCTTGTGCTTAA
43027080 TGAGGAA
1 TGAGGAA
43027087 GCAAATTTGG
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:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (20 bp):
TGAGGAAAGCTTGTGCTTAA
Found at i:43027380 original size:9 final size:9
Alignment explanation
Indices: 43027363--43027392 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
43027353 CTTTTTCTCC
43027363 AAAACCCTA
1 AAAACCCTA
*
43027372 AAAATCCTA
1 AAAACCCTA
43027381 AAAACCCTA
1 AAAACCCTA
43027390 AAA
1 AAA
43027393 TCCAAAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAACCCTA
Found at i:43027392 original size:17 final size:17
Alignment explanation
Indices: 43027363--43027402 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
43027353 CTTTTTCTCC
43027363 AAAACCCTAAAAATCCTA
1 AAAACCCTAAAAATCC-A
43027381 AAAACCCT-AAAATCCA
1 AAAACCCTAAAAATCCA
43027397 AAAACC
1 AAAACC
43027403 TACAAGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.32
17 7 0.32
18 8 0.36
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAACCCTAAAAATCCA
Found at i:43041120 original size:9 final size:9
Alignment explanation
Indices: 43041108--43041260 Score: 55
Period size: 9 Copynumber: 16.0 Consensus size: 9
43041098 TATGACTTTT
43041108 TTTTTATAA
1 TTTTTATAA
*
43041117 TTTTCATAA
1 TTTTTATAA
*
43041126 GTTTATATCAA
1 -TTTTTAT-AA
* *
43041137 TTTTAATCA
1 TTTTTATAA
43041146 TTTTTATAGAA
1 TTTTTAT--AA
* *
43041157 TTTTAATACG
1 TTTTTATA-A
43041167 TTTTTATAAA
1 TTTTTAT-AA
*
43041177 ATTTTA-AA
1 TTTTTATAA
43041185 TATTTTGA-ATA
1 T-TTTT-ATA-A
43041196 TGTTTTATTAA
1 T-TTTTA-TAA
*
43041207 -TTTTAT-T
1 TTTTTATAA
43041214 TTTTTATAA
1 TTTTTATAA
43041223 TTTTTTTATAA
1 --TTTTTATAA
* *
43041234 TTTATTAGAT
1 TTT-TTATAA
43041244 TTTTTAT-A
1 TTTTTATAA
43041252 TTTTTATAA
1 TTTTTATAA
43041261 AATTATGTCT
Statistics
Matches: 106, Mismatches: 21, Indels: 34
0.66 0.13 0.21
Matches are distributed among these distances:
8 16 0.15
9 32 0.30
10 31 0.29
11 26 0.25
12 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:43041158 original size:20 final size:21
Alignment explanation
Indices: 43041135--43041183 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
43041125 AGTTTATATC
*
43041135 AATTTTAAT-CATTTTTATAG
1 AATTTTAATACATTTTTATAA
*
43041155 AATTTTAATACGTTTTTATAA
1 AATTTTAATACATTTTTATAA
43041176 AATTTTAA
1 AATTTTAA
43041184 ATATTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
AATTTTAATACATTTTTATAA
Found at i:43041227 original size:11 final size:11
Alignment explanation
Indices: 43041211--43041236 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43041201 TATTAATTTT
43041211 ATTTTTTTATA
1 ATTTTTTTATA
43041222 ATTTTTTTATA
1 ATTTTTTTATA
43041233 ATTT
1 ATTT
43041237 ATTAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:43041291 original size:11 final size:10
Alignment explanation
Indices: 43041127--43041302 Score: 68
Period size: 10 Copynumber: 18.1 Consensus size: 10
43041117 TTTTCATAAG
*
43041127 TTTATATCAAT
1 TTTATAT-ATT
43041138 TTTA-ATCATT
1 TTTATAT-ATT
* *
43041148 TTTATAGAAT
1 TTTATATATT
43041158 TTTA-ATACGTT
1 TTTATATA--TT
* *
43041169 TTTATAAAAT
1 TTTATATATT
*
43041179 TTTAAATATT
1 TTTATATATT
*
43041189 TTGA-ATATGT
1 TTTATATAT-T
*
43041199 TTTAT-TAAT
1 TTTATATATT
43041208 TTTAT-T-TT
1 TTTATATATT
43041216 TTTATA-ATT
1 TTTATATATT
* *
43041225 TTTTTATA-A
1 TTTATATATT
*
43041234 TTTATTAGATT
1 TTTA-TATATT
43041245 TTT-TATATT
1 TTTATATATT
* *
43041254 TTTATAAAAT
1 TTTATATATT
* * *
43041264 TATGTCTATT
1 TTTATATATT
*
43041274 TTCATATATT
1 TTTATATATT
43041284 TTTA-ATATT
1 TTTATATATT
43041293 TTTA-ATATT
1 TTTATATATT
43041302 T
1 T
43041303 AATGATCTTA
Statistics
Matches: 121, Mismatches: 32, Indels: 26
0.68 0.18 0.15
Matches are distributed among these distances:
8 6 0.05
9 46 0.38
10 54 0.45
11 13 0.11
12 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (10 bp):
TTTATATATT
Found at i:43044225 original size:127 final size:127
Alignment explanation
Indices: 43043994--43044255 Score: 443
Period size: 127 Copynumber: 2.1 Consensus size: 127
43043984 TTGTGTATGG
* *
43043994 CATGACTTTACTAGCAACAGTGGAATTCATAGCTCAATTAGACCATGCGTATGTAACTCACGTGT
1 CATGACTTTACTAGAAACAGTGGAATTCATAGCTCAATTAGACCATGCGTATGTAACTCACGTGC
* * *
43044059 TTTGAAATAAGTGGAGGCTTATGCTTTAAAAATGGTCAAGCCAATAGTCGGTACGTTGGGTA
66 TTTGAAATAAGTGGAGGCTTATGCTCTAAAAATGATCAAGCCAATAGTCGGTACGCTGGGTA
*
43044121 CATGACTTTACTAGAAACAGTGGAATTCATAGCTCAATTAGACCATGCGTATGTAACTCATGTGC
1 CATGACTTTACTAGAAACAGTGGAATTCATAGCTCAATTAGACCATGCGTATGTAACTCACGTGC
* **
43044186 TTTGAAATAAGTGGAGGCTTATGCTCTAAAGATGATCAAGCTGATAGTCGGTACGCTGGGTA
66 TTTGAAATAAGTGGAGGCTTATGCTCTAAAAATGATCAAGCCAATAGTCGGTACGCTGGGTA
43044248 CATGACTT
1 CATGACTT
43044256 GTGTATGGTG
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (127 bp):
CATGACTTTACTAGAAACAGTGGAATTCATAGCTCAATTAGACCATGCGTATGTAACTCACGTGC
TTTGAAATAAGTGGAGGCTTATGCTCTAAAAATGATCAAGCCAATAGTCGGTACGCTGGGTA
Found at i:43045371 original size:20 final size:19
Alignment explanation
Indices: 43045346--43045438 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 19
43045336 ATTCCAAAAA
43045346 TAATATTATTTTAATAGATT
1 TAATATTATTTTAATA-ATT
**
43045366 TAATATTAAATT-A-AATT
1 TAATATTATTTTAATAATT
*
43045383 TAATACTTATATTAATAGTATT
1 TAATA-TTATTTTAATA--ATT
*
43045405 T--TATTAATTTAAT-ATT
1 TAATATTATTTTAATAATT
43045421 TAAGTTATTATTTTAATA
1 TAA--TATTATTTTAATA
43045439 TTAAATTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
16 4 0.07
17 8 0.14
18 7 0.12
19 10 0.18
20 24 0.42
22 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (19 bp):
TAATATTATTTTAATAATT
Found at i:43045505 original size:62 final size:59
Alignment explanation
Indices: 43045432--43045548 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
43045422 AAGTTATTAT
* * *
43045432 TTTAATATTAAATTTAATTTAATGTCTATCTTGTAGATAAATATTCTATTAATTTAATAAGA
1 TTTAATATTAAATTTAATCTAATATCTATC-T-T-GATAAATATTATATTAATTTAATAAGA
*
43045494 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAAT
1 TTTAATATTAAATTTAATCTAATATCTATCTTGATAAATATTATATTAATTTAAT
43045549 GTTAAAGTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.43
60 1 0.02
61 1 0.02
62 27 0.53
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (59 bp):
TTTAATATTAAATTTAATCTAATATCTATCTTGATAAATATTATATTAATTTAATAAGA
Found at i:43046274 original size:27 final size:27
Alignment explanation
Indices: 43046224--43046308 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
43046214 TCACGTTCTG
* *
43046224 GCGGACTTACCTCATGTAAACTGTCTCA
1 GCGGACTTACC-CATGTTAACTGTCCCA
* *
43046252 GCGGACTTACCCATGTTCACTGTCCCG
1 GCGGACTTACCCATGTTAACTGTCCCA
* ** *
43046279 GAGGACTTACCTGTGTTTACTGTCCCA
1 GCGGACTTACCCATGTTAACTGTCCCA
43046306 GCG
1 GCG
43046309 AACTGTTTGT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 36 0.77
28 11 0.23
ACGTcount: A:0.19, C:0.31, G:0.22, T:0.28
Consensus pattern (27 bp):
GCGGACTTACCCATGTTAACTGTCCCA
Found at i:43050803 original size:33 final size:33
Alignment explanation
Indices: 43050766--43050842 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
43050756 GCAGACTATC
* *
43050766 TGTTCTATGTTT-CTTATCCCACCGAACTTTCTT
1 TGTTCTATGTTTAC-TATCCCAACGAACTATCTT
* *
43050799 TGTTCTGTGTTTACTATCCCAACGGACTATCTT
1 TGTTCTATGTTTACTATCCCAACGAACTATCTT
43050832 TGTTCTATGTT
1 TGTTCTATGTT
43050843 AATTGTCACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 37 0.97
34 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.13, T:0.48
Consensus pattern (33 bp):
TGTTCTATGTTTACTATCCCAACGAACTATCTT
Found at i:43051025 original size:58 final size:58
Alignment explanation
Indices: 43050924--43051061 Score: 143
Period size: 58 Copynumber: 2.4 Consensus size: 58
43050914 CTACCATAGT
* ** * ** * *
43050924 GTCTTTCATCTATGGTCTTACACCGTATACCTTATACTTTGTACTATAC-AGCCATGGC
1 GTCTTTCATCCATGGTCTTATGCCATATACCTTATACCATGTACCATACTA-CCATGAC
* * *
43050982 GTCTTTCATCCATGGTCTTATGCCATATACCTTTTACCATGTACCATGCTACCATGAT
1 GTCTTTCATCCATGGTCTTATGCCATATACCTTATACCATGTACCATACTACCATGAC
* *
43051040 GTCTTTCATCCACGATCTTATG
1 GTCTTTCATCCATGGTCTTATG
43051062 TTACCTACCT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
58 65 0.98
59 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (58 bp):
GTCTTTCATCCATGGTCTTATGCCATATACCTTATACCATGTACCATACTACCATGAC
Found at i:43054794 original size:22 final size:23
Alignment explanation
Indices: 43054768--43054810 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
43054758 TAACATCTTT
43054768 TTACCT-A-TTTACAAAATTACCC
1 TTACCTAACTTTA-AAAATTACCC
43054790 TTACCTAACTTTAAAAATTAC
1 TTACCTAACTTTAAAAATTAC
43054811 TCAATTGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (23 bp):
TTACCTAACTTTAAAAATTACCC
Found at i:43056240 original size:25 final size:25
Alignment explanation
Indices: 43056204--43056253 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
43056194 TCATTCATAT
43056204 CTATGTCACTAAATATATTTAAATA
1 CTATGTCACTAAATATATTTAAATA
* *
43056229 CTATGTCCCTAAATGTATTTAAATA
1 CTATGTCACTAAATATATTTAAATA
43056254 TGTAGTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (25 bp):
CTATGTCACTAAATATATTTAAATA
Found at i:43064824 original size:16 final size:16
Alignment explanation
Indices: 43064803--43064834 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43064793 TAACTTATTT
43064803 CATTTCTAGTCAAAAC
1 CATTTCTAGTCAAAAC
*
43064819 CATTTCTAGTCCAAAC
1 CATTTCTAGTCAAAAC
43064835 TTTATAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.31
Consensus pattern (16 bp):
CATTTCTAGTCAAAAC
Found at i:43068583 original size:12 final size:13
Alignment explanation
Indices: 43068553--43068585 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
43068543 TGCTATCTGG
43068553 TACACATAGTAGCC
1 TACACATAGTA-CC
43068567 TACACATAGTA-C
1 TACACATAGTACC
43068579 TACACAT
1 TACACAT
43068586 GTGACCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:43068614 original size:51 final size:52
Alignment explanation
Indices: 43068552--43068739 Score: 267
Period size: 51 Copynumber: 3.7 Consensus size: 52
43068542 ATGCTATCTG
*
43068552 GTACACATAGTAGCCTACACATAGTACTACACATGTGACCAATA-CCATCCA
1 GTACACATAGTAGCCTACACATAGTACTACACATGTGACCAATAGCTATCCA
* * *
43068603 GTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAA-AGCTATCCG
1 GTACACATAGTAGCCTACACATAGTACTACACATGTGACCAATAGCTATCCA
* * *
43068654 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC-ATAGCTATCTTA
1 GTACACATAGTAGCCTACACATAGTACTACACATGTGACCAATAGCTATC-CA
*
43068706 -TACTCATAGTAGCCTACACATAGTACTACACATG
1 GTACACATAGTAGCCTACACATAGTACTACACATG
43068740 AGTTCTCATG
Statistics
Matches: 123, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
50 2 0.02
51 121 0.98
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (52 bp):
GTACACATAGTAGCCTACACATAGTACTACACATGTGACCAATAGCTATCCA
Found at i:43070925 original size:24 final size:24
Alignment explanation
Indices: 43070872--43070917 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
43070862 TCTTTCTAGA
* *
43070872 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAGCATTTATTAGAATAAT
43070896 ATATTTAGCATTTATTAGAATA
1 ATATTTAGCATTTATTAGAATA
43070918 GTTTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGAATAAT
Found at i:43072947 original size:50 final size:50
Alignment explanation
Indices: 43072832--43073071 Score: 241
Period size: 50 Copynumber: 4.8 Consensus size: 50
43072822 GAATATAACA
* * * * ** * * * *
43072832 TGCCAAAGCTATGTCCTAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * ** *
43072881 TGCCAA-GCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * ** *
43072930 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* *
43072980 TGCCAACGCTATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* *
43073030 TGCTAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
43073072 TTACCCAAAT
Statistics
Matches: 158, Mismatches: 31, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
48 30 0.19
49 11 0.07
50 117 0.74
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:43075222 original size:24 final size:24
Alignment explanation
Indices: 43075172--43075223 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
43075162 TTTCTAGAAG
* *
43075172 ATTTAGTATTTATTAGTAGAATAT
1 ATTTAGCATTTATTAGCAGAATAT
* *
43075196 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCAGAATAT
43075220 ATTT
1 ATTT
43075224 GACCTACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCAGAATAT
Found at i:43075871 original size:31 final size:32
Alignment explanation
Indices: 43075777--43075871 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 32
43075767 TAATAATAGT
* * *
43075777 TATATATGTATTTTTTTGTAATAGTTATATATGA
1 TATATAT-TA-TTTTATGTAATAGTAATATATTA
*
43075811 TATTATATTATATTAT-TAATAGTACATATATTA
1 TA-TATATTATTTTATGTAATAGTA-ATATATTA
*
43075844 TAT-TATTATTTTATGTATTAGTAATATA
1 TATATATTATTTTATGTAATAGTAATATA
43075872 CTAATTTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
31 15 0.29
32 15 0.29
33 13 0.25
34 4 0.08
35 5 0.10
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (32 bp):
TATATATTATTTTATGTAATAGTAATATATTA
Found at i:43080622 original size:42 final size:42
Alignment explanation
Indices: 43080563--43080647 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
43080553 ATAAGGTGAG
43080563 AGTTTTTAAATCTTACTTCAACCTACATTGCCGTTTTCAATC
1 AGTTTTTAAATCTTACTTCAACCTACATTGCCGTTTTCAATC
43080605 AGTTTTTAAATCTTACTTCAACCTACATTGCCGTTTTCAATC
1 AGTTTTTAAATCTTACTTCAACCTACATTGCCGTTTTCAATC
43080647 A
1 A
43080648 CCTCCGGAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (42 bp):
AGTTTTTAAATCTTACTTCAACCTACATTGCCGTTTTCAATC
Found at i:43081128 original size:6 final size:6
Alignment explanation
Indices: 43081117--43081148 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
43081107 CACGGCCTCG
43081117 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
43081149 GTCGGCGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.69, G:0.00, T:0.16
Consensus pattern (6 bp):
CCTCCA
Found at i:43083710 original size:16 final size:16
Alignment explanation
Indices: 43083685--43083719 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43083675 TCTCCTTTTT
*
43083685 TTTTCCTTCTTTTTCC
1 TTTTCCTTCTTTCTCC
*
43083701 TTTTCTTTCTTTCTCC
1 TTTTCCTTCTTTCTCC
43083717 TTT
1 TTT
43083720 CCTCCTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCCTTCTTTCTCC
Found at i:43084322 original size:24 final size:25
Alignment explanation
Indices: 43084280--43084333 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
43084270 ATATTTACAA
* * *
43084280 TTTTTTAAATTAGATAAATATGTCG
1 TTTTTTAAATTAGACAAATAGGCCG
*
43084305 TTTTTT-AATTAGCCAAATAGGCCG
1 TTTTTTAAATTAGACAAATAGGCCG
43084329 TTTTT
1 TTTTT
43084334 GGAGAGAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (25 bp):
TTTTTTAAATTAGACAAATAGGCCG
Found at i:43087170 original size:40 final size:40
Alignment explanation
Indices: 43087116--43087193 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
43087106 ATATCAGGAA
* * *
43087116 TTAGCCATGAATCTATCATATCGTCTATTATGTGAGCCCT
1 TTAGCCATAAATCTATCATATCGTCCATTATATGAGCCCT
*
43087156 TTAGTCATAAATCTATCATATCGTCCATTATATGAGCC
1 TTAGCCATAAATCTATCATATCGTCCATTATATGAGCC
43087194 ATCGAGACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (40 bp):
TTAGCCATAAATCTATCATATCGTCCATTATATGAGCCCT
Found at i:43088490 original size:25 final size:24
Alignment explanation
Indices: 43088462--43088508 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
43088452 ATCCGAGCAA
*
43088462 TATAACGGGAAGCTCACAAAGAGCC
1 TATAACAGGAAGCTC-CAAAGAGCC
*
43088487 TATAACAGGTAGCTCCAAAGAG
1 TATAACAGGAAGCTCCAAAGAG
43088509 TAATTAACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.15
Consensus pattern (24 bp):
TATAACAGGAAGCTCCAAAGAGCC
Found at i:43088516 original size:24 final size:24
Alignment explanation
Indices: 43088464--43088571 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
43088454 CCGAGCAATA
*
43088464 TAACGGGAAGCTCACAAAGAGCCT-A-
1 TAACGGGTAGCTC-CAAAGAG--TAAT
*
43088489 TAACAGGTAGCTCCAAAGAGTAAT
1 TAACGGGTAGCTCCAAAGAGTAAT
* *
43088513 TAACGGGTAGCTTCAAAAAGTAAT
1 TAACGGGTAGCTCCAAAGAGTAAT
** ** *
43088537 TAACGAATAGCTCTGAAGAGCAAT
1 TAACGGGTAGCTCCAAAGAGTAAT
43088561 TAACGGGTAGC
1 TAACGGGTAGC
43088572 ACTTGATAGC
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 54 0.81
25 11 0.16
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (24 bp):
TAACGGGTAGCTCCAAAGAGTAAT
Found at i:43088643 original size:26 final size:26
Alignment explanation
Indices: 43088614--43088674 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
43088604 AGCACTAACA
*
43088614 GGAAGCTCACAAAGAGCC-TTTAATCG
1 GGAAGCTCACAAAGAGCCATATAAT-G
*
43088640 GGAAGCTCACGAAGAGCCATATAATG
1 GGAAGCTCACAAAGAGCCATATAATG
*
43088666 GGACGCTCA
1 GGAAGCTCA
43088675 TAAGAGCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.16
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCATATAATG
Found at i:43096370 original size:707 final size:710
Alignment explanation
Indices: 43094980--43096379 Score: 1920
Period size: 707 Copynumber: 2.0 Consensus size: 710
43094970 TATGGGTGAC
*
43094980 ATCTAAGTGTACTTTTTAGAAAAATTTGTACAAAGAACTTCTGTTTGTTAAGACATTGTTTTTTA
1 ATCTAAGTGTACTTTTTAGAAAAATTTGTACAAAGAACTTATGTTTGTTAAGACATTGTTTTTTA
* * *
43095045 TGAAACCTTGTGAAAATTCATGCTTTGGATATTAAATATTATCTGTTGTTTAATAAAGTTACTAT
66 TGAAACCTAGTGAAAATTCATGCTTTGGATATTAAATATTATATGATGTTTAATAAAGTTACTAT
* * * * *
43095110 ACTTGAGTTTATGCGCCATAGGATTTAAATATTATAATTACTCCAATAATGGTTTAATTCAAACA
131 ACTTAAGTTTATACACCATAAGATTTAAACATTATAATTACTCCAATAATGGTTTAATTCAAACA
* *
43095175 TTGAAGTTTTACAAAGCTATTGCCAGAACTGATTTTTTCAATTTAAGATGATTTCTAAGTAGTGA
196 TTGAAGTTTTACAAAGCTATTACCAGAACTGATATTTTCAATTTAAGATGATTTCTAAGTAGTGA
* ** * *
43095240 CACATTATACTCAAATTCTTTCTAAAGGATTGGGTTTGGCGTGTTACAGGAAACACACCCCGATT
261 CACATCATACTCAAATTCTTTCTAAAGGATCAGGTTTGGCGTGTTACAGGAAACAAACCCCAATT
* * *
43095305 TCTTCCAACACTCGCCTTTATGTCTGTTTCCATACAATTCACCACTCGATATATCAACATCTCTA
326 TCTTCCAACACTCGCCTTTATGTCTCTTTCCACACAATTCACAACTCGATATATCAACATCTCTA
* * * * * * *
43095370 ACTGAGCCTCTCACACTACCTACAGACATTGTTGACTGTCGATCTCGGCCTCTCTCGGATCTAGC
391 ACTGAGCCTCTCACACAACCTACAAACACTATCGACTATCGATCTCGGCCTCTCTCAGATCTAGC
** ** * *
43095435 AAATCTCAGAGCTAATCTCCAATGCTCTGGAGACTCCCTTGCCCGTTTAGGCAACAGATGAGAGC
456 AAATCTCAGAGCTAATCTCCAATGCTCTCAAGACTCCCTAACCCATTTAGGCAACAAATGAGAGC
* *
43095500 TAGAAGTCCAGACTCATTTCTCAAATGCTCCAGAAGGTTCCAATTTCTTGTCTAGGCCCATCACT
521 TAAAAGTCCAGACTCATTTCTCAAATGCTCCAGAAGGTTCCAATTTCTTGTCTAGGACCATCACT
* * * * *
43095565 TGCTTGACCATCTTTACCCGTTCAAAGAGGTCAGTGAACTATTTTATTCTATGTAAAACCAACTG
586 TACTCGACCATCTTTACCCATTCAAAGAGGTCAGTGAACTATTTTACTCTATGCAAAACCAACTG
* ** **
43095630 AACTATGAGCTCATCGTGCAAACCCTGAAGAAATCATTTACAAAACTTCTATTTGTACAT
651 AACTATGACCTCATCACGCAAACCCCAAAGAAATCATTTACAAAACTTCTATTTGTACAT
* *
43095690 ATCTAAGTGTA-TTTTTAGAAGAATTTGTACAAAGAACTTATGTTTGTTAAGACCTTG-TTTTTA
1 ATCTAAGTGTACTTTTTAGAAAAATTTGTACAAAGAACTTATGTTTGTTAAGACATTGTTTTTTA
*
43095753 TGAAACCTGAGTGAAAATTCATGTTTTGGATATTAAATATTATATGATGTTTAATAAAGTTACTA
66 TGAAACCT-AGTGAAAATTCATGCTTTGGATATTAAATATTATATGATGTTTAATAAAGTTACTA
* * *
43095818 TACTTAAGTTTATATACCATAAGATTTAACCATTATAATTACTTCAATAATGGTTTAATTCAAAC
130 TACTTAAGTTTATACACCATAAGATTTAAACATTATAATTACTCCAATAATGGTTTAATTCAAAC
* *
43095883 ATTGAAGTTTTACAAAGTTATTACCAGAACT-A-ATTTTGAATTTAAGATGATTTCTAAGTAGTG
195 ATTGAAGTTTTACAAAGCTATTACCAGAACTGATATTTTCAATTTAAGATGATTTCTAAGTAGTG
* ** *
43095946 ACACATCATGCTCGGATTCTTTCTAAAGGATCAGGTTTGGCGTGTTACA-GAAACAAACCTCAAT
260 ACACATCATACTCAAATTCTTTCTAAAGGATCAGGTTTGGCGTGTTACAGGAAACAAACCCCAA-
* * * *
43096010 TTTCTTCTAACACTCGCCTTTATGTCTCTTTCCACAGAATTCATAACTCGGTATATCAACATCTC
324 TTTCTTCCAACACTCGCCTTTATGTCTCTTTCCACACAATTCACAACTCGATATATCAACATCTC
* * * *
43096075 TAACTTG-GCCTTTCACACAACCTACAAACACTATCGGCTATTGATCTCGGCTCTCTCTTAGATC
389 TAAC-TGAGCCTCTCACACAACCTACAAACACTATCGACTATCGATCTCGGC-CTCTCTCAGATC
* * * * ** * *
43096139 TGGTAGAT-TCGGAGCTGGTCTCCTATGCTCTCAAGACTCTCTAACCCATTTAGGCAACAAATGA
452 TAGCAAATCTCAGAGCTAATCTCCAATGCTCTCAAGACTCCCTAACCCATTTAGGCAACAAATGA
* * **
43096203 GAGCTAAAAGTGCC-GACTCGTTTCTCAAATGCTCTAGAAGGTTCCGGTTTCTTGTCTAGGACCA
517 GAGCTAAAAGT-CCAGACTCATTTCTCAAATGCTCCAGAAGGTTCCAATTTCTTGTCTAGGACCA
* ** * * *
43096267 TCGCTTACTCGACCATCTTTGTCCATTCAGTA-AGGTCA-TCGAACTCTTTTACTCTATGCGAAA
581 TCACTTACTCGACCATCTTTACCCATTCA-AAGAGGTCAGT-GAACTATTTTACTCTATGCAAAA
*
43096330 CCAACTGAACTATGACCTCATCACGTAAACCCCAAAGAAATCATTTACAA
644 CCAACTGAACTATGACCTCATCACGCAAACCCCAAAGAAATCATTTACAA
43096380 CTTTCTTCTT
Statistics
Matches: 600, Mismatches: 83, Indels: 17
0.86 0.12 0.02
Matches are distributed among these distances:
706 12 0.02
707 361 0.60
708 35 0.06
709 181 0.30
710 11 0.02
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (710 bp):
ATCTAAGTGTACTTTTTAGAAAAATTTGTACAAAGAACTTATGTTTGTTAAGACATTGTTTTTTA
TGAAACCTAGTGAAAATTCATGCTTTGGATATTAAATATTATATGATGTTTAATAAAGTTACTAT
ACTTAAGTTTATACACCATAAGATTTAAACATTATAATTACTCCAATAATGGTTTAATTCAAACA
TTGAAGTTTTACAAAGCTATTACCAGAACTGATATTTTCAATTTAAGATGATTTCTAAGTAGTGA
CACATCATACTCAAATTCTTTCTAAAGGATCAGGTTTGGCGTGTTACAGGAAACAAACCCCAATT
TCTTCCAACACTCGCCTTTATGTCTCTTTCCACACAATTCACAACTCGATATATCAACATCTCTA
ACTGAGCCTCTCACACAACCTACAAACACTATCGACTATCGATCTCGGCCTCTCTCAGATCTAGC
AAATCTCAGAGCTAATCTCCAATGCTCTCAAGACTCCCTAACCCATTTAGGCAACAAATGAGAGC
TAAAAGTCCAGACTCATTTCTCAAATGCTCCAGAAGGTTCCAATTTCTTGTCTAGGACCATCACT
TACTCGACCATCTTTACCCATTCAAAGAGGTCAGTGAACTATTTTACTCTATGCAAAACCAACTG
AACTATGACCTCATCACGCAAACCCCAAAGAAATCATTTACAAAACTTCTATTTGTACAT
Found at i:43099747 original size:20 final size:19
Alignment explanation
Indices: 43099716--43099755 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
43099706 TAATTAGTTT
*
43099716 TAAATTAAACTTAATTTAA
1 TAAATTAAACTTAAATTAA
43099735 TAAATTAAAACTTAAATTAA
1 TAAATT-AAACTTAAATTAA
43099755 T
1 T
43099756 TAAGCTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTAAACTTAAATTAA
Found at i:43100621 original size:88 final size:88
Alignment explanation
Indices: 43100471--43100664 Score: 284
Period size: 88 Copynumber: 2.2 Consensus size: 88
43100461 CATAAAGCCC
* * *
43100471 TCAAACTTTCTTAGAAAAAGCAATTAAGCCTCTACAGTTTTTTGCACTCATTTGGGTACTTGAAC
1 TCAAACCTT-TTAAAAAAAGCAATTAAGCCTCTACAGTTTTTTGCACTCAATTGGGTACTTGAAC
43100536 TTTCAAAATGCATCAAAAAGACCA
65 TTTCAAAATGCATCAAAAAGACCA
* **
43100560 TCAAACCTTTTAAAAAAAGTAATTAAG-CTCCTACTTTTTTTTGCACTCAATTGGGTACTTGAAC
1 TCAAACCTTTTAAAAAAAGCAATTAAGCCT-CTACAGTTTTTTGCACTCAATTGGGTACTTGAAC
* *
43100624 TTTCAAAATGCATCAAAACGACCC
65 TTTCAAAATGCATCAAAAAGACCA
43100648 TCAAA-CTTTTAAAAAAA
1 TCAAACCTTTTAAAAAAA
43100665 TAAAATAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
87 14 0.15
88 74 0.77
89 8 0.08
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (88 bp):
TCAAACCTTTTAAAAAAAGCAATTAAGCCTCTACAGTTTTTTGCACTCAATTGGGTACTTGAACT
TTCAAAATGCATCAAAAAGACCA
Found at i:43100806 original size:8 final size:8
Alignment explanation
Indices: 43100793--43100878 Score: 55
Period size: 8 Copynumber: 9.6 Consensus size: 8
43100783 AGAAATTAGA
43100793 AAAAATAT
1 AAAAATAT
43100801 AAAAATCAT
1 AAAAAT-AT
43100810 AAAAATATAT
1 -AAAA-ATAT
*
43100820 AAAAATTGT
1 AAAAA-TAT
*
43100829 AAAATTTTAT
1 AAAA--ATAT
*
43100839 AAAAATCGT
1 AAAAAT-AT
43100848 AAAAATAT
1 AAAAATAT
43100856 AAAAAAATAT
1 --AAAAATAT
*
43100866 AGAAATAT
1 AAAAATAT
43100874 AAAAA
1 AAAAA
43100879 AATTATAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
8 20 0.33
9 19 0.31
10 20 0.33
11 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (8 bp):
AAAAATAT
Found at i:43100811 original size:9 final size:9
Alignment explanation
Indices: 43100771--43100888 Score: 76
Period size: 9 Copynumber: 12.6 Consensus size: 9
43100761 ATTCAAATAT
43100771 TAAAAATTTA
1 TAAAAA-TTA
*
43100781 TTAGAAATTA
1 -TAAAAATTA
* *
43100791 GAAAAAATA
1 TAAAAATTA
*
43100800 TAAAAATCA
1 TAAAAATTA
43100809 TAAAAATATA
1 TAAAAAT-TA
*
43100819 TAAAAATTG
1 TAAAAATTA
*
43100828 TAAAATTTTA
1 TAAAA-ATTA
**
43100838 TAAAAATCG
1 TAAAAATTA
43100847 TAAAAA-TA
1 TAAAAATTA
*
43100855 TAAAAAAATA
1 T-AAAAATTA
*
43100865 TAGAAATATA
1 TAAAAAT-TA
*
43100875 AAAAAATTA
1 TAAAAATTA
43100884 TAAAA
1 TAAAA
43100889 TTTTATAAAG
Statistics
Matches: 81, Mismatches: 21, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
8 1 0.01
9 47 0.58
10 28 0.35
11 5 0.06
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:43100814 original size:19 final size:19
Alignment explanation
Indices: 43100792--43100888 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 19
43100782 TAGAAATTAG
43100792 AAAAA-ATATAAAAATCAT
1 AAAAATATATAAAAATCAT
**
43100810 AAAAATATATAAAAATTGT
1 AAAAATATATAAAAATCAT
* * *
43100829 AAAATTTTATAAAAATCGT
1 AAAAATATATAAAAATCAT
*
43100848 AAAAATATAAAAAAAT-AT
1 AAAAATATATAAAAATCAT
* * *
43100866 AGAAATATAAAAAAATTAT
1 AAAAATATATAAAAATCAT
43100885 AAAA
1 AAAA
43100889 TTTTATAAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
18 21 0.32
19 45 0.68
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAATATATAAAAATCAT
Found at i:43100834 original size:56 final size:55
Alignment explanation
Indices: 43100792--43100897 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 55
43100782 TAGAAATTAG
* * *
43100792 AAAAAATATAAAAATCATAAAAATATATAAAAATTGTAAAATTTTATAAAAATCGTA
1 AAAAAATAAAAAAAT-ATAAAAATATAAAAAAATTATAAAATTTTATAAAAATC-TA
* *
43100849 AAAATATAAAAAAATATAGAAATATAAAAAAATTATAAAATTTTATAAA
1 AAAAAATAAAAAAATATAAAAATATAAAAAAATTATAAAATTTTATAAA
43100898 GTCGTAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 31 0.70
57 13 0.30
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (55 bp):
AAAAAATAAAAAAATATAAAAATATAAAAAAATTATAAAATTTTATAAAAATCTA
Found at i:43100927 original size:21 final size:21
Alignment explanation
Indices: 43100885--43100929 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
43100875 AAAAAATTAT
* *
43100885 AAAATTTTATAAAGTCGTAAG
1 AAAATTATATAAAATCGTAAG
43100906 AAAATTATATAAAAT-GTAAAG
1 AAAATTATATAAAATCGT-AAG
43100927 AAA
1 AAA
43100930 TATAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAATTATATAAAATCGTAAG
Found at i:43101126 original size:19 final size:19
Alignment explanation
Indices: 43101104--43101175 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 19
43101094 TATTTTTATG
43101104 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
***
43101123 ATTTTT-TATTTTTTTACA
1 ATTTTTATAAAATTTTACA
* * *
43101141 TTTTTTATAAAAATTTAATA
1 ATTTTTAT-AAAATTTTACA
*
43101161 ATTTTTCTAAAATTT
1 ATTTTTATAAAATTT
43101176 ATTATTTATT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 14 0.35
19 14 0.35
20 12 0.30
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:43101387 original size:91 final size:92
Alignment explanation
Indices: 43101249--43101423 Score: 246
Period size: 91 Copynumber: 1.9 Consensus size: 92
43101239 TTTGAAATAT
** * * * *
43101249 TTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAATACCCAGTTGAGT-TAAGAAGAAAAAGCA
1 TTTGAGGACCTTTTTGATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAAAAAG-A
43101313 GGGGCTTAATTGTTT-TTTTAAAAGAAG
65 GGGGCTTAATTGTTTCTTTTAAAAGAAG
* * *
43101340 TTTGAGGACCTTTTTGATGCATTTTGAAAGTTCAAGTGCTCAATTGAGTGCAAAAAAAAAAAGAG
1 TTTGAGGACCTTTTTGATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAAAAAGAG
43101405 GGGCTTAATTGTTTCTTTT
66 GGGCTTAATTGTTTCTTTT
43101424 TTTAAAAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
91 59 0.81
92 14 0.19
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (92 bp):
TTTGAGGACCTTTTTGATGCATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAAAAAGAG
GGGCTTAATTGTTTCTTTTAAAAGAAG
Found at i:43104742 original size:24 final size:23
Alignment explanation
Indices: 43104715--43104790 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
43104705 AGATATTTAT
*
43104715 ATTATTTATTTATATAATATATAA
1 ATTAATTATTTATATAATAT-TAA
** *
43104739 ATTAATTATAAAGTATATTATTAA
1 ATTAATTATTTA-TATAATATTAA
*
43104763 ATTAATTATATTATA-AATATTAT
1 ATTAATTAT-TTATATAATATTAA
43104786 ATTAA
1 ATTAA
43104791 GAAATAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.26
24 23 0.55
25 8 0.19
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTAATTATTTATATAATATTAA
Found at i:43104758 original size:12 final size:11
Alignment explanation
Indices: 43104729--43104772 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
43104719 TTTATTTATA
43104729 TAATATATAAAT
1 TAAT-TATAAAT
*
43104741 TAATTATAAAG
1 TAATTATAAAT
43104752 TATATTATTAAAT
1 TA-ATTA-TAAAT
43104765 TAATTATA
1 TAATTATA
43104773 TTATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:43104784 original size:14 final size:17
Alignment explanation
Indices: 43104752--43104789 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
43104742 AATTATAAAG
43104752 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
43104769 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
43104783 TATATTA
1 TATATTA
43104790 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:43105026 original size:15 final size:17
Alignment explanation
Indices: 43105008--43105039 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43104998 CAGAATAGAA
43105008 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
43105023 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
43105040 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:43105240 original size:12 final size:12
Alignment explanation
Indices: 43105223--43105254 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
43105213 GCGTGATTCA
43105223 TGTTGAATAAAT
1 TGTTGAATAAAT
43105235 TGTTGAATAAAT
1 TGTTGAATAAAT
43105247 TGTTGAAT
1 TGTTGAAT
43105255 TAGGGATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (12 bp):
TGTTGAATAAAT
Found at i:43105727 original size:3 final size:3
Alignment explanation
Indices: 43105719--43105774 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
43105709 GTGAGGTAAG
43105719 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43105767 TAT TAT TA
1 TAT TAT TA
43105775 AGATGAGTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:43108964 original size:45 final size:45
Alignment explanation
Indices: 43108900--43108993 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
43108890 AATAGATACT
* * * *
43108900 CGGTGGATTCAGTACATAGCAACCACCTTATTAATCAGTGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
* *
43108945 CGGTGGAATCAGCACATAGCAACCACTTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
43108990 CGGT
1 CGGT
43108994 TCACATAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:43109056 original size:51 final size:50
Alignment explanation
Indices: 43108998--43109181 Score: 217
Period size: 51 Copynumber: 3.6 Consensus size: 50
43108988 TTCGGTTCAC
*
43108998 ATAGTAGCCTGCACATAGTACTACACATGTGATCATTACCATCCGATACGT
1 ATAGTAGCCTGCACATAGTACTACACACGTGATCA-TACCATCCGATACGT
* * *
43109049 ATAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATTCGATACGT
1 ATAGTAGCCTGCACATAGTACTACACACGTGATC-ATACCATCCGATACGT
* * * * * * **
43109100 ATAGTAGCCTGCACATAGTACAACACATGCGA-CCTATCATTCCGGTACAC
1 ATAGTAGCCTGCACATAGTACTACACACGTGATCATACCA-TCCGATACGT
*
43109150 GTAGTAGCCTGCACATAGTACTACACACGTGA
1 ATAGTAGCCTGCACATAGTACTACACACGTGA
43109182 CCATCACTTT
Statistics
Matches: 112, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 35 0.31
51 74 0.66
52 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (50 bp):
ATAGTAGCCTGCACATAGTACTACACACGTGATCATACCATCCGATACGT
Found at i:43109178 original size:101 final size:102
Alignment explanation
Indices: 43108998--43109181 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 102
43108988 TTCGGTTCAC
* * * **
43108998 ATAGTAGCCTGCACATAGTACTACACATGTGATCATTACCATCCGATACGTATAGTAGCCTGCAC
1 ATAGTAGCCTGCACATAGTACAACACATGCGATCACTACCATCCGATACACATAGTAGCCTGCAC
43109063 ATAGTACTACACACGTGATCGAAACTATTCGATACGT
66 ATAGTACTACACACGTGATCGAAACTATTCGATACGT
* * *
43109100 ATAGTAGCCTGCACATAGTACAACACATGCGA-C-CTATCATTCCGGTACACGTAGTAGCCTGCA
1 ATAGTAGCCTGCACATAGTACAACACATGCGATCACTACCA-TCCGATACACATAGTAGCCTGCA
43109163 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
43109182 CCATCACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.53
102 30 0.41
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (102 bp):
ATAGTAGCCTGCACATAGTACAACACATGCGATCACTACCATCCGATACACATAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATTCGATACGT
Done.