Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 123 of 172
Found at i:34938245 original size:7 final size:8
Alignment explanation
Indices: 34938210--34938261 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
34938200 TAATTATTAT
*
34938210 TATTCTAA
1 TATTTTAA
*
34938218 TATTTTGA
1 TATTTTAA
34938226 TATTTTAA
1 TATTTTAA
34938234 TATTTT-A
1 TATTTTAA
34938241 TATTTTATA
1 TATTTTA-A
*
34938250 TATTTTAT
1 TATTTTAA
34938258 TATT
1 TATT
34938262 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:34944044 original size:21 final size:22
Alignment explanation
Indices: 34944015--34944061 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
34944005 CAGAAGGAGT
*
34944015 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
34944037 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
34944058 GAGT
1 GAGT
34944062 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:34945525 original size:24 final size:24
Alignment explanation
Indices: 34945484--34945552 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
34945474 AAATGAAAAA
*
34945484 AATAATAATATAGT-ATAACTTTTA-
1 AATAATAATACA-TAATAA-TTTTAG
*
34945508 AGTAATAATACATAATAATTTTAG
1 AATAATAATACATAATAATTTTAG
* *
34945532 AATAATAATACACAATGATTT
1 AATAATAATACATAATAATTT
34945553 CGAAAACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 6 0.16
24 32 0.84
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
AATAATAATACATAATAATTTTAG
Found at i:34945655 original size:3 final size:3
Alignment explanation
Indices: 34945647--34945681 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
34945637 ATAGTACATA
*
34945647 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34945682 AAGGTTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34947528 original size:13 final size:13
Alignment explanation
Indices: 34947512--34947536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34947502 TACTTTATCA
34947512 TAAATTCTAGTAT
1 TAAATTCTAGTAT
34947525 TAAATTCTAGTA
1 TAAATTCTAGTA
34947537 GTAATAATAT
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:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TAAATTCTAGTAT
Found at i:34953084 original size:16 final size:16
Alignment explanation
Indices: 34953063--34953099 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
34953053 TTGTACTCTC
34953063 TTTTTTTT--ACTGTGA
1 TTTTTTTTCCACTG-GA
34953078 TTTTTTTTCCACTGGA
1 TTTTTTTTCCACTGGA
34953094 TTTTTT
1 TTTTTT
34953100 CTAGTAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 8 0.40
17 4 0.20
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.68
Consensus pattern (16 bp):
TTTTTTTTCCACTGGA
Found at i:34958851 original size:2 final size:2
Alignment explanation
Indices: 34958844--34958868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34958834 TGAATGTTAG
34958844 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 T
34958869 TTTTATTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34965785 original size:34 final size:34
Alignment explanation
Indices: 34965742--34965811 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
34965732 ACGATAAGTC
34965742 TGGCAATACCTCAATTGACTCAACTAATATAACA
1 TGGCAATACCTCAATTGACTCAACTAATATAACA
34965776 TGGCAATACCTCAATTGACTCAACTAATATAACA
1 TGGCAATACCTCAATTGACTCAACTAATATAACA
34965810 TG
1 TG
34965812 AAACATGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (34 bp):
TGGCAATACCTCAATTGACTCAACTAATATAACA
Found at i:34976759 original size:115 final size:114
Alignment explanation
Indices: 34976572--34976899 Score: 417
Period size: 115 Copynumber: 2.9 Consensus size: 114
34976562 AAAATAAGTA
* * * * * *
34976572 TTAGCGGCATTTTTTAAAAAGCACCGCAAAA-AAATAAGCCAAACGACGCCGTATTCTGAGCTTT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCAAAATAACTAAGCCCAACGACGCCGTTTTCTGAGCTTT
*
34976636 CGCAGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAAGGCTT
66 CGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAAGGCTT
* * *
34976685 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAATCTAAGCCCAACGACGCTGTTTTCTAAGCTT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCAAAATAA-CTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
34976750 TCGCGGATTTAGTGGCTTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTT
65 TCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAAGGCTT
** * *
34976800 TT-GTAGCGTTTTTGATAAAGCGCCGCAAAATAAACTAAGCCCAACGATGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAT-AACTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * * *
34976864 TCACGGATTTAGAGGCGATTCTTAATAAAGCGCCGC
65 TCGCGGATTTAGTGGCGTTTTTTAGT-AAGCGCCGC
34976900 AAAATAAACT
Statistics
Matches: 185, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
113 27 0.15
114 74 0.40
115 84 0.45
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAAAAAGCGCCGCAAAATAACTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAAGGCTT
Found at i:34976855 original size:114 final size:115
Alignment explanation
Indices: 34976589--34976880 Score: 419
Period size: 115 Copynumber: 2.6 Consensus size: 115
34976579 CATTTTTTAA
* * * *
34976589 AAAGCACCGCAAAA-AAA-TAAGCCAAACGACGCCGTATTCTGAGCTTTCGCAGATTTAGTGGCG
1 AAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGGATTTAGTGGCG
* *
34976652 TTTTTTAGTAAGCGCCGCTAATGCTCAAGGCTTTTAGCGGCGTTTTTGAG
66 TTTTTTAGGAAGCGCCGCTAATGCTCAAGGCTTTTAGCAGCGTTTTTGAG
* * * *
34976702 AAAGCGCCGCAAAATAATCTAAGCCCAACGACGCTGTTTTCTAAGCTTTCGCGGATTTAGTGGCT
1 AAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGGATTTAGTGGCG
* * *
34976767 TTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTT-GTAGCGTTTTTGAT
66 TTTTTTAGGAAGCGCCGCTAATGCTCAAGGCTTTTAGCAGCGTTTTTGAG
* * *
34976816 AAAGCGCCGCAAAATAAACTAAGCCCAACGATGCCGTTTTCTGAGCTTTCACGGATTTAGAGGCG
1 AAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGGATTTAGTGGCG
34976881 ATTCTTAATA
Statistics
Matches: 157, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
113 13 0.08
114 71 0.45
115 73 0.46
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (115 bp):
AAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGGATTTAGTGGCG
TTTTTTAGGAAGCGCCGCTAATGCTCAAGGCTTTTAGCAGCGTTTTTGAG
Found at i:34977029 original size:188 final size:188
Alignment explanation
Indices: 34976702--34977053 Score: 528
Period size: 188 Copynumber: 1.9 Consensus size: 188
34976692 CGTTTTTGAG
* * * *
34976702 AAAGCGCCGCAAAATAATCTAAGCCCAACGACGCTGTTTTCTAAGCTTTCGCGGATTTAGTGGCT
1 AAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGCGAATTTAGTGGCG
* * * *
34976767 TTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTTGTAGCGTTTTTGATAAAGCGCCGCAAAATA
66 TTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTGTGAGAAAGCGCCGCAAAATA
34976832 AACTAAGCCCAACGATGCCGTTTTCTGAGCTTTCACGGATTTAGAGGCGATTCTTAAT
131 AACTAAGCCCAACGATGCCGTTTTCTGAGCTTTCACGGATTTAGAGGCGATTCTTAAT
* * * *
34976890 AAAGCGCCGCAAAATAAACTAAGTCCAACGACGCCGTTTTCTGAGCTTTTGCGAATTTAGTGTCG
1 AAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGCGAATTTAGTGGCG
* *
34976955 TTTTTTAGGATA-CGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTGTGAGAAAGCGTCGCAAAA-
66 TTTTTTAGGA-AGCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTGTGAGAAAGCGCCGCAAAAT
* *
34977018 AGACATAAGCCCAACGATGCTGTTTTCTGAGCTTTC
130 AAAC-TAAGCCCAACGATGCCGTTTTCTGAGCTTTC
34977054 GGGGGATTTA
Statistics
Matches: 146, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
187 3 0.02
188 142 0.97
189 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (188 bp):
AAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGCGAATTTAGTGGCG
TTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTGTGAGAAAGCGCCGCAAAATA
AACTAAGCCCAACGATGCCGTTTTCTGAGCTTTCACGGATTTAGAGGCGATTCTTAAT
Found at i:34977208 original size:14 final size:14
Alignment explanation
Indices: 34977189--34977218 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34977179 ATGGGTTTAG
34977189 GGATTATGGATTAA
1 GGATTATGGATTAA
*
34977203 GGATTATGGTTTAA
1 GGATTATGGATTAA
34977217 GG
1 GG
34977219 GTTGAGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (14 bp):
GGATTATGGATTAA
Found at i:34977251 original size:15 final size:15
Alignment explanation
Indices: 34977230--34977272 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
34977220 TTGAGATTTA
34977230 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
34977245 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
34977260 ACGTTT-GGGGTTA
1 AGGTTTAGGGGTTA
34977273 AGTGCTAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.16, C:0.02, G:0.47, T:0.35
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:34977492 original size:15 final size:14
Alignment explanation
Indices: 34977471--34977519 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
34977461 CATATTTTAA
*
34977471 GGTTTAGGGAGTAT
1 GGTTTAGGGACTAT
*
34977485 GAGTTTAGGGATTAT
1 G-GTTTAGGGACTAT
*
34977500 GGATTAGGGACTAT
1 GGTTTAGGGACTAT
34977514 GGTTTA
1 GGTTTA
34977520 AGGGTTAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (14 bp):
GGTTTAGGGACTAT
Found at i:34977506 original size:29 final size:27
Alignment explanation
Indices: 34977474--34977531 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
34977464 ATTTTAAGGT
*
34977474 TTAGGGAGTATGAGTTT-AGGGATTATGGA
1 TTAGGGACTATG-GTTTAAGGG-TTA-GGA
34977503 TTAGGGACTATGGTTTAAGGGTTAGGA
1 TTAGGGACTATGGTTTAAGGGTTAGGA
34977530 TT
1 TT
34977532 TAAGGTTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 5 0.19
28 7 0.26
29 15 0.56
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (27 bp):
TTAGGGACTATGGTTTAAGGGTTAGGA
Found at i:34977620 original size:35 final size:37
Alignment explanation
Indices: 34977521--34977597 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
34977511 TATGGTTTAA
* * * * *
34977521 GGGTTAGGATTTAAGG-TTTAGGGGTTAGGGGTTTAG
1 GGGTTAAGAGTTAAGGATTTAAGGTTTAGGGGTTCAG
34977557 GGGTTAAGAGTTAAGGATTTAAGGTTTAGGGGTTCAG
1 GGGTTAAGAGTTAAGGATTTAAGGTTTAGGGGTTCAG
34977594 GGGT
1 GGGT
34977598 CGAGTTAAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 14 0.40
37 21 0.60
ACGTcount: A:0.22, C:0.01, G:0.43, T:0.34
Consensus pattern (37 bp):
GGGTTAAGAGTTAAGGATTTAAGGTTTAGGGGTTCAG
Found at i:34978102 original size:136 final size:138
Alignment explanation
Indices: 34977896--34978151 Score: 380
Period size: 136 Copynumber: 1.9 Consensus size: 138
34977886 CAAAACGGCG
* *
34977896 TCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTATGCAAAACGCCGCAAAAGATAACA
1 TCATTTTGTTCAAAACGAAATAATATTTTGCGGCATTTTTATGCAAAACGCCGCAAAAGATAACA
* *
34977961 AATAGCGGCGCTTTCT-AT-AAAAACGCCGC-AA-AAATAAATCAATTTATAGAAAACAAAATAG
66 AATAGCGGCG-TTTCTCATGAAAAACGCCGCAAACAAATAAAT-AAATTATAAAAAACAAAATAG
34978022 CAAAATTGCA
129 CAAAATTGCA
*
34978032 TCATTTTGTTCAAAACGAAATAATATTTTGTGGCATTTTTATAG-AAAACGCCGCAAAAGATAAG
1 TCATTTTGTTCAAAACGAAATAATATTTTGCGGCATTTTTAT-GCAAAACGCCGCAAAAGATAA-
*
34978096 C-AATAGCGGCGTTTTTCATGAAAAACGCCGCAAACAAATAAATAAATTATAAAAAA
64 CAAATAGCGGCGTTTCTCATGAAAAACGCCGCAAACAAATAAATAAATTATAAAAAA
34978152 TTATTTACAT
Statistics
Matches: 108, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
135 4 0.04
136 70 0.65
137 13 0.12
138 13 0.12
139 8 0.07
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (138 bp):
TCATTTTGTTCAAAACGAAATAATATTTTGCGGCATTTTTATGCAAAACGCCGCAAAAGATAACA
AATAGCGGCGTTTCTCATGAAAAACGCCGCAAACAAATAAATAAATTATAAAAAACAAAATAGCA
AAATTGCA
Found at i:34978400 original size:105 final size:104
Alignment explanation
Indices: 34978144--34978749 Score: 520
Period size: 105 Copynumber: 5.5 Consensus size: 104
34978134 TAAATAAATT
* * * * * *
34978144 ATAAAAAATTATT-TACATAGAAAAACGGCGCCGTTTTTTTATCAAAATG-AATTAACGGCGTTT
1 ATAAAAAATT-TTGTGCATAGCAAAACGGCGTC-ATTTTGT-TCAAAATGAAATT-GCGGCGTTT
**
34978207 TTTATAAAAACGCCGCAAAAAAGTAAATCAATCTATAAAAAACAAA
62 TTCCTAAAAACGCCGCAAAAAA-TAAATCAAT-T-TAAAAAACAAA
* * *
34978253 ATAAAAAATTTTGTGCACAGCAAAACGGCGTCATTTTATTCAAATTGAAATTGCGGCGTTTTTCC
1 ATAAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATTGCGGCGTTTTTCC
*
34978318 TAAAAACGCCGCAAAAAATAAATCAATTTAAAAGATCAAA
66 TAAAAACGCCGCAAAAAATAAATCAATTTAAAA-AACAAA
** * *
34978358 ATAAAAAATTGCGTCCATAGCAAAACTGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCG
1 ATAAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAAATG----AA-A--TTGCGGCG
* ** *
34978423 TTTTTCAC-AAAAACGCCGCAAAATATAAGCAATAGCGGCGTTTTAGCAGAGAAAATAAATAA
59 TTTTTC-CTAAAAACGCCGCAAAAAAT-A--AAT-----CAATTT---A-A-AAAACAA---A
* * * * * *
34978485 ATTTAAAAAATTTATTTGTATAGCAAAACGGCGCCGTTTTTCTTCAAAATGAAATAGCGGCGTTT
1 A--TAAAAAATTT-TGTGCATAGCAAAACGGCGTC-ATTTTGTTCAAAATGAAATTGCGGCGTTT
*
34978550 TTAAC-AAAAACGCCGCAAAAAAGTAAATCAATTTATAAAAACAAA
62 TT-CCTAAAAACGCCGCAAAAAA-TAAATCAATTTA-AAAAACAAA
* * * * *
34978595 AT-AAAATTTTTGTGCATAGCAAAACGGCGACATTTTGTTCAAATTGAAGTTGCGGCGTTTTCCC
1 ATAAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATTGCGGCGTTTTTCC
34978659 TAAAAACGCCGCAAAAAATAAATCAATTTTAAAAAACAAA
66 TAAAAACGCCGCAAAAAATAAATCAA-TTTAAAAAACAAA
*
34978699 ATAAAAAATTTTGTGCATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAT
1 ATAAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAT
34978750 AATATTTTGC
Statistics
Matches: 406, Mismatches: 55, Indels: 76
0.76 0.10 0.14
Matches are distributed among these distances:
104 25 0.06
105 135 0.33
106 27 0.07
107 42 0.10
108 12 0.03
109 27 0.07
110 3 0.01
112 31 0.08
113 8 0.02
114 2 0.00
115 3 0.01
117 4 0.01
120 4 0.01
122 3 0.01
123 1 0.00
124 34 0.08
125 3 0.01
126 1 0.00
127 4 0.01
129 9 0.02
130 15 0.04
131 13 0.03
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (104 bp):
ATAAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATTGCGGCGTTTTTCC
TAAAAACGCCGCAAAAAATAAATCAATTTAAAAAACAAA
Found at i:34978663 original size:341 final size:350
Alignment explanation
Indices: 34978018--34978768 Score: 1067
Period size: 341 Copynumber: 2.2 Consensus size: 350
34978008 AGAAAACAAA
* * * * * *
34978018 ATAGCAAAATTGCATCATTTTGTTCAAAACGAAATAATATTTTGTGGCATTTTTATAGAAAACGC
1 ATAGCAAAACTGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTACAGAAAACGC
*
34978083 CGCAAAAGATAAGCAATAGCGGCGTTTTTCATGAAAAACGCCGCAAACAAATAAATAAATTATAA
66 CGCAAAAGATAAGCAATAGCGGCG-TTTT-AT----AACGCAGCAAACAAATAAATAAATTATAA
* * * *
34978148 AAAATTATTTACATAGAAAAACGGCGCCGTTTTTTTATCAAAATGAATTAACGGCGTTTTTTATA
125 AAAATTATTTACATAGAAAAACGGCGCCGTTTTTCTATCAAAATGAAATAACGGCGTTTTTAACA
34978213 AAAACGCCGCAAAAAAGTAAATCAATCTATAAAAAACAAAATAAAAAATTTTGTGCACAGCAAAA
190 AAAACGCCGCAAAAAAGTAAATCAATCTATAAAAAACAAAATAAAAAATTTTGTGCACAGCAAAA
* *
34978278 CGGCGTCATTTTATTCAAATTGAAATTGCGGCGTTTTTCCTAAAAACGCCGCAAAAAATAAATCA
255 CGGCGACATTTTATTCAAATTGAAATTGCGGCGTTTTCCCTAAAAACGCCGCAAAAAATAAATCA
*
34978343 A-TTTAAAAGATCAAAATAAAAAATTGCGTCC
320 ATTTTAAAA-AACAAAATAAAAAATTGCGTCC
34978374 ATAGCAAAACTGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCACA-AAAACG
1 ATAGCAAAACTGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTT-ACAGAAAACG
* *
34978438 CCGCAAAATATAAGCAATAGCGGCG-TTT-T-A-GCAG-AGA-AAATAAATAAATT-TAAAAAAT
65 CCGCAAAAGATAAGCAATAGCGGCGTTTTATAACGCAGCAAACAAATAAATAAATTATAAAAAA-
** * *
34978496 TTATTTGTATAGCAAAACGGCGCCGTTTTTCT-TCAAAATGAAATAGCGGCGTTTTTAACAAAAA
129 TTATTTACATAGAAAAACGGCGCCGTTTTTCTATCAAAATGAAATAACGGCGTTTTTAACAAAAA
* * *
34978560 CGCCGCAAAAAAGTAAATCAATTTAT-AAAAACAAAAT-AAAATTTTTGTGCATAGCAAAACGGC
194 CGCCGCAAAAAAGTAAATCAATCTATAAAAAACAAAATAAAAAATTTTGTGCACAGCAAAACGGC
* *
34978623 GACATTTTGTTCAAATTGAAGTTGCGGCGTTTTCCCTAAAAACGCCGCAAAAAATAAATCAATTT
259 GACATTTTATTCAAATTGAAATTGCGGCGTTTTCCCTAAAAACGCCGCAAAAAATAAATCAATTT
** *
34978688 TAAAAAACAAAATAAAAAATTTTGTGC
324 TAAAAAACAAAATAAAAAATTGCGTCC
* *
34978715 ATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTT
1 ATAGCAAAACTGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTT
34978769 GTATAGCAAA
Statistics
Matches: 362, Mismatches: 30, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
341 152 0.42
342 18 0.05
343 60 0.17
344 41 0.11
345 2 0.01
346 3 0.01
347 1 0.00
352 1 0.00
354 3 0.01
356 79 0.22
357 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (350 bp):
ATAGCAAAACTGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTACAGAAAACGC
CGCAAAAGATAAGCAATAGCGGCGTTTTATAACGCAGCAAACAAATAAATAAATTATAAAAAATT
ATTTACATAGAAAAACGGCGCCGTTTTTCTATCAAAATGAAATAACGGCGTTTTTAACAAAAACG
CCGCAAAAAAGTAAATCAATCTATAAAAAACAAAATAAAAAATTTTGTGCACAGCAAAACGGCGA
CATTTTATTCAAATTGAAATTGCGGCGTTTTCCCTAAAAACGCCGCAAAAAATAAATCAATTTTA
AAAAACAAAATAAAAAATTGCGTCC
Found at i:34980549 original size:25 final size:25
Alignment explanation
Indices: 34980521--34980626 Score: 71
Period size: 25 Copynumber: 4.2 Consensus size: 25
34980511 TGGGTTCAAC
*
34980521 CTTAATAATACCTTAACTTACTTAA
1 CTTAATAATACCTTAACTTACATAA
*
34980546 CTTACATAATACAC--CACTTACATAA
1 CTTA-ATAATAC-CTTAACTTACATAA
* *
34980571 CTT-A-AATAACTT-ACATAATACTTAA
1 CTTAATAATACCTTAAC-T--TACATAA
*
34980596 CTTTAATAATA-CATAACTTACATAA
1 C-TTAATAATACCTTAACTTACATAA
34980621 CTTAAT
1 CTTAAT
34980627 TACATTATAC
Statistics
Matches: 64, Mismatches: 6, Indels: 23
0.69 0.06 0.25
Matches are distributed among these distances:
21 1 0.02
22 6 0.09
23 2 0.03
24 5 0.08
25 30 0.47
26 9 0.14
27 5 0.08
28 6 0.09
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (25 bp):
CTTAATAATACCTTAACTTACATAA
Found at i:34980573 original size:9 final size:9
Alignment explanation
Indices: 34980534--34980624 Score: 79
Period size: 9 Copynumber: 10.8 Consensus size: 9
34980524 AATAATACCT
*
34980534 TAACTTACT
1 TAACTTACA
34980543 TAACTTACA
1 TAACTTACA
34980552 TAA--TACA
1 TAACTTACA
**
34980559 CCACTTACA
1 TAACTTACA
*
34980568 TAACTTAAA
1 TAACTTACA
34980577 TAACTTACA
1 TAACTTACA
*
34980586 TAA--TACT
1 TAACTTACA
34980593 TAACTTTA-A
1 TAAC-TTACA
34980602 TAA--TACA
1 TAACTTACA
34980609 TAACTTACA
1 TAACTTACA
34980618 TAACTTA
1 TAACTTA
34980625 ATTACATTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
6 2 0.03
7 15 0.23
9 46 0.71
10 2 0.03
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (9 bp):
TAACTTACA
Found at i:34982401 original size:20 final size:20
Alignment explanation
Indices: 34982365--34982414 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
34982355 CTGCAGCTTA
34982365 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGA-GCGGCAGCGAGAG
* *
34982386 AAGCAGAGCTGCAGCGAGGG
1 AAGCAGAGCGGCAGCGAGAG
34982406 AAGCAGAGC
1 AAGCAGAGC
34982415 AGTGTAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.34, C:0.20, G:0.42, T:0.04
Consensus pattern (20 bp):
AAGCAGAGCGGCAGCGAGAG
Found at i:34982786 original size:43 final size:43
Alignment explanation
Indices: 34982734--34982976 Score: 236
Period size: 43 Copynumber: 5.6 Consensus size: 43
34982724 TCTGTCAAAA
* * * *
34982734 TTAGTGGCGTTTTTAAAAAAAGCGCCGCTAAAGGTCATGGTCT
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGACATGATCT
*** * *
34982777 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGAACATGACCT
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCT-AAAGGACATGATCT
* * * * * *
34982821 TTAGTGGCGTTTGTAGAGAAAGCGCCGCCAAAGAACATAATCT
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGACATGATCT
* *
34982864 TTAGCGGCGTTTGTGAAAAAAGCTCCGCTAAAGGACATGATCT
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGACATGATCT
* * * *
34982907 TTAGCGGCGTTTG-AGGAATAAGCGCCGCTAAAGTACATGACCT
1 TTAGCGGCGTTTGTA-AAAAAAGCGCCGCTAAAGGACATGATCT
* * *
34982950 TTAGCAGCATTTATAAAAATAAGCGCC
1 TTAGCGGCGTTTGTAAAAA-AAGCGCC
34982977 ACAAATGTTA
Statistics
Matches: 161, Mismatches: 35, Indels: 7
0.79 0.17 0.03
Matches are distributed among these distances:
43 119 0.74
44 42 0.26
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (43 bp):
TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGACATGATCT
Found at i:34982865 original size:87 final size:86
Alignment explanation
Indices: 34982734--34982954 Score: 257
Period size: 87 Copynumber: 2.6 Consensus size: 86
34982724 TCTGTCAAAA
* * * ** * **
34982734 TTAGTGGCGTTTTTAAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAG
1 TTAGTGGCGTTTGTAGAGAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGAAAAAAG
34982799 CGCCGCTAAAAGAACATGACCT
66 CGCCGCT-AAAGAACATGACCT
* *
34982821 TTAGTGGCGTTTGTAGAGAAAGCGCCGCCAAAGAACATAATCTTTAGCGGCGTTTGTGAAAAAAG
1 TTAGTGGCGTTTGTAGAGAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGAAAAAAG
* * *
34982886 CTCCGCTAAAGGACATGATCT
66 CGCCGCTAAAGAACATGACCT
* * *
34982907 TTAGCGGCGTTTG-AG-GAATAAGCGCCGCTAAAGTACATGACCTTTAGC
1 TTAGTGGCGTTTGTAGAG-A-AAGCGCCGCTAAAGAACATGATCTTTAGC
34982955 AGCATTTATA
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
84 1 0.01
85 3 0.03
86 49 0.43
87 61 0.54
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (86 bp):
TTAGTGGCGTTTGTAGAGAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGAAAAAAG
CGCCGCTAAAGAACATGACCT
Found at i:34982974 original size:130 final size:130
Alignment explanation
Indices: 34982734--34982976 Score: 328
Period size: 130 Copynumber: 1.9 Consensus size: 130
34982724 TCTGTCAAAA
* * * * *
34982734 TTAGTGGCGTTTTTAAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAG
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTGTAGGAAAAG
** * * * *
34982799 CGCCGCTAAAAGAACATGACCTTTAGTGGCGTTTGTAGAGAAAGCGCCGCCAAAGAACATAATCT
66 CGCCGCTAAAAGAACATGACCTTTAGCAGCATTTATAAAAAAAGCGCCGCCAAAGAACATAATCT
* *
34982864 TTAGCGGCGTTTGTGAAAAAAGCTCCGCTAAAGGACATGATCTTTAGCGGCGTTTG-AGGAATAA
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTGTAGGAA-AA
*
34982928 GCGCCGCT-AAAGTACATGACCTTTAGCAGCATTTATAAAAATAAGCGCC
65 GCGCCGCTAAAAGAACATGACCTTTAGCAGCATTTATAAAAA-AAGCGCC
34982977 ACAAATGTTA
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
129 30 0.31
130 67 0.69
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (130 bp):
TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTGTAGGAAAAG
CGCCGCTAAAAGAACATGACCTTTAGCAGCATTTATAAAAAAAGCGCCGCCAAAGAACATAATCT
Found at i:34983357 original size:43 final size:42
Alignment explanation
Indices: 34983263--34983509 Score: 215
Period size: 43 Copynumber: 5.7 Consensus size: 42
34983253 TGTTGGTCTA
** **** *
34983263 TAGCGGCGCTTCTAGCACAAACGCCGCTAAAGATTAGGGTCTT
1 TAGCGGCGCTT-TTCCACAAACGCCGCTAAAGACCCTGATCTT
* * * * *
34983306 TAGTGGCGCTTTTCCATAAAACGCTGCAAAAGACCCTGATCTA
1 TAGCGGCGCTTTTCCA-CAAACGCCGCTAAAGACCCTGATCTT
** * * *
34983349 TAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTT
1 TAGCGGCGCTT-TTCCACAAACGCCGCTAAAGACCCTGATCTT
* * *
34983392 TAGTGGCGCTTTTCCCACAAACGCCGCTGAAGACCATGATCTT
1 TAGCGGCGCTTTT-CCACAAACGCCGCTAAAGACCCTGATCTT
* * *
34983435 TAGGGGCGCTTTTTCCACAAACGCCGCGAAAGACCCTTATCTT
1 TAGCGGCGC-TTTTCCACAAACGCCGCTAAAGACCCTGATCTT
* *
34983478 TAGCGGCGCTTTTACCAAAAACGCCACTAAAG
1 TAGCGGCGCTTTT-CCACAAACGCCGCTAAAG
34983510 GCCAACACCT
Statistics
Matches: 160, Mismatches: 39, Indels: 10
0.77 0.19 0.05
Matches are distributed among these distances:
42 7 0.04
43 146 0.91
44 7 0.04
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (42 bp):
TAGCGGCGCTTTTCCACAAACGCCGCTAAAGACCCTGATCTT
Found at i:34983404 original size:86 final size:86
Alignment explanation
Indices: 34983259--34983502 Score: 269
Period size: 86 Copynumber: 2.8 Consensus size: 86
34983249 AAGGTGTTGG
* * *
34983259 TCTATAGCGGCGCTTCTAGCACAAACGCCGCTAAAG-A-TTAGGGTCTTTAGTGGCGCTTTT-CC
1 TCTATAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACCTA--ATCTTTAGTGGCGCTTTTACC
* *
34983321 ATAAAACGCTGCAAAAGACCCTGA
64 A-AAAACGCCGCAAAAGACCATGA
* * * *
34983345 TCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGTGGCGCTTTTCCCAC
1 TCTATAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACCTAATCTTTAGTGGCGCTTTTACCAA
**
34983410 AAACGCCGCTGAAGACCATGA
66 AAACGCCGCAAAAGACCATGA
* * * * * * * *
34983431 TCTTTAGGGGCGCTTTTTCCACAAACGCCGCGAAAGACCCTTATCTTTAGCGGCGCTTTTACCAA
1 TCTATAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACCTAATCTTTAGTGGCGCTTTTACCAA
34983496 AAACGCC
66 AAACGCC
34983503 ACTAAAGGCC
Statistics
Matches: 133, Mismatches: 22, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
86 127 0.95
87 4 0.03
88 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (86 bp):
TCTATAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACCTAATCTTTAGTGGCGCTTTTACCAA
AAACGCCGCAAAAGACCATGA
Found at i:34983522 original size:86 final size:86
Alignment explanation
Indices: 34983363--34983534 Score: 209
Period size: 86 Copynumber: 2.0 Consensus size: 86
34983353 GGCGCTTCGA
* * * * * *
34983363 CCACAAACGCCACTAAAGAACCTAATCTTTAGTGGCGCTTTTCCCACAAACGCCGCTGAAGACCA
1 CCACAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTTACCAAAAACGCCACTAAAGACCA
** *
34983428 TGATCTTTAGGGGCGCTTTTT
66 ACACCTTTAGGGGCGCTTTTT
* * * *
34983449 CCACAAACGCCGCGAAAGACCCTTATCTTTAGCGGCGCTTTTACCAAAAACGCCACTAAAGGCCA
1 CCACAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTTACCAAAAACGCCACTAAAGACCA
* *
34983514 ACACCTTTAGTGGCGTTTTTT
66 ACACCTTTAGGGGCGCTTTTT
34983535 TTTCAAAACG
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (86 bp):
CCACAAACGCCACGAAAGAACCTAATCTTTAGCGGCGCTTTTACCAAAAACGCCACTAAAGACCA
ACACCTTTAGGGGCGCTTTTT
Found at i:34983522 original size:129 final size:129
Alignment explanation
Indices: 34983278--34983533 Score: 318
Period size: 129 Copynumber: 2.0 Consensus size: 129
34983268 GCGCTTCTAG
** * * *
34983278 CACAAACGCCGCTAAAGATTAGGGTCTTTAGTGGCGCTTTTCCATAAAACGCTGCAAAAGACCCT
1 CACAAACGCCGCTAAAGACCAGGATCTTTAGGGGCGCTTTTCCATAAAACGCCGCAAAAGACCCT
* * *
34983343 GATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGTGGCGCTTTTCC
66 GATCTATAGCGGCGCTTCGACCAAAAACGCCACTAAAGAACCAAACCTTTAGTGGCGCTTTTCC
* * * *
34983407 CACAAACGCCGCTGAAGACCATGATCTTTAGGGGCGCTTTTTCCA-CAAACGCCGCGAAAGACCC
1 CACAAACGCCGCTAAAGACCAGGATCTTTAGGGGCGC-TTTTCCATAAAACGCCGCAAAAGACCC
* * ** * *
34983471 TTATCTTTAGCGGCGCTTTTACCAAAAACGCCACTAAAG-GCCAACACCTTTAGTGGCGTTTTT
65 TGATCTATAGCGGCGCTTCGACCAAAAACGCCACTAAAGAACCAA-ACCTTTAGTGGCGCTTTT
34983534 TTTTCAAAAC
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
128 3 0.03
129 97 0.91
130 7 0.07
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (129 bp):
CACAAACGCCGCTAAAGACCAGGATCTTTAGGGGCGCTTTTCCATAAAACGCCGCAAAAGACCCT
GATCTATAGCGGCGCTTCGACCAAAAACGCCACTAAAGAACCAAACCTTTAGTGGCGCTTTTCC
Found at i:34983886 original size:21 final size:21
Alignment explanation
Indices: 34983860--34983917 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
34983850 TTTGACGCTG
34983860 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTTTAGC
**
34983881 CTCTGCTTCCCTCATTTTAGC
1 CTCTGCTTCCCTCGCTTTAGC
34983902 CTCTGCTTCCCTCGCT
1 CTCTGCTTCCCTCGCT
34983918 GTAACATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.05, C:0.43, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTTTAGC
Found at i:34983952 original size:21 final size:21
Alignment explanation
Indices: 34983928--34983972 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34983918 GTAACATGTA
*
34983928 CTTCTCTCACTGCTGCCTCTG
1 CTTCTCTCACTGCCGCCTCTG
**
34983949 CTTCTCTTGCTGCCGCCTCTG
1 CTTCTCTCACTGCCGCCTCTG
34983970 CTT
1 CTT
34983973 TAAGCTGCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.42, G:0.16, T:0.40
Consensus pattern (21 bp):
CTTCTCTCACTGCCGCCTCTG
Found at i:34984025 original size:66 final size:66
Alignment explanation
Indices: 34983943--34984087 Score: 213
Period size: 66 Copynumber: 2.2 Consensus size: 66
34983933 CTCACTGCTG
* *
34983943 CCTCTGCTTCTCTTGCTGCCGCCTCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
34984006 GAA
64 GAA
* * *
34984009 CCTCAGCTTCTCTTGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
34984074 A
66 A
34984075 CCTCAGCTTCTCT
1 CCTCAGCTTCTCT
34984088 CGATGTTGCC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.12, C:0.28, G:0.18, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:34984105 original size:66 final size:65
Alignment explanation
Indices: 34983943--34984113 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
34983933 CTCACTGCTG
* * * * *
34983943 CCTCTGCTTCTCTTGCTGCCGCCTCTGCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGA
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTTTAAGTTG-TGCTGGAGTTCTTCATACTTTCGTTGA
34984008 A
65 A
* * * *
34984009 CCTCAGCTTCTCTTGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTG
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTTTAAGTTGT-GCTGGAGTTCTTCATA-CTTTCGTTG
34984073 AA
64 AA
* *
34984075 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGTG
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTTTAAGTTGTG
34984114 TAATTTGCTC
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 2 0.02
66 87 0.94
67 4 0.04
ACGTcount: A:0.12, C:0.27, G:0.19, T:0.41
Consensus pattern (65 bp):
CCTCAGCTTCTCTCGATGCTGCCTCTGCTTTAAGTTGTGCTGGAGTTCTTCATACTTTCGTTGAA
Found at i:34989537 original size:9 final size:9
Alignment explanation
Indices: 34989520--34989950 Score: 134
Period size: 9 Copynumber: 49.2 Consensus size: 9
34989510 TAAGTATAAT
*
34989520 TAAGCTATG
1 TAAGTTATG
34989529 TAAGTTATG
1 TAAGTTATG
34989538 T-A-TTATG
1 TAAGTTATG
34989545 TAAGTTAT-
1 TAAGTTATG
*
34989553 TTA-TTATG
1 TAAGTTATG
* *
34989561 AAAATTATG
1 TAAGTTATG
*
34989570 TAAGTTGTG
1 TAAGTTATG
34989579 T-A-TTATG
1 TAAGTTATG
*
34989586 -AA--AAT-
1 TAAGTTATG
*
34989591 TATGTTATG
1 TAAGTTATG
34989600 TAAGTTATG
1 TAAGTTATG
* *
34989609 TAAGTCATA
1 TAAGTTATG
34989618 TAAGTTATG
1 TAAGTTATG
34989627 T-A-TTATG
1 TAAGTTATG
34989634 TAAGTTATG
1 TAAGTTATG
34989643 TAAGTTAT-
1 TAAGTTATG
*
34989651 TTA-TTATG
1 TAAGTTATG
* * *
34989659 AAAGATAAG
1 TAAGTTATG
34989668 TAAGTTATG
1 TAAGTTATG
* *
34989677 TAATTTACG
1 TAAGTTATG
*
34989686 -AA-TAAT-
1 TAAGTTATG
***
34989692 TAAAAAAATG
1 T-AAGTTATG
34989702 TAAGTTATG
1 TAAGTTATG
34989711 TAAG-T-TG
1 TAAGTTATG
34989718 TAAGTTATG
1 TAAGTTATG
*
34989727 TATA-ATAT-
1 TA-AGTTATG
**
34989735 TAA-TTAAC
1 TAAGTTATG
34989743 TAAGTTATG
1 TAAGTTATG
*
34989752 TAATTTATG
1 TAAGTTATG
*
34989761 TATA-ATAT-
1 TA-AGTTATG
34989769 TAA-TTAAT-
1 TAAGTT-ATG
34989777 TAAGTTATG
1 TAAGTTATG
*
34989786 TAATTTATG
1 TAAGTTATG
34989795 TATA-TTAAT-
1 TA-AGTT-ATG
34989804 TAAGTTATG
1 TAAGTTATG
*
34989813 TAATTTATG
1 TAAGTTATG
*
34989822 TATAATATTAATG
1 --TAA-GTT-ATG
34989835 TAAGTTATG
1 TAAGTTATG
*
34989844 TATA-ATATG
1 TA-AGTTATG
*
34989853 TATAATATTAATG
1 --TAA-GTT-ATG
*
34989866 CAAGTTATG
1 TAAGTTATG
34989875 TAAGTTATG
1 TAAGTTATG
*
34989884 TATA-ATAT-
1 TA-AGTTATG
**
34989892 TAA-TTAAC
1 TAAGTTATG
34989900 TAAGTTATG
1 TAAGTTATG
*
34989909 TAATTTATG
1 TAAGTTATG
*
34989918 TATAATATTAATG
1 --TAA-GTT-ATG
34989931 TAAGTTATG
1 TAAGTTATG
*
34989940 TAATTTATG
1 TAAGTTATG
34989949 TA
1 TA
34989951 TATTAATTAA
Statistics
Matches: 317, Mismatches: 58, Indels: 94
0.68 0.12 0.20
Matches are distributed among these distances:
6 3 0.01
7 41 0.13
8 41 0.13
9 187 0.59
10 15 0.05
11 16 0.05
12 5 0.02
13 9 0.03
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:34989546 original size:16 final size:16
Alignment explanation
Indices: 34989525--34989644 Score: 105
Period size: 16 Copynumber: 7.9 Consensus size: 16
34989515 ATAATTAAGC
34989525 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
34989541 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
34989557 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
34989566 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* *
34989582 TATGAAAATTATG--T
1 TATGTAAGTTATGTAT
34989596 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
34989614 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
34989630 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
34989645 AGTTATTTAT
Statistics
Matches: 82, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
9 6 0.07
10 2 0.02
12 1 0.01
14 12 0.15
15 2 0.02
16 45 0.55
17 1 0.01
18 13 0.16
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:34989567 original size:25 final size:25
Alignment explanation
Indices: 34989539--34989675 Score: 113
Period size: 25 Copynumber: 5.6 Consensus size: 25
34989529 TAAGTTATGT
34989539 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
34989564 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
34989589 ATTA--T--GTTATGTAAGTTATGTAA
1 ATTATGTAAGTTAT-TTA-TTATGAAA
* * * * *
34989612 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
*
34989637 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
*
34989662 GA-TAAGTAAGTTAT
1 -ATTATGTAAGTTAT
34989676 GTAATTTACG
Statistics
Matches: 89, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
21 4 0.04
22 1 0.01
23 10 0.11
25 68 0.76
26 1 0.01
27 5 0.06
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:34989727 original size:25 final size:25
Alignment explanation
Indices: 34989699--34989762 Score: 51
Period size: 25 Copynumber: 2.5 Consensus size: 25
34989689 AATTAAAAAA
34989699 ATGTAAGTTATGTAAGT-TGTAAGTT
1 ATGTAA-TTATGTAAGTATGTAAGTT
* * **
34989724 ATGTATAATAT-TAATTAACTAAGTT
1 ATGTA-ATTATGTAAGTATGTAAGTT
34989749 ATGTAATTTATGTA
1 ATGTAA-TTATGTA
34989763 TAATATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
24 5 0.17
25 22 0.73
26 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGTAATTATGTAAGTATGTAAGTT
Found at i:34989835 original size:22 final size:24
Alignment explanation
Indices: 34989782--34989851 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 24
34989772 TTAATTAAGT
*
34989782 TATGTAATTTATGTATATTAATTAA
1 TATGTAATTTATGTATAAT-ATTAA
34989807 GTTATGTAATTTATGTATAATATT-A
1 --TATGTAATTTATGTATAATATTAA
*
34989832 -ATGTAAGTTATGTATAATAT
1 TATGTAATTTATGTATAATAT
34989852 GTATAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
22 19 0.46
25 1 0.02
26 3 0.07
27 18 0.44
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (24 bp):
TATGTAATTTATGTATAATATTAA
Found at i:34989938 original size:22 final size:22
Alignment explanation
Indices: 34989906--34990056 Score: 123
Period size: 22 Copynumber: 7.4 Consensus size: 22
34989896 TAACTAAGTT
34989906 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
*
34989928 ATGTAAGTTATG--TAAT-TT-
1 ATGTAATTTATGTATAATATTA
* *
34989946 ATGTATATTAAT-TAACTAA-GTT-
1 ATGTA-ATTTATGT-A-TAATATTA
34989968 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
* *
34989990 AT-TAA-TTA-AT-TAA-GTT-
1 ATGTAATTTATGTATAATATTA
34990006 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
*
34990028 ATGTAAGTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
34990050 AT-TAATT
1 ATGTAATT
34990057 AAGTTATGTA
Statistics
Matches: 103, Mismatches: 11, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.02
17 5 0.05
18 11 0.11
19 8 0.08
20 13 0.13
21 17 0.17
22 47 0.46
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (22 bp):
ATGTAATTTATGTATAATATTA
Found at i:34989938 original size:56 final size:56
Alignment explanation
Indices: 34989749--34990853 Score: 896
Period size: 56 Copynumber: 18.2 Consensus size: 56
34989739 TAACTAAGTT
* *
34989749 ATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATATTAATTAA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAAT-ATT-A
* * *
34989807 GTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGT-ATAATATGTATAATATTAATGCA
1 ---ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT-TTATGTATAATA-T--T---
34989868 A
56 A
*
34989869 GTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
1 ---ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
*
34989928 ATGTAAGTTATGTAATTTATGTATATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGT-A--TA---ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
* * * *
34989990 AT-TAA-TTAAT-TA-AGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATTAA
1 ATGTAAGTT-ATGTATA-ATAT-TAA-TTA-AT-TAA-GTT-ATGTAA--T-T-TAT-GTA-TAA
34990051 TTAATTAA
52 -T-ATT-A
*
34990059 GTTATGTAACTTATGTATAATATTAATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ---ATGTAAGTTATGTATAATATTAATTAA----TTAAGTTATGTAATTTATGTATAATATTA
34990122 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
* * * *
34990178 AT-TAA-TTAAT-TA-AGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATTAA
1 ATGTAAGTT-ATGTATA-ATAT-TAA-TTA-AT-TAA-GTT-ATGTAA--T-T-TAT-GTA-TAA
34990239 TTAATTAA
52 -T-ATT-A
*
34990247 GTTATGTAACTTATGTATAATATTAATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ---ATGTAAGTTATGTATAATATTAATTAA----TTAAGTTATGTAATTTATGTATAATATTA
34990310 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
*
34990366 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAACTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
* * * *
34990422 AT-TAA-TTAAT-TA-AGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATTA
1 ATGTAAGTT-ATGTATA-ATAT-TAA-TTA-AT-TAA-GTT-ATGTAATTTATGTATAATATTA
* * * *
34990482 ATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGT-ATAATAT-TAATTAATT
1 A-T--GTAAGTTATGT-A--TA-ATATTA-ATTAAT-TAAGTTATGTAAT-TTATGT-A-TAA-T
* *
34990545 AAGTT
53 -ATTA
*
34990550 ATGTAACTTATGTATAATATTAATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATAT----TAATTAATTAAGTTATGTAATTTATGTATAATATTA
34990610 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
34990666 ATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGT-A--TA---ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
*
34990728 ATGTAAGTTATGTATAATATTAATTAATTAGGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
*
34990784 ATGTAAGTTATGTATAATATTAATTCATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
34990840 ATGTAAGTTATGTA
1 ATGTAAGTTATGTA
34990854 ATCTATGTAT
Statistics
Matches: 885, Mismatches: 52, Indels: 219
0.77 0.04 0.19
Matches are distributed among these distances:
53 2 0.00
54 17 0.02
55 19 0.02
56 296 0.33
57 7 0.01
58 29 0.03
59 14 0.02
60 112 0.13
61 34 0.04
62 130 0.15
63 19 0.02
64 30 0.03
65 48 0.05
66 20 0.02
67 12 0.01
68 19 0.02
69 9 0.01
70 2 0.00
72 22 0.02
73 20 0.02
74 20 0.02
75 4 0.00
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (56 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
Found at i:34990004 original size:38 final size:38
Alignment explanation
Indices: 34989952--34990217 Score: 179
Period size: 38 Copynumber: 7.1 Consensus size: 38
34989942 ATTTATGTAT
34989952 ATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
1 ATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
*
34989990 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
** * * *
34990028 ATGTAAGTTATGTATA-ATAT-TAATTAAT-TA-AGTTATGTA
1 AT-TAA-TTAACTA-AGTTATGTAATTTATGTATA-ATAT-TA
*
34990067 ACTT-ATGT-A-TAA--TAT-TAATTAAT-TAATTAAGTTATGTA
1 A-TTAAT-TAACTAAGTTATGTAATTTATGT-A-TAA--TAT-TA
* * *
34990105 ATTTATGT-A-TAATATTAATGTAAGTTATGTATAATATTA
1 ATTAAT-TAACTAA-GTT-ATGTAATTTATGTATAATATTA
34990144 ATTAA-T---TAAGTTATGTAATTTATGTATAATATTA
1 ATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
*
34990178 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
34990216 AT
1 AT
34990218 GTAAGTTATG
Statistics
Matches: 192, Mismatches: 13, Indels: 46
0.76 0.05 0.18
Matches are distributed among these distances:
34 38 0.20
35 5 0.03
36 5 0.03
37 6 0.03
38 91 0.47
39 20 0.10
40 12 0.06
41 2 0.01
42 5 0.03
43 7 0.04
44 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (38 bp):
ATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
Found at i:34990096 original size:94 final size:94
Alignment explanation
Indices: 34989749--34990729 Score: 1044
Period size: 94 Copynumber: 10.6 Consensus size: 94
34989739 TAACTAAGTT
*
34989749 ATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATG--------T-A-T-ATTAA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAA
34989803 TTAAGTTATGTAATTTATGTATAATATTA
66 TTAAGTTATGTAATTTATGTATAATATTA
* *
34989832 ATGTAAGTTATGTATAATATGTATAATATTAATGCAAGTTATGTAAGTTATGTAT-A-A-T-ATT
1 ATGTAAGTTATGTATAATA--T-T-A-ATTAAT-TAAGTTATGTAATTTATGTATAATATTAATT
*
34989893 AATTAACTAAGTTATGTAATTTATGTATAATATTA
60 AATTAATTAAGTTATGTAATTTATGTATAATATTA
*
34989928 ATGTAAGTTATGTAATTTATGTATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATT
1 ATGTAAGTTATGT-A--TA---ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATT
34989993 AATTAATTAAGTTATGTAATTTATGTATAATATTA
60 AATTAATTAAGTTATGTAATTTATGTATAATATTA
*
34990028 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAACTTATGTATAATATTAATTAATTAA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAA
34990093 TTAAGTTATGTAATTTATGTATAATATTA
66 TTAAGTTATGTAATTTATGTATAATATTA
34990122 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAA
34990187 TTAAGTTATGTAATTTATGTATAATATTA
66 TTAAGTTATGTAATTTATGTATAATATTA
*
34990216 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAACTTATGTATAATATTAATTAATTAA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAA
34990281 TTAAGTTATGTAATTTATGTATAATATTA
66 TTAAGTTATGTAATTTATGTATAATATTA
34990310 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTT
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT-TAA-TT
* * *
34990375 -ATGTATA-ATAT-TAA-TTA-AT-TAA-GTT-
64 AAT-TA-AGTTATGTAATTTATGTATAATATTA
*
34990400 ATGTAACTTATGTATAATATTAATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTA
1 ATGTAAGTTATGTAT-A-A-T-ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT-TA
* * *
34990465 AGTT-ATGTATA-ATAT-TAA-TTA-AT-TAA-GTT-
61 A-TTAAT-TA-AGTTATGTAATTTATGTATAATATTA
* * * *
34990494 ATGTAATTTATGTATAATATTAA-T--GTAAGTTATGT-A--TA-ATATTA-ATTAATTAAGTT-
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAA-TTA
* * *
34990550 ATGTAACTTATGT-ATAATAT-TA-ATTAATTA
65 AT-TAAGTTATGTAAT-TTATGTATAAT-ATTA
* *
34990580 AT-TAAGTTATG--TAAT-TT-ATGT-A-TAATATTAATGTAAGTTATGTATAATATTAA----T
1 ATGTAAGTTATGTATAATATTAAT-TAATTAA-GTT-ATGTAATTTATGTATAATATTAATTAAT
34990634 TAATTAAGTTATGTAATTTATGTATAATATTA
63 TAATTAAGTTATGTAATTTATGTATAATATTA
34990666 ATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
1 ATGTAAGTTATGT-A--TA---ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
34990730 GTAAGTTATG
Statistics
Matches: 796, Mismatches: 34, Indels: 122
0.84 0.04 0.13
Matches are distributed among these distances:
80 1 0.00
81 16 0.02
82 9 0.01
83 34 0.04
84 4 0.01
85 29 0.04
86 17 0.02
87 22 0.03
88 8 0.01
89 21 0.03
90 24 0.03
91 4 0.01
92 7 0.01
93 3 0.00
94 410 0.52
95 11 0.01
96 97 0.12
97 15 0.02
98 5 0.01
99 5 0.01
100 51 0.06
102 3 0.00
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (94 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAA
TTAAGTTATGTAATTTATGTATAATATTA
Found at i:34990125 original size:22 final size:22
Alignment explanation
Indices: 34990062--34990150 Score: 93
Period size: 22 Copynumber: 4.4 Consensus size: 22
34990052 TAATTAAGTT
*
34990062 ATGTAACTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
* *
34990084 AT-TAA-TTA-AT-TAA-GTT-
1 ATGTAATTTATGTATAATATTA
34990100 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
*
34990122 ATGTAAGTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
34990144 AT-TAATT
1 ATGTAATT
34990151 AAGTTATGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
16 2 0.04
17 5 0.09
18 6 0.11
19 2 0.04
20 6 0.11
21 9 0.16
22 25 0.45
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (22 bp):
ATGTAATTTATGTATAATATTA
Found at i:34990261 original size:150 final size:150
Alignment explanation
Indices: 34989749--34990785 Score: 909
Period size: 150 Copynumber: 6.8 Consensus size: 150
34989739 TAACTAAGTT
* *
34989749 ATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATATTAATTAAGTTATGT
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAAT-ATT-A---ATGT
* * *
34989814 AATTTATGTATA-ATATTAA-T--GTAAGTTATGT-ATAATATGTATAATATTAATGCAAGTT-A
61 AA-TTATGTATAGATATTAATTAATTAAGTTATGTAAT-TTATGTATAATATTAAT-TAA-TTAA
*
34989873 TGTAAGTTATGTATAATATTAAT-TAACTAA-GTT-
122 T-TAAGTTATG--TAAT-TT-ATGT-A-TAATATTA
* * *
34989906 ATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGTATATTAATTAACTAAGTT
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATG--TA-TAA-T-A-T---TA
*
34989968 ATGTAATTTATGTATAATATTAATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTA
57 ATGTAA-TTATGTAT-AGA-T-ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT-TA
* * *
34990033 AGTT-ATGTATA-ATAT-TAA-TTA-AT-TAA-GTT-
117 A-TTAAT-TA-AGTTATGTAATTTATGTATAATATTA
*
34990062 ATGTAACTTATGTATAATATTAATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTA
1 ATGTAAGTTATGTAT-A-A-T-ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTA
34990127 AGTTATGTATA-ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAATTAA
62 A-TTATGTATAGATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAATTAA
34990191 GTTATGTAATTTATGTATAATATTA
126 GTTATGTAATTTATGTATAATATTA
*
34990216 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAACTTATGTATAATATTAAT-TAATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAATT-
* * * *
34990280 AT-TA-AGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAT-A-A-T-ATTAATTAATT
65 ATGTATAGATAT-TAA-TTA-AT-TAA-GTT-ATGTAATTTATGTATAATATTAATTAATTAATT
34990339 AAGTTATGTAATTTATGTATAATATTA
124 AAGTTATGTAATTTATGTATAATATTA
*
34990366 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAACTTATGTATAATATTAAT-TAATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAATT-
* * * *
34990430 AT-TA-AGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAT-A-A-T-ATTAATTAATT
65 ATGTATAGATAT-TAA-TTA-AT-TAA-GTT-ATGTAATTTATGTATAATATTAATTAATTAATT
34990489 AAGTTATGTAATTTATGTATAATATTA
124 AAGTTATGTAATTTATGTATAATATTA
*
34990516 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAACTTATGTATAATATTAAT-TAATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAATT-
* * * *
34990580 AT-TA-AGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAT-A-A-T-ATTAATTAATT
65 ATGTATAGATAT-TAA-TTA-AT-TAA-GTT-ATGTAATTTATGTATAATATTAATTAATTAATT
34990639 AAGTTATGTAATTTATGTATAATATTA
124 AAGTTATGTAATTTATGTATAATATTA
34990666 ATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
1 ATGTAAGTTATGT-A--TA---ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
*
34990731 TAAGTTATGTATA-ATATTAATTAATTAGGTTATGTAATTTATGTATAATATTAAT
60 TAA-TTATGTATAGATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
34990786 GTAAGTTATG
Statistics
Matches: 799, Mismatches: 26, Indels: 111
0.85 0.03 0.12
Matches are distributed among these distances:
147 2 0.00
148 14 0.02
149 16 0.02
150 436 0.55
151 6 0.01
152 23 0.03
153 12 0.02
154 64 0.08
155 2 0.00
156 69 0.09
157 35 0.04
158 27 0.03
159 7 0.01
160 11 0.01
161 4 0.01
162 9 0.01
163 19 0.02
165 40 0.05
166 3 0.00
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (150 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAATTA
TGTATAGATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAATTAATTAAGTTAT
GTAATTTATGTATAATATTA
Found at i:34990669 original size:22 final size:22
Alignment explanation
Indices: 34990644--34990756 Score: 107
Period size: 22 Copynumber: 5.4 Consensus size: 22
34990634 TAATTAAGTT
34990644 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
*
34990666 ATGTAAGTTATG--TAAT-TT-
1 ATGTAATTTATGTATAATATTA
* *
34990684 ATGTATATTAAT-TAATTAA-GTT-
1 ATGTA-ATTTATGT-A-TAATATTA
34990706 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
*
34990728 ATGTAAGTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
34990750 AT-TAATT
1 ATGTAATT
34990757 AGGTTATGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
18 5 0.07
19 6 0.08
20 7 0.09
21 12 0.16
22 45 0.60
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
ATGTAATTTATGTATAATATTA
Found at i:34990787 original size:22 final size:22
Alignment explanation
Indices: 34990762--34990807 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
34990752 TAATTAGGTT
*
34990762 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
34990784 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
34990806 AT
1 AT
34990808 TCATTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:34994980 original size:14 final size:14
Alignment explanation
Indices: 34994961--34995028 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
34994951 ATGACCGTTG
34994961 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
34994975 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
34994990 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
34995003 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
34995016 AAACCTTAAATCT
1 AAACCCTAAATCT
34995029 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:34994984 original size:15 final size:15
Alignment explanation
Indices: 34994964--34995001 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
34994954 ACCGTTGAAA
34994964 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
34994979 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
34994994 CCCTAAAT
1 CCCTAAAT
34995002 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:34995604 original size:41 final size:41
Alignment explanation
Indices: 34995559--34995742 Score: 126
Period size: 41 Copynumber: 4.5 Consensus size: 41
34995549 AGGTAAATAC
* * *
34995559 ATTAGCGGCGCTTAGCTACAAACGCAGCTGAAGA-CAGGAGA
1 ATTAGCGGCGCTTAGCTAAAAACGCAGCTAAAGATC-CGAGA
* * * * *
34995600 ATTAGTGGCGCTAAGTTAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTTAGCTAAAAACGCAGCTAAAGATCCGAGA
** * * * * *
34995641 ATTAGCGGCGCTTATATAAAAACACCGCCAAAG-GCCAGAGC
1 ATTAGCGGCGCTTAGCTAAAAACGCAGCTAAAGATCC-GAGA
* *
34995682 ATTAGCGGCG-TTCAGATAAAAACGCCA-CGAAA-ATCCGAGA
1 ATTAGCGGCGCTT-AGCTAAAAACG-CAGCTAAAGATCCGAGA
* *
34995722 ATGAGCGGCGCTTAGATAAAA
1 ATTAGCGGCGCTTAGCTAAAA
34995743 CTACCGCTAA
Statistics
Matches: 115, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
40 24 0.21
41 89 0.77
42 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.16
Consensus pattern (41 bp):
ATTAGCGGCGCTTAGCTAAAAACGCAGCTAAAGATCCGAGA
Found at i:35002421 original size:14 final size:14
Alignment explanation
Indices: 35002404--35002449 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
35002394 TAAAAAAATG
35002404 TTATTAAATTATTA
1 TTATTAAATTATTA
*
35002418 TTATTAAATTAGTA
1 TTATTAAATTATTA
35002432 TTATTAAATTATTA
1 TTATTAAATTATTA
35002446 TTAT
1 TTAT
35002450 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:35003357 original size:3 final size:3
Alignment explanation
Indices: 35003349--35003401 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
35003339 GTGAGGTAAG
35003349 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
35003397 TAT TA
1 TAT TA
35003402 GTGTGAATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35003583 original size:24 final size:26
Alignment explanation
Indices: 35003556--35003611 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
35003546 TTAATTATCG
35003556 ATTGAAAGGTG-GAAA-AGTGATTGA
1 ATTGAAAGGTGAGAAATAGTGATTGA
* *
35003580 ATTGAAAATGTGAGAAATTGTGATTGA
1 ATTG-AAAGGTGAGAAATAGTGATTGA
35003607 ATTGA
1 ATTGA
35003612 GGTAATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 6 0.22
26 5 0.19
27 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.30
Consensus pattern (26 bp):
ATTGAAAGGTGAGAAATAGTGATTGA
Found at i:35003775 original size:20 final size:22
Alignment explanation
Indices: 35003715--35003779 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
35003705 GCTTTGCCGA
35003715 TCAGGCACTTTATGTGTCGTATC
1 TCAGGCAC-TTATGTGTCGTATC
**
35003738 TCAGGCACCTCGTGTGTCGT-T-
1 TCAGGCA-CTTATGTGTCGTATC
*
35003759 TTAGGCACTTATGTGTCGTAT
1 TCAGGCACTTATGTGTCGTAT
35003780 ACTGATCAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 10 0.29
21 7 0.20
22 1 0.03
23 16 0.46
24 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAGGCACTTATGTGTCGTATC
Found at i:35005157 original size:16 final size:17
Alignment explanation
Indices: 35005136--35005168 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35005126 ATTTTCTTTA
35005136 TTATTAAATT-AGTATT
1 TTATTAAATTAAGTATT
*
35005152 TTATTAATTTAAGTATT
1 TTATTAAATTAAGTATT
35005169 GAATATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTATTAAATTAAGTATT
Found at i:35015815 original size:14 final size:16
Alignment explanation
Indices: 35015798--35015835 Score: 62
Period size: 14 Copynumber: 2.5 Consensus size: 16
35015788 TCTTATTCTG
35015798 TTTTATTTA-TTTA-T
1 TTTTATTTATTTTATT
35015812 TTTTATTTATTTTATT
1 TTTTATTTATTTTATT
35015828 TTTTATTT
1 TTTTATTT
35015836 CGAAATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 9 0.41
15 4 0.18
16 9 0.41
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTTATTTTATT
Found at i:35016247 original size:12 final size:12
Alignment explanation
Indices: 35016197--35016268 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 12
35016187 CACATACACG
*
35016197 TACATATTTTTA
1 TACATATTTATA
*
35016209 TAACTTATTTATA
1 T-ACATATTTATA
* * *
35016222 TATATATATGTA
1 TACATATTTATA
*
35016234 TACATACTTATA
1 TACATATTTATA
*
35016246 T--ATTTTTATA
1 TACATATTTATA
35016256 TACATATTTATA
1 TACATATTTATA
35016268 T
1 T
35016269 TCTTGTATTT
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
10 8 0.18
12 26 0.59
13 10 0.23
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (12 bp):
TACATATTTATA
Found at i:35016248 original size:22 final size:22
Alignment explanation
Indices: 35016220--35016268 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
35016210 AACTTATTTA
*
35016220 TATATATATATGTATACATACT
1 TATATATATATATATACATACT
* * *
35016242 TATATATTTTTATATACATATT
1 TATATATATATATATACATACT
35016264 TATAT
1 TATAT
35016269 TCTTGTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (22 bp):
TATATATATATATATACATACT
Found at i:35016303 original size:23 final size:23
Alignment explanation
Indices: 35016277--35016321 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35016267 ATTCTTGTAT
*
35016277 TTTTATAAT-TTTGTTCACGTTTC
1 TTTTA-AATATTTATTCACGTTTC
*
35016300 TTTTAATTATTTATTCACGTTT
1 TTTTAAATATTTATTCACGTTT
35016322 TCATCATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTTAAATATTTATTCACGTTTC
Found at i:35022363 original size:24 final size:23
Alignment explanation
Indices: 35022319--35022364 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
35022309 TATGATTTTT
*
35022319 TTTTATTTTATATGTTCAATTAC
1 TTTTATTTTATATATTCAATTAC
* *
35022342 TTTTAGTTTTATTTATTTAATTA
1 TTTTA-TTTTATATATTCAATTA
35022365 AAGATTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTATTTTATATATTCAATTAC
Found at i:35026423 original size:13 final size:13
Alignment explanation
Indices: 35026405--35026429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35026395 AAATCTGTTT
35026405 TGAGTGCTGCTCA
1 TGAGTGCTGCTCA
35026418 TGAGTGCTGCTC
1 TGAGTGCTGCTC
35026430 TTGTTAAGGC
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:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (13 bp):
TGAGTGCTGCTCA
Found at i:35026887 original size:16 final size:16
Alignment explanation
Indices: 35026866--35026907 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35026856 TTATTAAATT
*
35026866 ATATATTTTAATTATA
1 ATATATTTTAATAATA
35026882 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
35026897 AT-TATGTTTAA
1 ATATAT-TTTAA
35026908 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:35026892 original size:15 final size:15
Alignment explanation
Indices: 35026857--35026898 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35026847 TTAAGAATTT
*
35026857 TATTAAATTAT-ATA
1 TATTTAATTATAATA
35026871 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
35026885 TATTTAATAATAAT
1 TATTTAATTATAAT
35026899 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:35027038 original size:18 final size:17
Alignment explanation
Indices: 35027010--35027044 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35027000 ATTATTAAGA
*
35027010 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35027027 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35027045 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35027043 original size:157 final size:157
Alignment explanation
Indices: 35026844--35027150 Score: 569
Period size: 157 Copynumber: 2.0 Consensus size: 157
35026834 AGAATATTAG
*
35026844 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
*
35026909 TATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAAATTAAATAACAATAACAATAA
66 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAATAA
35026974 TAATTTACCAAAACAAATTTCTGCTAA
131 TAATTTACCAAAACAAATTTCTGCTAA
*
35027001 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTGTGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
*
35027066 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
66 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAATAA
*
35027131 TCATTTACCAAAACAAATTT
131 TAATTTACCAAAACAAATTT
35027151 ATGATAAGGG
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (157 bp):
TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAATAA
TAATTTACCAAAACAAATTTCTGCTAA
Found at i:35027290 original size:45 final size:44
Alignment explanation
Indices: 35027209--35027299 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
35027199 ATCTCTATTC
* *
35027209 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCAATA
*** *
35027253 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCAATA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCAATA
35027298 CA
1 CA
35027300 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCAATA
Found at i:35027301 original size:16 final size:16
Alignment explanation
Indices: 35027280--35027347 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
35027270 GATTTGCTAT
*
35027280 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
35027296 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
35027312 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
* *
35027328 TACATCTTTAATCCAA
1 TACACCTCTAATCCAA
35027344 TACA
1 TACA
35027348 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.35, C:0.34, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:35030947 original size:20 final size:21
Alignment explanation
Indices: 35030924--35030962 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35030914 GCAATTACAC
*
35030924 AATT-ATTGACTAAATTTCAA
1 AATTCATTCACTAAATTTCAA
*
35030944 AATTCTTTCACTAAATTTC
1 AATTCATTCACTAAATTTC
35030963 TGAAATTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (21 bp):
AATTCATTCACTAAATTTCAA
Found at i:35034892 original size:10 final size:10
Alignment explanation
Indices: 35034873--35034950 Score: 57
Period size: 10 Copynumber: 7.2 Consensus size: 10
35034863 AGAAGAAGAG
*
35034873 AAGAAGAAAA
1 AAGAAAAAAA
35034883 AAGAAAAAAA
1 AAGAAAAAAA
* *
35034893 TAGAGGAAGAAA
1 -A-AGAAAAAAA
*
35034905 AAGAGAGAAAA
1 AAGA-AAAAAA
35034916 AAGAAAGAAAAA
1 AAG-AA-AAAAA
35034928 AAGAAAAAAA
1 AAGAAAAAAA
*
35034938 AATAAATAAAA
1 AAGAAA-AAAA
35034949 AA
1 AA
35034951 CAGCAGGCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 21 0.39
11 18 0.33
12 15 0.28
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:35034902 original size:23 final size:21
Alignment explanation
Indices: 35034874--35034938 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
35034864 GAAGAAGAGA
35034874 AGAAGAAAAAAGAAAAAAATAG
1 AGAAGAAAAAAGAAAAAAA-AG
*
35034896 AGGAAGAAAAAGAGAGAAAAAAG
1 A-GAAGAAAAA-AGAAAAAAAAG
35034919 A-AAGAAAAAAAGAAAAAAAA
1 AGAAG-AAAAAAGAAAAAAAA
35034939 ATAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 12 0.32
22 6 0.16
23 12 0.32
24 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
AGAAGAAAAAAGAAAAAAAAG
Found at i:35034939 original size:33 final size:32
Alignment explanation
Indices: 35034873--35034939 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
35034863 AGAAGAAGAG
* * *
35034873 AAGAAGAAAAAAGAAAAAAATAGAGGAAGAAA
1 AAGAAGAAAAAAGAAAAAAATAAAGAAAAAAA
35034905 AAGAGAGAAAAAAGAAAGAAAA-AAAGAAAAAAA
1 AAGA-AGAAAAAAGAAA-AAAATAAAGAAAAAAA
35034938 AA
1 AA
35034940 TAAATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 4 0.13
33 22 0.73
34 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (32 bp):
AAGAAGAAAAAAGAAAAAAATAAAGAAAAAAA
Found at i:35035577 original size:15 final size:16
Alignment explanation
Indices: 35035557--35035586 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35035547 TAAAAAAAAA
35035557 TTTCGTGT-TTTAAAT
1 TTTCGTGTCTTTAAAT
35035572 TTTCGTGTCTTTAAA
1 TTTCGTGTCTTTAAA
35035587 AATTACTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (16 bp):
TTTCGTGTCTTTAAAT
Found at i:35035649 original size:18 final size:18
Alignment explanation
Indices: 35035615--35035649 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35035605 AATTTTCGAC
*
35035615 TTTTCGCGTTTTCAAAAG
1 TTTTCGCGTTTTAAAAAG
*
35035633 TTTTCGTGTTTTAAAAA
1 TTTTCGCGTTTTAAAAA
35035650 ACAAAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TTTTCGCGTTTTAAAAAG
Found at i:35035678 original size:23 final size:23
Alignment explanation
Indices: 35035634--35035723 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
35035624 TTTCAAAAGT
*
35035634 TTTCGTGTTTTAAAA-AACAAAAA
1 TTTCGTGTTTTAAAATGA-AAAAA
* *
35035657 ATTCGCGTTTTAAAATGAAAAAA
1 TTTCGTGTTTTAAAATGAAAAAA
* *
35035680 TTTTCGTGTTTTCAAATGAAAAAT
1 -TTTCGTGTTTTAAAATGAAAAAA
35035704 TTTCGTGTTTTAAAAT-AAAA
1 TTTCGTGTTTTAAAATGAAAA
35035724 CAAAAAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.07
23 33 0.58
24 20 0.35
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (23 bp):
TTTCGTGTTTTAAAATGAAAAAA
Found at i:35035777 original size:37 final size:36
Alignment explanation
Indices: 35035728--35035800 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
35035718 ATAAAACAAA
*
35035728 AAAAAACTCCCGT-CTTTCAGAAATTTTCGTGTTTTC
1 AAAAAACTCCCGTGCTTTCA-AAATTTTCATGTTTTC
* *
35035764 AAAAAATTGCCCGTGTTTTCAAAATTTTCATGTTTTC
1 AAAAAACT-CCCGTGCTTTCAAAATTTTCATGTTTTC
35035801 GTGTTTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 7 0.22
37 20 0.62
38 5 0.16
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (36 bp):
AAAAAACTCCCGTGCTTTCAAAATTTTCATGTTTTC
Found at i:35035823 original size:19 final size:19
Alignment explanation
Indices: 35035799--35035990 Score: 103
Period size: 18 Copynumber: 10.8 Consensus size: 19
35035789 TTTCATGTTT
35035799 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
* *
35035818 TCGTGTTTTTTAAAAAAAT-
1 TCGTG-TTTTCAAAAAATTC
*
35035837 TCATGTTTT-AAAAAA-T-
1 TCGTGTTTTCAAAAAATTC
* *
35035853 TCATGTTTTC--GAAATTC
1 TCGTGTTTTCAAAAAATTC
* * *
35035870 TCATGTTTTC-AAAATTTT
1 TCGTGTTTTCAAAAAATTC
*
35035888 TCGTG---TCAAAGAATTC
1 TCGTGTTTTCAAAAAATTC
* * * *
35035904 TCATG-TATCGAAAATTTC
1 TCGTGTTTTCAAAAAATTC
*
35035922 -CTTGTTTTCAAAAAAATTC
1 TCGTGTTTTC-AAAAAATTC
35035941 T-GTGTTTTCAAAAAATT-
1 TCGTGTTTTCAAAAAATTC
35035958 TCCGTG-TTTC-AAAAA-TC
1 T-CGTGTTTTCAAAAAATTC
35035975 TTCGTGTTTTCAAAAA
1 -TCGTGTTTTCAAAAA
35035991 TTATTATTGT
Statistics
Matches: 136, Mismatches: 20, Indels: 34
0.72 0.11 0.18
Matches are distributed among these distances:
15 5 0.04
16 21 0.15
17 29 0.21
18 40 0.29
19 30 0.22
20 11 0.08
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (19 bp):
TCGTGTTTTCAAAAAATTC
Found at i:35035824 original size:27 final size:25
Alignment explanation
Indices: 35035775--35035826 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
35035765 AAAAATTGCC
*
35035775 CGTGTTTTCAAAATTTTCATGTTTT
1 CGTGTTTTCAAAATTCTCATGTTTT
*
35035800 CGTGTTTTCAAAAAATTCTCGTGTTTT
1 CGTGTTTTC--AAAATTCTCATGTTTT
35035827 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (25 bp):
CGTGTTTTCAAAATTCTCATGTTTT
Found at i:35035851 original size:16 final size:17
Alignment explanation
Indices: 35035825--35035861 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
35035815 TTCTCGTGTT
35035825 TTTTAAAAAAATTCATG
1 TTTTAAAAAAATTCATG
35035842 TTTT-AAAAAATTCATG
1 TTTTAAAAAAATTCATG
35035858 TTTT
1 TTTT
35035862 CGAAATTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTTAAAAAAATTCATG
Found at i:35035875 original size:17 final size:17
Alignment explanation
Indices: 35035837--35035885 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
35035827 TTAAAAAAAT
* *
35035837 TCATGTTTTAAAAAAT-
1 TCATGTTTTCAAAATTC
*
35035853 TCATGTTTTCGAAATTC
1 TCATGTTTTCAAAATTC
35035870 TCATGTTTTCAAAATT
1 TCATGTTTTCAAAATT
35035886 TTTCGTGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (17 bp):
TCATGTTTTCAAAATTC
Found at i:35035991 original size:18 final size:17
Alignment explanation
Indices: 35035797--35035992 Score: 100
Period size: 19 Copynumber: 11.1 Consensus size: 17
35035787 ATTTTCATGT
35035797 TTTCGTGTTTTCAAAAAA
1 TTTCGTGTTTTC-AAAAA
*
35035815 TTCTCGTGTTTTTTAAAAAA
1 TT-TCGTG--TTTTCAAAAA
* *
35035835 ATTCATGTTTT-AAAAA
1 TTTCGTGTTTTCAAAAA
* * *
35035851 ATTCATGTTTTC-GAAA
1 TTTCGTGTTTTCAAAAA
* *
35035867 TTCTCATGTTTTCAAAATT
1 TT-TCGTGTTTTCAAAA-A
35035886 TTTCGTG---TCAAAGAA
1 TTTCGTGTTTTCAAA-AA
* * *
35035901 TTCTCATG-TATCGAAAA
1 TT-TCGTGTTTTCAAAAA
*
35035918 TTTCCTTGTTTTCAAAAAA
1 TTT-CGTGTTTTC-AAAAA
*
35035937 ATTCTGTGTTTTCAAAAAA
1 TTTC-GTGTTTTC-AAAAA
35035956 TTTCCGTG-TTTCAAAAA
1 TTT-CGTGTTTTCAAAAA
35035973 TCTTCGTGTTTTCAAAAA
1 T-TTCGTGTTTTCAAAAA
35035991 TT
1 TT
35035993 ATTATTGTGT
Statistics
Matches: 143, Mismatches: 17, Indels: 37
0.73 0.09 0.19
Matches are distributed among these distances:
15 7 0.05
16 26 0.18
17 32 0.22
18 32 0.22
19 35 0.24
20 7 0.05
21 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (17 bp):
TTTCGTGTTTTCAAAAA
Found at i:35036003 original size:38 final size:36
Alignment explanation
Indices: 35035923--35036008 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 36
35035913 GAAAATTTCC
35035923 TTGT-TTTCAAAAAAATTCTGTGTTTTCAAAAAATT
1 TTGTGTTTCAAAAAAATTCTGTGTTTTCAAAAAATT
* **
35035958 TCCGTGTTTCAAAAATCTTC-GTGTTTTCAAAAATTATT
1 T-TGTGTTTCAAAAAAATTCTGTGTTTTCAAAAA--ATT
35035996 ATTGTGTTTCAAA
1 -TTGTGTTTCAAA
35036009 GTTCTCGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
35 1 0.02
36 15 0.36
37 12 0.29
38 13 0.31
39 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (36 bp):
TTGTGTTTCAAAAAAATTCTGTGTTTTCAAAAAATT
Found at i:35041702 original size:8 final size:8
Alignment explanation
Indices: 35041680--35041751 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
35041670 TATGCCTGAA
35041680 AAAAAAAG
1 AAAAAAAG
*
35041688 AGAAAAAAA
1 A-AAAAAAG
35041697 ACAAAAAAGG
1 A-AAAAAA-G
35041707 AACAAAAA-
1 AA-AAAAAG
*
35041715 AACAAAAG
1 AAAAAAAG
35041723 AAAAAAAG
1 AAAAAAAG
35041731 AAAAAACA-
1 AAAAAA-AG
*
35041739 AATAAAAG
1 AAAAAAAG
35041747 AAAAA
1 AAAAA
35041752 GGAAAATCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
7 5 0.10
8 25 0.49
9 15 0.29
10 6 0.12
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:35041704 original size:19 final size:18
Alignment explanation
Indices: 35041680--35041751 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 18
35041670 TATGCCTGAA
35041680 AAAAAAAGAGAAAAAAAAC
1 AAAAAAAGA-AAAAAAAAC
*
35041699 AAAAAAGGAACAAAAAAAC
1 AAAAAAAGAA-AAAAAAAC
*
35041718 AAAAGAAAAAAAGAAAAAAC
1 AAAA-AAAGAAA-AAAAAAC
35041738 AAATAAAAGAAAAA
1 AAA-AAAAGAAAAA
35041752 GGAAAATCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.02
19 23 0.51
20 20 0.44
21 1 0.02
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.01
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAAAC
Found at i:35041726 original size:24 final size:22
Alignment explanation
Indices: 35041690--35041757 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 22
35041680 AAAAAAAGAG
*
35041690 AAAAAAAACAAAAAAGGAACAAA
1 AAAAAAAAGAAAAAAGGAA-AAA
*
35041713 AAAACAAAAGAAAAAAAGAAAAA
1 AAAA-AAAAGAAAAAAGGAAAAA
35041736 ACAAATAAAAG-AAAAAGGAAAA
1 A-AAA-AAAAGAAAAAAGGAAAA
35041758 TCAAGATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.46
24 21 0.54
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.01
Consensus pattern (22 bp):
AAAAAAAAGAAAAAAGGAAAAA
Found at i:35042613 original size:30 final size:29
Alignment explanation
Indices: 35042579--35042636 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
35042569 ACCTGATGTT
*
35042579 TTTTTGAAACCCTGTTTCTTTCAAGAAATA
1 TTTTTAAAACCCTGTTTCTTTCAA-AAATA
** *
35042609 TTTTTAAAATTCTGTTTTTTTCAAAAAT
1 TTTTTAAAACCCTGTTTCTTTCAAAAAT
35042637 CAACTCATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (29 bp):
TTTTTAAAACCCTGTTTCTTTCAAAAATA
Found at i:35043069 original size:79 final size:77
Alignment explanation
Indices: 35042609--35043913 Score: 1535
Period size: 76 Copynumber: 16.9 Consensus size: 77
35042599 TCAAGAAATA
*
35042609 TTTTTAAAATTCTGTTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTG-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
35042673 ACGCTAAGGTATT
65 ACGCTGAGGTATT
35042686 TTTTT-AATTTCTGTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTG--TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
35042750 CACGCTGAGGTATTTT
64 CACGCTGAGGTA--TT
*
35042766 TTTTTAAATTTCTGTTTTTTTCAAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTG-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
35042831 ACGTTGAGGTATT
65 ACGCTGAGGTATT
35042844 TTTTTAATTTAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TTTTT-A---AATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
*
35042909 GTCACGCTGATGTA--
62 GTCACGCTGAGGTATT
35042923 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTG-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
35042988 ACGCTGAGGTATT
65 ACGCTGAGGTATT
35043001 TTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTG--TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
35043066 CACGCTAAGGTATTT
64 CACGCTGAGGTA-TT
*
35043081 TTTTTAATTTTCTGCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTG-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
35043145 ACGCTGAGGTATTT
65 ACGCTGAGGTA-TT
* * *
35043159 TTTTTATTTAATTTCTACTTTTTTCAAAAACTCAACTCATAATACAGAGGTGAGTTGAGTCTCGG
1 TTTTTA---AATTTCT-GTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
35043224 GTCACGCTGAGGTA--
62 GTCACGCTGAGGTATT
*
35043238 TTTTTAAATTTCTTCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTC-TGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
35043303 ACGCTGAGGTA--
65 ACGCTGAGGTATT
* **
35043314 TTTTT-AATTTATGTCTTTTTTTAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTGT-TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
35043378 ACGCTGAGGTA--
65 ACGCTGAGGTATT
* * *
35043389 TTTTT-AATTTATGCCTTTTTT-TAAAAATCAACTCAT-ATCGCGAGAGGTGAGTTGAGCCTCGG
1 TTTTTAAATTTCTG--TTTTTTCAAAAAATCAACTCATAAT-AC-AGAGGTGAGTTGAGCCTCGG
*
35043451 GTCACGCCGAGGTATT
62 GTCACGCTGAGGTATT
* * * * * *
35043467 TCTTTTAAATTTATG-TTTTTCAAAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTTGGA
1 T-TTTTAAATTTCTGTTTTTTC-AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
* * *
35043531 CCATGCCGAGGTATT
63 TCACGCTGAGGTATT
* * *
35043546 TCTTTTAAATTTCTG-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGT
1 T-TTTTAAATTTCTGTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT
*
35043609 CACACTGAGGTA--
64 CACGCTGAGGTATT
* * * * * **
35043621 TTTTTAAATTTATG-TTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTTTGGAC
1 TTTTTAAATTTCTGTTTTTTC-AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT
* *
35043685 CATGCCGAGGTATT
64 CACGCTGAGGTATT
* * *
35043699 TCTTTTAAATTTCT-ATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 T-TTTTAAATTTCTGTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT
35043762 CACGCTGAGGTA--
64 CACGCTGAGGTATT
* * * *
35043774 TTTTTCAA-TTCATG-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGG
1 TTTTTAAATTTC-TGTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT
35043836 CACATG-TCGAGGTA--
64 CAC--GCT-GAGGTATT
* * * * *
35043850 TTTTT-AATTTTTG-TTTTTC-GAAGATCAACTCATAATCCAGGAGGTGAGTTGAGCTTCGGGTC
1 TTTTTAAATTTCTGTTTTTTCAAAAAATCAACTCATAATACA-GAGGTGAGTTGAGCCTCGGGTC
35043912 AC
65 AC
35043914 ACGCCGAGCT
Statistics
Matches: 1115, Mismatches: 68, Indels: 92
0.87 0.05 0.07
Matches are distributed among these distances:
73 3 0.00
74 80 0.07
75 150 0.13
76 235 0.21
77 113 0.10
78 137 0.12
79 168 0.15
80 91 0.08
81 79 0.07
82 59 0.05
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (77 bp):
TTTTTAAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCA
CGCTGAGGTATT
Found at i:35043183 original size:315 final size:311
Alignment explanation
Indices: 35042607--35043913 Score: 1620
Period size: 315 Copynumber: 4.2 Consensus size: 311
35042597 TTTCAAGAAA
*
35042607 TATTTTTAAAATTCTGTTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAAATTTCTG-TTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* * *
35042672 CACGCTAAGGTATTTTTTTAATTTCTGTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAG
65 CACGCTGAGGTA--TTTTTAATTTATGCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAG
* *
35042737 TTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTTAAATTTCTGTTTTTTTCAAAAAATTAACTCA
128 TTGAGCCTCGGGTCACGCTGAGGTA-TTTTTTTTAAATTTCTGCTTTTTTC-AAAAATCAACTCA
* * *
35042802 TAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGTTGAGGTATTTTTTTAATTTAATT-TCTGTTT
191 TAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTATTTAATTCTATG-TT
*
35042865 TTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGATG
255 TTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
35042921 TATTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAAATTTCTG-TTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
*
35042986 TCACGCTGAGGTATTTTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTG
64 TCACGCTGAGGTA--TTTTT-AATTTATGCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTG
* *
35043051 AGTTGAGCCTCGGGTCACGCTAAGGTATTTTTTTTAATTTTCTGCTTTTTTCAAAAATCAACTCA
126 AGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTCTGCTTTTTTCAAAAATCAACTCA
35043116 TAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTATTTAATTTCTACT-T
191 TAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTATTTAA-TTCTA-TGT
* *
35043179 TTTTCAAAAACTCAACTCATAATAC-AGAGGTGAGTTGAGTCTCGGGTCACGCTGAGG
254 TTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
*
35043236 TATTTTTAAATTTCTTCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAAATTTC-TGTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
35043301 TCACGCTGAGGTATTTTTAATTTATGTCTTTTTTT--AAAAATCAACTCATAATACAGAGGTGAG
64 TCACGCTGAGGTATTTTTAATTTATG-CTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAG
* *
35043364 TTGAGCCTCGGGTCACGCTGAGGTA---TTTTT-AATTTATGCCTTTTTTTAAAAATCAACTCAT
128 TTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTCTG-CTTTTTTCAAAAATCAACTCAT
* * *
35043425 -ATCGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTCTTTTA---AATT-TATGTTT
192 AAT-ACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTATTTAATTCTATGTTT
* * * * ** * *
35043485 TTCAAAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTTGGACCATGCCGAGG
256 TTC-AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
* * *
35043542 TATTTCTTTTAAATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCG
1 TA--T-TTTTAAATTTCTGTTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCG
* * *
35043606 GGTCACACTGAGGTATTTTTAAATTTATG---TTTTTCAAAAAAATCAACTCATATTGCAAGAGG
62 GGTCACGCTGAGGTATTTTT-AATTTATGCTTTTTTTC-AAAAAATCAACTCATAATAC-AGAGG
* * ** * * * *
35043668 TGAGTTGAGCTTTGGACCATGCCGAGGTATTTCTTTTAAATTTCT--ATTTTTCAAAAATCAACT
124 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTCTGCTTTTTTCAAAAATCAACT
* * *
35043731 CATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-----TTT-TTCAATTC-ATGT
189 CATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTATTTAATTCTATGT
* * *
35043789 TTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATG-TCGAGG
254 TTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCAC--GCT-GAGG
* * * * *
35043848 TATTTTT-AATTTTTG-TTTTTCGAAGATCAACTCATAATCCAGGAGGTGAGTTGAGCTTCGGGT
1 TATTTTTAAATTTCTGTTTTTTCAAAAATCAACTCATAATACA-GAGGTGAGTTGAGCCTCGGGT
35043911 CAC
65 CAC
35043914 ACGCCGAGCT
Statistics
Matches: 893, Mismatches: 65, Indels: 82
0.86 0.06 0.08
Matches are distributed among these distances:
301 1 0.00
302 50 0.06
303 5 0.01
304 57 0.06
305 19 0.02
306 66 0.07
307 68 0.08
308 65 0.07
309 107 0.12
310 1 0.00
311 56 0.06
312 13 0.01
313 13 0.01
314 86 0.10
315 214 0.24
316 71 0.08
317 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (311 bp):
TATTTTTAAATTTCTGTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGGTATTTTTAATTTATGCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTG
AGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTCTGCTTTTTTCAAAAATCAACTCATAATA
CGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTATTTAATTCTATGTTTTTCAA
AAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
Found at i:35044107 original size:17 final size:17
Alignment explanation
Indices: 35044077--35044110 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35044067 TTTCGTTTTA
*
35044077 AAAAAAATCCAAAAAAT
1 AAAAAAATCAAAAAAAT
*
35044094 AAAAAAATTAAAAAAAT
1 AAAAAAATCAAAAAAAT
35044111 TGCACTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAAATCAAAAAAAT
Found at i:35044745 original size:10 final size:10
Alignment explanation
Indices: 35044726--35044792 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 10
35044716 AGAAGAAGAG
*
35044726 AAGAAGAAAA
1 AAGAAAAAAA
35044736 AAGAAAAAAA
1 AAGAAAAAAA
*
35044746 GAGGAAGAAAAA
1 -AAGAA-AAAAA
35044758 GAGAGAAAAAAAGA
1 -A-AG-AAAAAA-A
35044772 AAGAAAAAAA
1 AAGAAAAAAA
*
35044782 AACAAAAAAA
1 AAGAAAAAAA
35044792 A
1 A
35044793 CAGCAGGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
10 20 0.42
11 10 0.21
12 9 0.19
13 6 0.12
14 3 0.06
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:35044758 original size:12 final size:11
Alignment explanation
Indices: 35044727--35044779 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 11
35044717 GAAGAAGAGA
35044727 AGAAGAAAAA-
1 AGAAGAAAAAG
35044737 AGAA-AAAAAG
1 AGAAGAAAAAG
35044747 AGGAAGAAAAAG
1 A-GAAGAAAAAG
*
35044759 AG-AGAAAAAA
1 AGAAGAAAAAG
35044769 AGAAAGAAAAA
1 AG-AAGAAAAA
35044780 AAAACAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
9 5 0.14
10 14 0.38
11 4 0.11
12 14 0.38
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AGAAGAAAAAG
Found at i:35044764 original size:24 final size:22
Alignment explanation
Indices: 35044721--35044791 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 22
35044711 AGACAAGAAG
35044721 AAGAGAAGAAGAAAAAAGAAAAA
1 AAGAGAAGAA-AAAAAAGAAAAA
*
35044744 AAGAGGAAGAAAAAGAGAGAAAAA
1 AAGA-GAAGAAAAA-AAAGAAAAA
*
35044768 AAGA-AAGAAAAAAAAACAAAAA
1 AAGAGAAG-AAAAAAAAGAAAAA
35044790 AA
1 AA
35044792 ACAGCAGGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 18 0.43
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (22 bp):
AAGAGAAGAAAAAAAAGAAAAA
Found at i:35044766 original size:22 final size:21
Alignment explanation
Indices: 35044728--35044791 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
35044718 AAGAAGAGAA
*
35044728 GAAGAAAAAAGAAAAAAAGAG
1 GAAGAAAAAAGAAAAAAAAAG
*
35044749 GAAGAAAAAGAGAGAAAAAAAG
1 GAAGAAAAA-AGAAAAAAAAAG
* *
35044771 AAAGAAAAAAAAACAAAAAAA
1 GAAGAAAAAAGAA-AAAAAAA
35044792 ACAGCAGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 11 0.31
22 25 0.69
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (21 bp):
GAAGAAAAAAGAAAAAAAAAG
Found at i:35044780 original size:12 final size:12
Alignment explanation
Indices: 35044735--35044781 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
35044725 GAAGAAGAAA
35044735 AAAGAAAAAAAG
1 AAAGAAAAAAAG
*
35044747 -AGGAAGAAAAAG
1 AAAGAA-AAAAAG
*
35044759 AGAGAAAAAAAG
1 AAAGAAAAAAAG
35044771 AAAGAAAAAAA
1 AAAGAAAAAAA
35044782 AACAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 4 0.14
12 22 0.76
13 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:35045479 original size:18 final size:18
Alignment explanation
Indices: 35045456--35045490 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35045446 AATTTTCGAA
35045456 TTTTCGTATTTTCAAAAG
1 TTTTCGTATTTTCAAAAG
* *
35045474 TTTTCGTGTTTTTAAAA
1 TTTTCGTATTTTCAAAA
35045491 AAAATTCCGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTTCGTATTTTCAAAAG
Found at i:35045515 original size:22 final size:22
Alignment explanation
Indices: 35045475--35045560 Score: 97
Period size: 23 Copynumber: 4.0 Consensus size: 22
35045465 TTTCAAAAGT
*
35045475 TTTCGTGTTTTTAAA--AAAAA
1 TTTCGTGTTTTAAAATGAAAAA
* *
35045495 TTCCGCGTTTTAAAATGAAAAAA
1 TTTCGTGTTTTAAAATG-AAAAA
*
35045518 TTTCGTGTTTTCAAATGAAAAA
1 TTTCGTGTTTTAAAATGAAAAA
35045540 TTTTCGTGTTTTAAAAT-AAAA
1 -TTTCGTGTTTTAAAATGAAAA
35045561 CAAAAAACAA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 12 0.22
22 9 0.16
23 34 0.62
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.41
Consensus pattern (22 bp):
TTTCGTGTTTTAAAATGAAAAA
Found at i:35045516 original size:23 final size:23
Alignment explanation
Indices: 35045489--35045560 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
35045479 GTGTTTTTAA
* *
35045489 AAAAAATTCCGCGTTTTAAAATG
1 AAAAAATTTCGTGTTTTAAAATG
*
35045512 AAAAAATTTCGTGTTTTCAAATG
1 AAAAAATTTCGTGTTTTAAAATG
*
35045535 AAAAATTTTCGTGTTTTAAAAT-
1 AAAAAATTTCGTGTTTTAAAATG
35045557 AAAA
1 AAAA
35045561 CAAAAAACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 4 0.09
23 40 0.91
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (23 bp):
AAAAAATTTCGTGTTTTAAAATG
Found at i:35045610 original size:18 final size:18
Alignment explanation
Indices: 35045589--35045818 Score: 107
Period size: 18 Copynumber: 12.4 Consensus size: 18
35045579 CCCGTCTTTA
35045589 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
**
35045607 AAAAATTGCCCGTGTTTTC
1 AAAAATT-TTCGTGTTTTC
35045626 AAAATTTTCATGTTTTCGTGTTTTC
1 AAAA-----A--TTTTCGTGTTTTC
* *
35045651 AAAAAATTCTCGTGTTTTTTTT
1 -AAAAATTTTCGTG---TTTTC
*
35045673 AAAAA--TTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
35045689 -GAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
35045706 AAAATTTTTCGTG---TC
1 AAAAATTTTCGTGTTTTC
* * *
35045721 AAAGAATTCTCATG-TATC
1 AAA-AATTTTCGTGTTTTC
* * * *
35045739 GAAAATTTCCTTATTTTC
1 AAAAATTTTCGTGTTTTC
**
35045757 AAAAAAATTCTGTGTTTTC
1 AAAAATTTTC-GTGTTTTC
35045776 AAAAAATTTTCGTG-TTTC
1 -AAAAATTTTCGTGTTTTC
*
35045794 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
35045812 AAAAATT
1 AAAAATT
35045819 ATTATTGTGT
Statistics
Matches: 156, Mismatches: 34, Indels: 44
0.67 0.15 0.19
Matches are distributed among these distances:
15 8 0.05
16 11 0.07
17 27 0.17
18 43 0.28
19 33 0.21
20 8 0.05
21 6 0.04
22 4 0.03
24 1 0.01
25 9 0.06
26 6 0.04
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:35045610 original size:19 final size:19
Alignment explanation
Indices: 35045588--35045816 Score: 90
Period size: 19 Copynumber: 12.3 Consensus size: 19
35045578 TCCCGTCTTT
35045588 AAAAAATTTTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
**
35045607 -AAAAATTGCCCGTGTTTTC
1 AAAAAATT-TTCGTGTTTTC
*
35045626 AAAATTTTCATGTTTTCGTGTTTTC
1 AAAA-----A-ATTTTCGTGTTTTC
* *
35045651 AAAAAATTCTCGTGTTTTTTT
1 AAAAAATTTTCGTG--TTTTC
* *
35045672 TAAAAA--TTCATGTTTTC
1 AAAAAATTTTCGTGTTTTC
* *
35045689 --GAAATTCTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
*
35045706 -AAAATTTTTCGTG---TC
1 AAAAAATTTTCGTGTTTTC
* * * *
35045721 AAAGAATTCTCATG-TATC
1 AAAAAATTTTCGTGTTTTC
* * * *
35045739 -GAAAATTTCCTTATTTTC
1 AAAAAATTTTCGTGTTTTC
*
35045757 AAAAAA-ATTCTGTGTTTTC
1 AAAAAATTTTC-GTGTTTTC
35045776 AAAAAATTTTCGTG-TTTC
1 AAAAAATTTTCGTGTTTTC
*
35045794 -AAAAATCTTCGTGTTTTC
1 AAAAAATTTTCGTGTTTTC
35045812 AAAAA
1 AAAAA
35045817 TTATTATTGT
Statistics
Matches: 152, Mismatches: 36, Indels: 44
0.66 0.16 0.19
Matches are distributed among these distances:
15 5 0.03
16 9 0.06
17 32 0.21
18 31 0.20
19 43 0.28
20 7 0.05
21 9 0.06
25 14 0.09
26 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (19 bp):
AAAAAATTTTCGTGTTTTC
Found at i:35045611 original size:36 final size:36
Alignment explanation
Indices: 35045572--35045642 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
35045562 AAAAAACAAA
*
35045572 AAAAACT-CCCGTCTTTAAAAAATTTTCGTGTTTTC
1 AAAAACTGCCCGTCTTTAAAAAATTTTCATGTTTTC
* * **
35045607 AAAAATTGCCCGTGTTTTCAAAATTTTCATGTTTTC
1 AAAAACTGCCCGTCTTTAAAAAATTTTCATGTTTTC
35045643 GTGTTTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (36 bp):
AAAAACTGCCCGTCTTTAAAAAATTTTCATGTTTTC
Found at i:35045666 original size:27 final size:25
Alignment explanation
Indices: 35045617--35045668 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
35045607 AAAAATTGCC
*
35045617 CGTGTTTTCAAAATTTTCATGTTTT
1 CGTGTTTTCAAAATTCTCATGTTTT
*
35045642 CGTGTTTTCAAAAAATTCTCGTGTTTT
1 CGTGTTTTC--AAAATTCTCATGTTTT
35045669 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (25 bp):
CGTGTTTTCAAAATTCTCATGTTTT
Found at i:35045808 original size:36 final size:38
Alignment explanation
Indices: 35045753--35045834 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 38
35045743 ATTTCCTTAT
35045753 TTTCAAAAAAATTCTGTGTTTTCAAAAA-ATT-TTCGTG
1 TTTCAAAAAAATTCTGTGTTTTCAAAAATATTATT-GTG
**
35045790 TTTCAAAAATCTTC-GTGTTTTCAAAAATTATTATTGTG
1 TTTCAAAAAAATTCTGTGTTTTCAAAAA-TATTATTGTG
35045828 TTTCAAA
1 TTTCAAA
35045835 GTTCTCGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 13 0.32
37 12 0.30
38 13 0.32
39 2 0.05
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (38 bp):
TTTCAAAAAAATTCTGTGTTTTCAAAAATATTATTGTG
Found at i:35053930 original size:12 final size:13
Alignment explanation
Indices: 35053905--35053933 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35053895 CTGAACAGAG
35053905 GGAAGAGAGAAGA
1 GGAAGAGAGAAGA
35053918 GGAAGAG-GAAGA
1 GGAAGAGAGAAGA
35053930 GGAA
1 GGAA
35053934 AAAATGATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (13 bp):
GGAAGAGAGAAGA
Found at i:35057482 original size:85 final size:85
Alignment explanation
Indices: 35057339--35057511 Score: 346
Period size: 85 Copynumber: 2.0 Consensus size: 85
35057329 TACGTTCATA
35057339 TCTTTCATTGTACTTTCATCTTGAGTTGTGAAAAGTTTAACACCCATACAGTTGCGAATTGATTG
1 TCTTTCATTGTACTTTCATCTTGAGTTGTGAAAAGTTTAACACCCATACAGTTGCGAATTGATTG
35057404 AGATGCCTTCCGATCTTAAT
66 AGATGCCTTCCGATCTTAAT
35057424 TCTTTCATTGTACTTTCATCTTGAGTTGTGAAAAGTTTAACACCCATACAGTTGCGAATTGATTG
1 TCTTTCATTGTACTTTCATCTTGAGTTGTGAAAAGTTTAACACCCATACAGTTGCGAATTGATTG
35057489 AGATGCCTTCCGATCTTAAT
66 AGATGCCTTCCGATCTTAAT
35057509 TCT
1 TCT
35057512 CCATTAGAGT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 88 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (85 bp):
TCTTTCATTGTACTTTCATCTTGAGTTGTGAAAAGTTTAACACCCATACAGTTGCGAATTGATTG
AGATGCCTTCCGATCTTAAT
Found at i:35059084 original size:89 final size:87
Alignment explanation
Indices: 35058878--35059090 Score: 223
Period size: 89 Copynumber: 2.4 Consensus size: 87
35058868 CATGTGAATA
** * * *
35058878 GTGAACATTGAAATTGAGGGAAACCATGTTTGTGGGGAAGTAATTCAGTGGTGGAAACCATAAAA
1 GTGAACATTGAAA-TGAGGGAAACCATGTTTGTGGGGAAGTAACACACTGGTAGAAACAATAAAA
* *
35058943 GGCGATTCAGGAACATGTCAATG
65 GGCAATTCAGGAACATATCAATG
* * * * ** *
35058966 GTTAACATTGAAATCAAAGAAAATTATGTTTATGGGGAAGTAACACAACT-GTAGAAACAATAGA
1 GTGAACATTGAAAT-GAGGGAAACCATGTTTGTGGGGAAGTAACAC-ACTGGTAGAAACAATA-A
35059030 AAGGCAATTCAGGAACATATCAATG
63 AAGGCAATTCAGGAACATATCAATG
*
35059055 GTGAACATTAAAACTGAGGGGAAA-CATGTTTGTGGG
1 GTGAACATTGAAA-TGA-GGGAAACCATGTTTGTGGG
35059091 TTAACTCAGT
Statistics
Matches: 99, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
87 1 0.01
88 45 0.45
89 48 0.48
90 5 0.05
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (87 bp):
GTGAACATTGAAATGAGGGAAACCATGTTTGTGGGGAAGTAACACACTGGTAGAAACAATAAAAG
GCAATTCAGGAACATATCAATG
Found at i:35063239 original size:11 final size:11
Alignment explanation
Indices: 35063220--35063315 Score: 60
Period size: 11 Copynumber: 9.0 Consensus size: 11
35063210 GGATTTAAGA
35063220 GAAATTTGAGAG
1 GAAA-TTGAGAG
35063232 GAAATTGAGAG
1 GAAATTGAGAG
* * *
35063243 TAAATTGTGAT
1 GAAATTGAGAG
*
35063254 TAAA-T-AG-G
1 GAAATTGAGAG
*
35063262 G-ATTTGAGA-
1 GAAATTGAGAG
35063271 GAAATTTG-GAAG
1 GAAA-TTGAG-AG
*
35063283 GAAATTAAGAG
1 GAAATTGAGAG
*
35063294 CAAATTGAGAG
1 GAAATTGAGAG
35063305 GAAATTGAGAG
1 GAAATTGAGAG
35063316 AATAATAGAA
Statistics
Matches: 64, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 4 0.06
10 3 0.05
11 46 0.72
12 9 0.14
ACGTcount: A:0.44, C:0.01, G:0.30, T:0.25
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:35063264 original size:51 final size:51
Alignment explanation
Indices: 35063204--35063300 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
35063194 AATAATTAAA
* *
35063204 AAATAGGGATTTAAGAGAAATTT-GAGAGGAAATTGAGAGTAAATTGTGATT
1 AAATAGGGATTTAAGAGAAATTTGGA-AGGAAATTAAGAGCAAATTGTGATT
*
35063255 AAATAGGGATTTGAGAGAAATTTGGAAGGAAATTAAGAGCAAATTG
1 AAATAGGGATTTAAGAGAAATTTGGAAGGAAATTAAGAGCAAATTG
35063301 AGAGGAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
51 40 0.95
52 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.28, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTGGAAGGAAATTAAGAGCAAATTGTGATT
Found at i:35070840 original size:22 final size:23
Alignment explanation
Indices: 35070787--35070842 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
35070777 CCCGTTTTTA
* * *
35070787 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
35070810 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
35070832 ATTAAAATTAA
1 ATTAAAATTAA
35070843 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:35070855 original size:16 final size:16
Alignment explanation
Indices: 35070818--35070857 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
35070808 TTAATAAAAT
* *
35070818 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
35070834 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
35070850 TAAAATTA
1 TAAAATTA
35070858 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:35070936 original size:59 final size:59
Alignment explanation
Indices: 35070868--35071007 Score: 271
Period size: 59 Copynumber: 2.4 Consensus size: 59
35070858 TCAAATTATT
*
35070868 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
35070927 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
35070986 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
35071008 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:35071001 original size:9 final size:9
Alignment explanation
Indices: 35070989--35071016 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
35070979 TTTATCAAAT
35070989 TATTAATTG
1 TATTAATTG
35070998 TATTAATTG
1 TATTAATTG
35071007 TATTAATTG
1 TATTAATTG
35071016 T
1 T
35071017 TGTAACAAAA
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:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:35071157 original size:23 final size:24
Alignment explanation
Indices: 35071110--35071155 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
35071100 AAATAAACTT
35071110 AAAATAAAAAAATATTATATTTTA
1 AAAATAAAAAAATATTATATTTTA
35071134 AAAATAAAAAAA-ATATATATTT
1 AAAATAAAAAAATAT-TATATTT
35071156 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATAAAAAAATATTATATTTTA
Found at i:35073228 original size:9 final size:9
Alignment explanation
Indices: 35073199--35073235 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
35073189 TGAGTTTTCG
35073199 AATTCGAAT
1 AATTCGAAT
*
35073208 AACTCGAAT
1 AATTCGAAT
35073217 AATTCGAAT
1 AATTCGAAT
*
35073226 AATTCAAAT
1 AATTCGAAT
35073235 A
1 A
35073236 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:35073498 original size:30 final size:32
Alignment explanation
Indices: 35073443--35073503 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
35073433 AAACCTTTTA
*
35073443 TTTTCCCCCAAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAAACTTTTACTCCCTTCCCAC
* *
35073474 TTTT-CCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAAACTTTTACTCCCTTCCCA
35073504 TCTTACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (32 bp):
TTTTCCCCCAAAAACTTTTACTCCCTTCCCAC
Found at i:35073761 original size:19 final size:19
Alignment explanation
Indices: 35073725--35073778 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
35073715 TATATCTACT
35073725 ATTTACATTATTAAATTAA
1 ATTTACATTATTAAATTAA
*
35073744 ATTTCACATT-TTATATT--
1 ATTT-ACATTATTAAATTAA
* *
35073761 ATTTATATTATTGAATTA
1 ATTTACATTATTAAATTA
35073779 TTTAGTCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
19 10 0.36
20 5 0.18
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTACATTATTAAATTAA
Found at i:35073778 original size:17 final size:17
Alignment explanation
Indices: 35073758--35073804 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
35073748 CACATTTTAT
35073758 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
35073775 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
35073793 A-TATTTATATTA
1 ATTATTTATATTA
35073805 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:35078104 original size:24 final size:26
Alignment explanation
Indices: 35078065--35078123 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
35078055 TAATTTTAAG
*
35078065 TATATTA-TTTATGATA-AATTGTTT
1 TATATTATTTTATGATAGAAGTGTTT
35078089 TATATTATTTTA-GATAGTAAGTGTTT
1 TATATTATTTTATGATAG-AAGTGTTT
*
35078115 TAAATTATT
1 TATATTATT
35078124 CCATATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 11 0.37
25 4 0.13
26 15 0.50
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (26 bp):
TATATTATTTTATGATAGAAGTGTTT
Found at i:35081003 original size:2 final size:2
Alignment explanation
Indices: 35080996--35081022 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35080986 TAGTTTTAGG
35080996 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35081023 GATCAGAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35082512 original size:3 final size:3
Alignment explanation
Indices: 35082504--35082540 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
35082494 AACCATTATC
35082504 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
35082541 AGTACATAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35082611 original size:21 final size:20
Alignment explanation
Indices: 35082585--35082626 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
35082575 CTAAACGTTT
35082585 AAAAAGGTA-AAGAAAGTAATA
1 AAAAAGGTAGAA-AAA-TAATA
35082606 AAAAAGGTAGAAAAATAATA
1 AAAAAGGTAGAAAAATAATA
35082626 A
1 A
35082627 TAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 12 0.60
22 2 0.10
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAAAGGTAGAAAAATAATA
Found at i:35082636 original size:13 final size:13
Alignment explanation
Indices: 35082618--35082646 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
35082608 AAAGGTAGAA
35082618 AAATAATAATAAT
1 AAATAATAATAAT
35082631 AAATAATAATAAT
1 AAATAATAATAAT
35082644 AAA
1 AAA
35082647 GTTCAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:35086440 original size:14 final size:14
Alignment explanation
Indices: 35086404--35086442 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
35086394 TTGTTTTATT
*
35086404 AAAAATGACTTCCG
1 AAAAATGATTTCCG
* *
35086418 GAAAATGATTTCTG
1 AAAAATGATTTCCG
35086432 AAAAATGATTT
1 AAAAATGATTT
35086443 ATATTTCTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (14 bp):
AAAAATGATTTCCG
Done.