Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 140 of 279
Found at i:45384960 original size:40 final size:40
Alignment explanation
Indices: 45384868--45385154 Score: 212
Period size: 40 Copynumber: 7.2 Consensus size: 40
45384858 TAGTAATTAT
* * *
45384868 CAAAATTTCT-ATGACTTTATCAAAAT-TTGTAACG-GTTAC
1 CAAAATTTCTAACGA-TTTATCAATATATT-TAACGATTTAC
* *
45384907 CAATAA-TTCTAAGGATTTATCAATATATTTAACGATTTAT
1 CAA-AATTTCTAACGATTTATCAATATATTTAACGATTTAC
* * * * * *
45384947 CAATATTTCTAAGGATATATCAATATATCTAACAATTTGC
1 CAAAATTTCTAACGATTTATCAATATATTTAACGATTTAC
* * *
45384987 AAAAAAATT-TAACGATTTATCAATA-ATTGTAACAATTTAC
1 -CAAAATTTCTAACGATTTATCAATATATT-TAACGATTTAC
* * * *
45385027 CAAAATATCTAACGATTGACCAATA-ATTTTAAAGATTTAC
1 CAAAATTTCTAACGATTTATCAATATA-TTTAACGATTTAC
* * *
45385067 CAAAATTTCTAAAGATTTACCAATATATTGT-ACGATTTTC
1 CAAAATTTCTAACGATTTATCAATATATT-TAACGATTTAC
** * * *
45385107 CAAAATTTCTAATAATTTATCAAAATATCTAATGATTTAC
1 CAAAATTTCTAACGATTTATCAATATATTTAACGATTTAC
*
45385147 CAATATTT
1 CAAAATTT
45385155 ATGAGACTTT
Statistics
Matches: 199, Mismatches: 37, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
39 31 0.16
40 159 0.80
41 9 0.05
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (40 bp):
CAAAATTTCTAACGATTTATCAATATATTTAACGATTTAC
Found at i:45385058 original size:60 final size:60
Alignment explanation
Indices: 45384903--45385094 Score: 151
Period size: 60 Copynumber: 3.2 Consensus size: 60
45384893 TTTGTAACGG
* * * * **
45384903 TTACCAATAAT-TCTAAGGATTTATCAAT-ATATTTAACGATTTATCAATATTTCTAAGGAT
1 TTACCAA-AATATCTAACGATTGACCAATAAT-TTTAACGATTTATCAATAATTCTAACAAT
* * * * * * * *
45384963 ATATCAATATATCTAACAATTTG-CAAAAAAATTTAACGATTTATCAATAATTGTAACAAT
1 TTACCAAAATATCTAACGA-TTGACCAATAATTTTAACGATTTATCAATAATTCTAACAAT
* *
45385023 TTACCAAAATATCTAACGATTGACCAATAATTTTAAAGATTTACCAA-AATTTCTAA-AGAT
1 TTACCAAAATATCTAACGATTGACCAATAATTTTAACGATTTATCAATAA-TTCTAACA-AT
*
45385083 TTACCAATATAT
1 TTACCAAAATAT
45385095 TGTACGATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
59 8 0.08
60 90 0.89
61 3 0.03
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (60 bp):
TTACCAAAATATCTAACGATTGACCAATAATTTTAACGATTTATCAATAATTCTAACAAT
Found at i:45385102 original size:60 final size:60
Alignment explanation
Indices: 45385021--45385152 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
45385011 AATTGTAACA
* *
45385021 ATTTACCAAAATATCTAACGATTGACCAATAATTT-TAA-AGATTTACCAAAATTTCTAAAG
1 ATTTACCAATATATCTAACGATTGACCAA-AATTTCTAATA-ATTTACCAAAATATCTAAAG
* ** * *
45385081 ATTTACCAATATAT-TGTACGATTTTCCAAAATTTCTAATAATTTATCAAAATATCTAATG
1 ATTTACCAATATATCT-AACGATTGACCAAAATTTCTAATAATTTACCAAAATATCTAAAG
45385141 ATTTACCAATAT
1 ATTTACCAATAT
45385153 TTATGAGACT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 6 0.10
60 55 0.89
61 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.38
Consensus pattern (60 bp):
ATTTACCAATATATCTAACGATTGACCAAAATTTCTAATAATTTACCAAAATATCTAAAG
Found at i:45385195 original size:20 final size:20
Alignment explanation
Indices: 45384864--45385195 Score: 119
Period size: 20 Copynumber: 16.6 Consensus size: 20
45384854 ATCTTAGTAA
*
45384864 TTATCAAAATTTCT-ATGACT
1 TTATCAATATTTCTAATGA-T
* * * *
45384884 TTATCAAAATTTGTAACG-G
1 TTATCAATATTTCTAATGAT
* * *
45384903 TTACCAATAATTCTAAGGAT
1 TTATCAATATTTCTAATGAT
*
45384923 TTATCAATATATT-TAACGAT
1 TTATCAATAT-TTCTAATGAT
*
45384943 TTATCAATATTTCTAAGGAT
1 TTATCAATATTTCTAATGAT
* * **
45384963 ATATCAATATATCTAACAAT
1 TTATCAATATTTCTAATGAT
* * * *
45384983 TTGCA-AAAAAATT-TAACGAT
1 TT--ATCAATATTTCTAATGAT
* * **
45385003 TTATCAATAATTGTAACAAT
1 TTATCAATATTTCTAATGAT
* * * *
45385023 TTACCAAAATATCTAACGAT
1 TTATCAATATTTCTAATGAT
* * *
45385043 TGACCAATAATTT-TAAAGAT
1 TTATCAAT-ATTTCTAATGAT
* * *
45385063 TTACCAAAATTTCTAAAGAT
1 TTATCAATATTTCTAATGAT
* * *
45385083 TTACCAATATATTGT-ACGAT
1 TTATCAATAT-TTCTAATGAT
* *
45385103 TT-TCCAAAATTTCTAATAAT
1 TTAT-CAATATTTCTAATGAT
* *
45385123 TTATCAAAATATCTAATGAT
1 TTATCAATATTTCTAATGAT
* * *
45385143 TTACCAATATTTATGA-GACT
1 TTATCAATATTTCTAATGA-T
45385163 TTATCCAAT-TTTCT-ATGATT
1 TTAT-CAATATTTCTAATGA-T
45385183 TTATCAATATTTC
1 TTATCAATATTTC
45385196 CAAAATTTCT
Statistics
Matches: 238, Mismatches: 56, Indels: 36
0.72 0.17 0.11
Matches are distributed among these distances:
18 1 0.00
19 35 0.15
20 182 0.76
21 19 0.08
22 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (20 bp):
TTATCAATATTTCTAATGAT
Found at i:45385280 original size:20 final size:20
Alignment explanation
Indices: 45385254--45385317 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
45385244 TGAATTTGTT
45385254 AAAATATCTAATGATTTACC
1 AAAATATCTAATGATTTACC
* **
45385274 AATATATCTAACAATTTACC
1 AAAATATCTAATGATTTACC
* * *
45385294 AAAATTTCTATTGATTTATC
1 AAAATATCTAATGATTTACC
45385314 AAAA
1 AAAA
45385318 CTTTTGAGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAATATCTAATGATTTACC
Found at i:45385459 original size:40 final size:40
Alignment explanation
Indices: 45385415--45385490 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
45385405 CACTTCACCT
* *
45385415 ATATTTCTAATGATTTACCAAAATTTTTAAGATTTTGTCA
1 ATATTTCTAATGATTCACCAAAATTTATAAGATTTTGTCA
45385455 ATATTTCTAATGATTCACCAAAATTTATAAGATTTT
1 ATATTTCTAATGATTCACCAAAATTTATAAGATTTT
45385491 ACCGATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (40 bp):
ATATTTCTAATGATTCACCAAAATTTATAAGATTTTGTCA
Found at i:45385499 original size:40 final size:40
Alignment explanation
Indices: 45385415--45385500 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
45385405 CACTTCACCT
* * **
45385415 ATATTTCTAATGATTTACCAAAATTTTTAAGATTTTGTCA
1 ATATTTCTAATGATTCACCAAAATTTATAAGATTTTACCA
*
45385455 ATATTTCTAATGATTCACCAAAATTTATAAGATTTTACCG
1 ATATTTCTAATGATTCACCAAAATTTATAAGATTTTACCA
45385495 ATATTT
1 ATATTT
45385501 GCAAAATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (40 bp):
ATATTTCTAATGATTCACCAAAATTTATAAGATTTTACCA
Found at i:45387137 original size:25 final size:23
Alignment explanation
Indices: 45387109--45387170 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 23
45387099 ATTTTGAAGT
* *
45387109 ATTTTTTATATTATATTATTTTGAC
1 ATTTTTTATATTAT-TTAGTTT-AA
* *
45387134 ATTTTGTATAATATTTAGTTTAA
1 ATTTTTTATATTATTTAGTTTAA
45387157 ATTTTTT-TATTATT
1 ATTTTTTATATTATT
45387171 ATCTGTACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 6 0.19
23 7 0.23
24 6 0.19
25 12 0.39
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (23 bp):
ATTTTTTATATTATTTAGTTTAA
Found at i:45389174 original size:11 final size:11
Alignment explanation
Indices: 45389139--45389174 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
45389129 TTTATAAGAA
*
45389139 TTTACCAAAAC
1 TTTACCAAAAT
45389150 TTTACCAAATAT
1 TTTACCAAA-AT
45389162 TTTACCAAAAT
1 TTTACCAAAAT
45389173 TT
1 TT
45389175 CAAACCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (11 bp):
TTTACCAAAAT
Found at i:45389351 original size:21 final size:20
Alignment explanation
Indices: 45389309--45389350 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
45389299 TTATATGAAC
*
45389309 TTACTAAAATATCTAACATT
1 TTACTAAAAGATCTAACATT
45389329 TTACTAAAAAGAT-TAACATT
1 TTACT-AAAAGATCTAACATT
45389349 TT
1 TT
45389351 TGGACTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (20 bp):
TTACTAAAAGATCTAACATT
Found at i:45389461 original size:21 final size:21
Alignment explanation
Indices: 45389435--45389474 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45389425 TTTATATAAA
*
45389435 TTTATCAAAATATCTAACATT
1 TTTATCAAAATATATAACATT
*
45389456 TTTATCAATATATATAACA
1 TTTATCAAAATATATAACA
45389475 ATTTACCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTATCAAAATATATAACATT
Found at i:45397432 original size:8 final size:8
Alignment explanation
Indices: 45397421--45397446 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
45397411 TAATTTTTTG
45397421 AATTTTAA
1 AATTTTAA
45397429 AATTTTAA
1 AATTTTAA
45397437 AATTTTAA
1 AATTTTAA
45397445 AA
1 AA
45397447 AATTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATTTTAA
Found at i:45398313 original size:14 final size:15
Alignment explanation
Indices: 45398280--45398315 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
45398270 AGTTTTAAAC
45398280 AAAAATGAATATTGT
1 AAAAATGAATATTGT
*
45398295 AAAAATGTATATTGT
1 AAAAATGAATATTGT
45398310 AAAAAT
1 AAAAAT
45398316 ATTAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:45404930 original size:13 final size:13
Alignment explanation
Indices: 45404912--45404939 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
45404902 TGTAATTGAC
45404912 TTCTCTGATTAAT
1 TTCTCTGATTAAT
45404925 TTCTCTGATTAAT
1 TTCTCTGATTAAT
45404938 TT
1 TT
45404940 GTGGTCCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (13 bp):
TTCTCTGATTAAT
Found at i:45409822 original size:56 final size:55
Alignment explanation
Indices: 45409736--45409846 Score: 177
Period size: 56 Copynumber: 2.0 Consensus size: 55
45409726 AAATTGTTGG
* * * *
45409736 GGGGGGGGGGGGAAAGACCAGCAGGGGACCAGTTTTTTAAGACTATCCCTGAGTA
1 GGGGGGGGGGAGAAAGACCAGCAGAGGACCAGTTATTTAAGACTATCACTGAGTA
45409791 NGGGGGGGGGGAGAAAGACCAGCAGAGGACCAGTTATTTAAGACTATCACTGAGTA
1 -GGGGGGGGGGAGAAAGACCAGCAGAGGACCAGTTATTTAAGACTATCACTGAGTA
45409847 TGCATGGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.29, C:0.15, G:0.38, T:0.17
Consensus pattern (55 bp):
GGGGGGGGGGAGAAAGACCAGCAGAGGACCAGTTATTTAAGACTATCACTGAGTA
Found at i:45419170 original size:25 final size:25
Alignment explanation
Indices: 45419135--45419198 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
45419125 CAACGGTGAA
45419135 AAATAAAGTAAATTCGTTCTTCTTTG
1 AAAT-AAGTAAATTCGTTCTTCTTTG
* *
45419161 AAATAAGTAATTTTCGTTTTTCTTTG
1 AAATAAGTAA-ATTCGTTCTTCTTTG
*
45419187 GAATAAG-AAATT
1 AAATAAGTAAATT
45419199 GAATAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 8 0.24
26 23 0.70
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
AAATAAGTAAATTCGTTCTTCTTTG
Found at i:45419176 original size:26 final size:26
Alignment explanation
Indices: 45419147--45419198 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
45419137 ATAAAGTAAA
*
45419147 TTCGTTCTTCTTTGAAATAAGTAATT
1 TTCGTTCTTCTTTGAAATAAGAAATT
* *
45419173 TTCGTTTTTCTTTGGAATAAGAAATT
1 TTCGTTCTTCTTTGAAATAAGAAATT
45419199 GAATAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (26 bp):
TTCGTTCTTCTTTGAAATAAGAAATT
Found at i:45419548 original size:16 final size:17
Alignment explanation
Indices: 45419515--45419582 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
45419505 ATATGTCACG
45419515 TTAATAAATAATTTAAAAA
1 TTAATAAA-AA-TTAAAAA
*
45419534 TT-ATAAAAATTAAAAT
1 TTAATAAAAATTAAAAA
*
45419550 TTAATAAAAA-T-AAAG
1 TTAATAAAAATTAAAAA
* *
45419565 TTCATAAAAATTTAAAA
1 TTAATAAAAATTAAAAA
45419582 T
1 T
45419583 AATTAGCATG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 12 0.29
16 10 0.24
17 13 0.31
18 5 0.12
19 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (17 bp):
TTAATAAAAATTAAAAA
Found at i:45423178 original size:25 final size:25
Alignment explanation
Indices: 45423143--45423206 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
45423133 CAACGGTGAA
45423143 AAATAAAGTAAATTCGTTCTTCTTTG
1 AAAT-AAGTAAATTCGTTCTTCTTTG
* *
45423169 AAATAAGTAATTTTCGTTTTTCTTTG
1 AAATAAGTAA-ATTCGTTCTTCTTTG
*
45423195 GAATAAG-AAATT
1 AAATAAGTAAATT
45423207 GAATAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 8 0.24
26 23 0.70
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
AAATAAGTAAATTCGTTCTTCTTTG
Found at i:45423184 original size:26 final size:26
Alignment explanation
Indices: 45423155--45423206 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
45423145 ATAAAGTAAA
*
45423155 TTCGTTCTTCTTTGAAATAAGTAATT
1 TTCGTTCTTCTTTGAAATAAGAAATT
* *
45423181 TTCGTTTTTCTTTGGAATAAGAAATT
1 TTCGTTCTTCTTTGAAATAAGAAATT
45423207 GAATAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (26 bp):
TTCGTTCTTCTTTGAAATAAGAAATT
Found at i:45423556 original size:16 final size:17
Alignment explanation
Indices: 45423523--45423590 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
45423513 ATATGTCACG
45423523 TTAATAAATAATTTAAAAA
1 TTAATAAA-AA-TTAAAAA
*
45423542 TT-ATAAAAATTAAAAT
1 TTAATAAAAATTAAAAA
*
45423558 TTAATAAAAA-T-AAAG
1 TTAATAAAAATTAAAAA
* *
45423573 TTCATAAAAATTTAAAA
1 TTAATAAAAATTAAAAA
45423590 T
1 T
45423591 AATTAGCATG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 12 0.29
16 10 0.24
17 13 0.31
18 5 0.12
19 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (17 bp):
TTAATAAAAATTAAAAA
Found at i:45426616 original size:113 final size:113
Alignment explanation
Indices: 45426418--45426643 Score: 452
Period size: 113 Copynumber: 2.0 Consensus size: 113
45426408 CCATCAAGAA
45426418 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
1 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
45426483 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTGTCATTAGAGGAGT
66 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTGTCATTAGAGGAGT
45426531 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
1 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
45426596 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTGTCATTAGAGGAGT
66 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTGTCATTAGAGGAGT
45426644 TTCAAAGGCA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (113 bp):
ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTGTCATTAGAGGAGT
Found at i:45426894 original size:187 final size:186
Alignment explanation
Indices: 45426579--45426952 Score: 678
Period size: 187 Copynumber: 2.0 Consensus size: 186
45426569 CAAGTCATGA
* *
45426579 CCCGAGTGCCTACCTGAATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTGTCATTAGAGGAGT
1 CCCGAGTGCCTACCTGAATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTGTCATTACA-GAGC
45426644 TTCAAAGGCATGCCTGGAGGGACAAAGATTCGCCGATAGTTCTCCACGGCAGTGGTATTTTTCTT
65 TTCAAAGGCATGCCTGGAGGGACAAAGATTCGCCGATAGTTCTCCACGGCAGTGGTATTTTTCTT
45426709 AAGTTTCTTTGCCAATGCACTTAAGAAGTCAGCCATGAAAACCCAGCCAAAAGAAGG
130 AAGTTTCTTTGCCAATGCACTTAAGAAGTCAGCCATGAAAACCCAGCCAAAAGAAGG
* *
45426766 CCCGAGTGCCTACCTGAATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATTCCCA-TG
1 CCCGAGTGCCTACCTGAATGTGCTTAAAAAGAACATTGACTCTCAGAGGCT-GTCATT-ACAGAG
45426830 CTTCAAAGGCATGCCTGGAGGGACAAAGATTCGCCGATAGTTCTCCACGGCAGTGGTATTTTTCT
64 CTTCAAAGGCATGCCTGGAGGGACAAAGATTCGCCGATAGTTCTCCACGGCAGTGGTATTTTTCT
45426895 TAAGTTTCTTTGCCAATGCACTTAAGAAGTCAGCCATGAAAACCCAGCCAAAAGAAGG
129 TAAGTTTCTTTGCCAATGCACTTAAGAAGTCAGCCATGAAAACCCAGCCAAAAGAAGG
45426953 ACCATTGCCT
Statistics
Matches: 181, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
187 174 0.96
188 6 0.03
189 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (186 bp):
CCCGAGTGCCTACCTGAATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTGTCATTACAGAGCT
TCAAAGGCATGCCTGGAGGGACAAAGATTCGCCGATAGTTCTCCACGGCAGTGGTATTTTTCTTA
AGTTTCTTTGCCAATGCACTTAAGAAGTCAGCCATGAAAACCCAGCCAAAAGAAGG
Found at i:45430252 original size:22 final size:21
Alignment explanation
Indices: 45430226--45430286 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
45430216 ATCTAAATTC
*
45430226 AAATTAAATAATAAAATTATCT
1 AAATTAAAT-ATAAAATTATAT
* *
45430248 AAATTTAAGTATAAAAATATAT
1 AAA-TTAAATATAAAATTATAT
*
45430270 AAATATTAATATAAAAT
1 AAAT-TAAATATAAAAT
45430287 ATTTTTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 25 0.81
23 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATTAAATATAAAATTATAT
Found at i:45434924 original size:25 final size:24
Alignment explanation
Indices: 45434890--45434937 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
45434880 ATGTATTAAA
* *
45434890 ATATTTTAATAGTTATATAATAAC
1 ATATTTTAATAATTAAATAATAAC
45434914 ATATATTTAATAATTAAATAATAA
1 ATAT-TTTAATAATTAAATAATAA
45434938 TTTGAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTTTAATAATTAAATAATAAC
Found at i:45436064 original size:3 final size:3
Alignment explanation
Indices: 45436056--45436081 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45436046 TGATCTGATG
45436056 AGT AGT AGT AGT AGT AGT AGT AGT AG
1 AGT AGT AGT AGT AGT AGT AGT AGT AG
45436082 GCAGTGGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
AGT
Found at i:45440719 original size:11 final size:12
Alignment explanation
Indices: 45440700--45440728 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
45440690 GGTAATAAAC
45440700 AAAAGATAAAAT
1 AAAAGATAAAAT
45440712 AAAA-ATAAAAT
1 AAAAGATAAAAT
45440723 AAAAGA
1 AAAAGA
45440729 ATGAATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAGATAAAAT
Found at i:45443784 original size:12 final size:12
Alignment explanation
Indices: 45443751--45443786 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
45443741 CAATTTGTGT
45443751 ATTGTTTTAAG-A
1 ATTGTTTT-AGTA
45443763 ATTGTTTTAGTA
1 ATTGTTTTAGTA
45443775 ATTGTTTTAGTA
1 ATTGTTTTAGTA
45443787 TCATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 2 0.09
12 21 0.91
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (12 bp):
ATTGTTTTAGTA
Found at i:45443849 original size:26 final size:24
Alignment explanation
Indices: 45443805--45443854 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
45443795 ATTTGTTTTA
*
45443805 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
45443829 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
45443855 TTTTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:45458960 original size:15 final size:15
Alignment explanation
Indices: 45458948--45458981 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
45458938 TAACAATAGT
45458948 AATAATAGTAATAAA
1 AATAATAGTAATAAA
45458963 AATAATAGCT-ATAAA
1 AATAATAG-TAATAAA
45458978 AATA
1 AATA
45458982 TTAACCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.94
16 1 0.06
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAATAGTAATAAA
Found at i:45459014 original size:3 final size:3
Alignment explanation
Indices: 45459000--45459053 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
45458990 GACAATAAAG
*
45459000 AAT AAT AGT AAT AAT AAT AAT -AT AGAT AAT AAT -AT ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT
45459044 AAT AAT AAT A
1 AAT AAT AAT A
45459054 GTTAGAGATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:45459268 original size:3 final size:3
Alignment explanation
Indices: 45459260--45459311 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
45459250 TATAAATATG
* * * *
45459260 ATA ATA ATA ATA ATG ATA ATG ATA ATA ATAA ATA AT- ATA GTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
45459305 ATA ATA A
1 ATA ATA A
45459312 AAGTAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45459272 original size:18 final size:18
Alignment explanation
Indices: 45459251--45459344 Score: 63
Period size: 18 Copynumber: 5.1 Consensus size: 18
45459241 AAATATAAGT
45459251 ATAAATATGATAATAATA
1 ATAAATATGATAATAATA
45459269 ATAATGATAATGATAATAATA
1 ATAA--AT-ATGATAATAATA
*
45459290 A-ATAATAT-AGTAGTAATA
1 ATA-AATATGA-TAATAATA
*
45459308 ATAAA-A-GTAAAATTAATA
1 ATAAATATG-ATAA-TAATA
*
45459326 GTAAAT-TGATAATAATA
1 ATAAATATGATAATAATA
45459343 AT
1 AT
45459345 GTACGTTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 23
0.67 0.07 0.26
Matches are distributed among these distances:
17 9 0.15
18 29 0.49
19 4 0.07
20 3 0.05
21 14 0.24
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (18 bp):
ATAAATATGATAATAATA
Found at i:45459306 original size:21 final size:22
Alignment explanation
Indices: 45459257--45459312 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
45459247 AAGTATAAAT
45459257 ATGATAATAAT-AATAATGATA
1 ATGATAATAATAAATAATGATA
45459278 ATGATAATAATAAATAAT-ATA
1 ATGATAATAATAAATAATGATA
*
45459299 GT-AGTAATAATAAA
1 ATGA-TAATAATAAA
45459313 AGTAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 1 0.03
21 25 0.78
22 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (22 bp):
ATGATAATAATAAATAATGATA
Found at i:45459682 original size:35 final size:32
Alignment explanation
Indices: 45459640--45459733 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 32
45459630 TATGCATAAC
45459640 AATAAAAATACAATATTAAAATATATATACGAGT
1 AATAAAAATACAATATTAAAATATATATAC-A-T
**
45459674 AATAAAAAATGTATCCGTATTAAAA-ATATATACAT
1 AAT-AAAAA--TA-CAATATTAAAATATATATACAT
45459709 AATAAAAATACAATATTTAAAATAT
1 AATAAAAATACAATA-TTAAAATAT
45459734 TTACACAGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
31 3 0.06
32 8 0.16
33 2 0.04
34 8 0.16
35 9 0.18
36 1 0.02
37 10 0.20
38 9 0.18
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (32 bp):
AATAAAAATACAATATTAAAATATATATACAT
Found at i:45459714 original size:17 final size:17
Alignment explanation
Indices: 45459656--45459718 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
45459646 AATACAATAT
45459656 TAAAATATATATACGAGTAA
1 TAAAA-ATATATAC-A-TAA
* * * *
45459676 TAAAAAATGTATCCGTAT
1 T-AAAAATATATACATAA
45459694 TAAAAATATATACATAA
1 TAAAAATATATACATAA
45459711 TAAAAATA
1 TAAAAATA
45459719 CAATATTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 20 0.59
18 3 0.09
20 7 0.21
21 4 0.12
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAAATATATACATAA
Found at i:45459864 original size:14 final size:14
Alignment explanation
Indices: 45459847--45459888 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
45459837 ACATAACATA
45459847 AATATCATATATAT
1 AATATCATATATAT
*
45459861 AATATC-TAAATAT
1 AATATCATATATAT
45459874 ACATA-CATATATAT
1 A-ATATCATATATAT
45459888 A
1 A
45459889 GTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATCATATATAT
Found at i:45460053 original size:15 final size:16
Alignment explanation
Indices: 45460028--45460058 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
45460018 TTAATAATAC
45460028 TATATAATATATATAA
1 TATATAATATATATAA
45460044 TATA-AATATATATAA
1 TATATAATATATATAA
45460059 GTATGACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATAATATATATAA
Found at i:45461359 original size:44 final size:44
Alignment explanation
Indices: 45461296--45461935 Score: 417
Period size: 44 Copynumber: 14.7 Consensus size: 44
45461286 AATTTTCAGC
**
45461296 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
* * * * **
45461340 CTGTTTCCCTACTGCTTAGGGGGTTAAGAT-C-TTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCG--AATTCAAT
* * ** *
45461384 CTGTTACCCTACTGCTTAGGGTTTTAAGGCCCATCGGCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
* * * *
45461428 CTGTTTCCCTACTGCTTAAGGGG-TAAAGAT-C-TTGTAAATTCAGA-
1 CTGTTACCCTACTGCTT-AGGGGTTTAAGGTCCATCG--AATTCA-AT
* * *
45461472 CTGTTACCCTACTGCTTAGGGTTTTAAGG-CCTATC-ACCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCC-ATCGA-ATTCAAT
* * * ** ** * * *
45461516 CTATTTCCCTACTGCTTAGGGGGTTAATATCTGT-AAATCCAAC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
*** *
45461559 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCTCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
* * * * *
45461603 CTGTTTCCCTACTGCTTAGGAGG-TTAAGATCTAT-AAATTCAAC
1 CTGTTACCCTACTGCTTAGG-GGTTTAAGGTCCATCGAATTCAAT
* * ** *
45461646 CTGTTACCTTACTGCTTAAGGGTTTAAGGTCCATCGCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
* * * * ** * *
45461690 CTGTTTCCTTACTGCTTAGGGGGTTAAGATCTGT-AAATTCAAC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
** *
45461733 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
* * * ** * *
45461777 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTCAAC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
* ** **
45461820 CTGTTACCCTACTGCCTAGGGGTTTAAGGTCCATCGTCTTTGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
* * * * ** * **
45461864 CTGTTTCACTACTGCTTAGGGGGTTAAGATCTGT-AAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
45461907 CTGTTACCCTACTGCTTAGGGGTTTAAGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGG
45461936 CTTGTGAATT
Statistics
Matches: 434, Mismatches: 140, Indels: 45
0.70 0.23 0.07
Matches are distributed among these distances:
42 6 0.01
43 159 0.37
44 257 0.59
45 9 0.02
46 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.35
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGAATTCAAT
Found at i:45461599 original size:87 final size:87
Alignment explanation
Indices: 45461290--45461935 Score: 1026
Period size: 87 Copynumber: 7.4 Consensus size: 87
45461280 ATCTAGAATT
* *
45461290 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCAATCTGTTTCCCTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC
45461355 TTAGGGGGTTAAGATCTTGTAAA
66 TTAGGGGGTTAAGATC-TGTAAA
* * * *
45461378 TTCAGCCTGTTACCCTACTGCTTAGGGTTTTAAGGCCCATCGGCTTCGATCTGTTTCCCTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC
* *
45461443 TTAAGGGGTAAAGATCTTGTAAA
66 TTAGGGGGTTAAGATC-TGTAAA
* * *
45461466 TTCAGA-CTGTTACCCTACTGCTTAGGGTTTTAAGG-CCTATCACCTTCGATCTATTTCCCTACT
1 TTCA-ACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCC-ATCGCCTTCGATCTGTTTCCCTACT
*
45461529 GCTTAGGGGGTTAATATCTGTAAA
64 GCTTAGGGGGTTAAGATCTGTAAA
* *
45461553 TCCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCTCCTTCGATCTGTTTCCCTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC
* *
45461618 TTAGGAGGTTAAGATCTATAAA
66 TTAGGGGGTTAAGATCTGTAAA
* * *
45461640 TTCAACCTGTTACCTTACTGCTTAAGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCTTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC
45461705 TTAGGGGGTTAAGATCTGTAAA
66 TTAGGGGGTTAAGATCTGTAAA
45461727 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC
45461792 TTAGGGGGTTAAGATCTGTAAA
66 TTAGGGGGTTAAGATCTGTAAA
* * * *
45461814 TTCAACCTGTTACCCTACTGCCTAGGGGTTTAAGGTCCATCGTCTTTGATCTGTTTCACTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC
45461879 TTAGGGGGTTAAGATCTGTAAA
66 TTAGGGGGTTAAGATCTGTAAA
*
45461901 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG
1 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
45461936 CTTGTGAATT
Statistics
Matches: 518, Mismatches: 36, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
86 1 0.00
87 363 0.70
88 154 0.30
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.35
Consensus pattern (87 bp):
TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC
TTAGGGGGTTAAGATCTGTAAA
Found at i:45462112 original size:64 final size:64
Alignment explanation
Indices: 45462011--45462134 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
45462001 GTAACTATGT
* *
45462011 TTATGCCAAATAATTAGGACGCTATGATTGAAATGAATCAAATGATCCTAACTAAATGTGATGC
1 TTATGCCAAATAACTAGGACGCTATGATCGAAATGAATCAAATGATCCTAACTAAATGTGATGC
* * * * *
45462075 TTATGTCAAATAACTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAATTAGATGTG
1 TTATGCCAAATAACTAGGACGCTATGATCGAAATGAATCAAATGATCCTAACTAAATGTG
45462135 TCACGAATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (64 bp):
TTATGCCAAATAACTAGGACGCTATGATCGAAATGAATCAAATGATCCTAACTAAATGTGATGC
Found at i:45467648 original size:39 final size:39
Alignment explanation
Indices: 45467565--45467640 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
45467555 AGCTCAAAGT
* * *
45467565 CTAATTGAAGCACATAAGTGCTAGACGGGAGCCCGAACA
1 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAACA
45467604 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAA
1 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAA
45467641 GGCTAACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (39 bp):
CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAACA
Found at i:45470455 original size:25 final size:25
Alignment explanation
Indices: 45470402--45470455 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
45470392 AAAATTTATA
* *
45470402 TGATAGGAAAATCTTATGAAAATAT
1 TGATAGGAAAATCTTATCAAAATAG
* **
45470427 TGATAGGAAAATTTTATCAATTTAG
1 TGATAGGAAAATCTTATCAAAATAG
45470452 TGAT
1 TGAT
45470456 TAGTTAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.37
Consensus pattern (25 bp):
TGATAGGAAAATCTTATCAAAATAG
Found at i:45479402 original size:5 final size:5
Alignment explanation
Indices: 45479392--45479419 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
45479382 TGCACTACCT
45479392 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
45479420 TTTATTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:45484332 original size:24 final size:24
Alignment explanation
Indices: 45484278--45484332 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
45484268 TTAATCTTTA
45484278 TACTATTAAAAAAATTAAACAAAGT
1 TACTATTAAAAAAATTAAAC-AAGT
* *
45484303 TA-TATTAAAATAAATTTAAC-ATT
1 TACTATTAAAA-AAATTAAACAAGT
45484326 TACTATT
1 TACTATT
45484333 TTAAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.15
24 12 0.46
25 10 0.38
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (24 bp):
TACTATTAAAAAAATTAAACAAGT
Found at i:45491982 original size:18 final size:17
Alignment explanation
Indices: 45491955--45491988 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
45491945 ATTTTTCAAG
45491955 TTTTAAAATTTTGAATT
1 TTTTAAAATTTTGAATT
45491972 TTTTGAAAATTTTGAAT
1 TTTT-AAAATTTTGAAT
45491989 ATGGACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTAAAATTTTGAATT
Found at i:45494256 original size:19 final size:21
Alignment explanation
Indices: 45494229--45494271 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
45494219 TTTAATCTGA
45494229 AAAAAATT-AAATTTAA-ATG
1 AAAAAATTAAAATTTAAGATG
*
45494248 AAAATATTAAAATTTAAGATG
1 AAAAAATTAAAATTTAAGATG
45494269 AAA
1 AAA
45494272 TTGTTGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 8 0.38
21 6 0.29
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAATTAAAATTTAAGATG
Found at i:45496362 original size:17 final size:17
Alignment explanation
Indices: 45496332--45496373 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
45496322 GTGAGATTAT
*
45496332 AAAATATAACAATAATTA
1 AAAAAATAACAATAA-TA
*
45496350 AAAGAATAA-AATAATA
1 AAAAAATAACAATAATA
45496366 AAAAAATA
1 AAAAAATA
45496374 TAAAAAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 5 0.24
18 7 0.33
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAATAACAATAATA
Found at i:45496376 original size:18 final size:18
Alignment explanation
Indices: 45496332--45496378 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
45496322 GTGAGATTAT
*
45496332 AAAATATAACAATAATTAA
1 AAAATATAA-AATAATAAA
*
45496351 AAGA-ATAAAATAATAAA
1 AAAATATAAAATAATAAA
45496368 AAAATATAAAA
1 AAAATATAAAA
45496379 AAACTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.46
18 10 0.42
19 3 0.12
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATATAAAATAATAAA
Found at i:45497409 original size:2 final size:2
Alignment explanation
Indices: 45497402--45497426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45497392 TAAAGAGAAA
45497402 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
45497427 AAAGTGTAAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:45501341 original size:21 final size:22
Alignment explanation
Indices: 45501315--45501361 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
45501305 CTCTGCTCAA
*
45501315 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
45501336 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
45501358 ACTC
1 ACTC
45501362 ACTCCTTCTG
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:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:45507260 original size:22 final size:21
Alignment explanation
Indices: 45507235--45507293 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
45507225 AAATAACAGT
45507235 AAAATAACGAGAAAATAGAAAG
1 AAAATAAC-AGAAAATAGAAAG
* * *
45507257 AAAACAACAGCAAAATAGTAGG
1 AAAATAACAG-AAAATAGAAAG
45507279 AAAATAACAAGAAAA
1 AAAATAAC-AGAAAA
45507294 CAACTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.68, C:0.08, G:0.15, T:0.08
Consensus pattern (21 bp):
AAAATAACAGAAAATAGAAAG
Found at i:45512024 original size:30 final size:30
Alignment explanation
Indices: 45511988--45512100 Score: 199
Period size: 30 Copynumber: 3.8 Consensus size: 30
45511978 CAATATCTCA
45511988 ATACCCATATCTTTGACTTTCCAATATTTG
1 ATACCCATATCTTTGACTTTCCAATATTTG
45512018 ATACCCATATCTTTGACTTTCCAATATTTG
1 ATACCCATATCTTTGACTTTCCAATATTTG
* *
45512048 ATACCCATATCTTTGACTTTCTATTATTTG
1 ATACCCATATCTTTGACTTTCCAATATTTG
*
45512078 ATACCCATATCTTTGATTTTCCA
1 ATACCCATATCTTTGACTTTCCA
45512101 TAAATATGGA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (30 bp):
ATACCCATATCTTTGACTTTCCAATATTTG
Found at i:45512032 original size:15 final size:15
Alignment explanation
Indices: 45511988--45512094 Score: 76
Period size: 15 Copynumber: 7.1 Consensus size: 15
45511978 CAATATCTCA
45511988 ATACCCATATCTTTG
1 ATACCCATATCTTTG
** *
45512003 ACTTTCCA-ATATTTG
1 A-TACCCATATCTTTG
45512018 ATACCCATATCTTTG
1 ATACCCATATCTTTG
** *
45512033 ACTTTCCA-ATATTTG
1 A-TACCCATATCTTTG
45512048 ATACCCATATCTTTG
1 ATACCCATATCTTTG
** * *
45512063 ACTTTCTAT-TATTTG
1 A-TACCCATATCTTTG
45512078 ATACCCATATCTTTG
1 ATACCCATATCTTTG
45512093 AT
1 AT
45512095 TTTCCATAAA
Statistics
Matches: 66, Mismatches: 20, Indels: 12
0.67 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 42 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (15 bp):
ATACCCATATCTTTG
Found at i:45516721 original size:30 final size:30
Alignment explanation
Indices: 45516681--45516764 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
45516671 CCAATATCTC
45516681 GATACCCATATCTTTGACTTTCCAATAGTT
1 GATACCCATATCTTTGACTTTCCAATAGTT
* * * *
45516711 GATAACCATATCTTTGACTTTCTATTATTT
1 GATACCCATATCTTTGACTTTCCAATAGTT
*
45516741 GATACCCATATCTTTGATTTTCCA
1 GATACCCATATCTTTGACTTTCCA
45516765 TAAATATGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.44
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCCAATAGTT
Found at i:45521189 original size:32 final size:32
Alignment explanation
Indices: 45521150--45521217 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
45521140 TCTGAAAAGT
45521150 AAAACAAAAATGAAAAGACATAAAATAAAATA
1 AAAACAAAAATGAAAAGACATAAAATAAAATA
45521182 AAAACAAAAATGAAAAGACATAAAATAAAATA
1 AAAACAAAAATGAAAAGACATAAAATAAAATA
45521214 AAAA
1 AAAA
45521218 AAGGAGGCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (32 bp):
AAAACAAAAATGAAAAGACATAAAATAAAATA
Found at i:45529071 original size:11 final size:11
Alignment explanation
Indices: 45529055--45529102 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
45529045 CTAAATAAAA
45529055 TAATAAAATAT
1 TAATAAAATAT
45529066 TAAT-AAATAT
1 TAATAAAATAT
* *
45529076 CTTATTAAATAT
1 -TAATAAAATAT
*
45529088 TAATAAAATAA
1 TAATAAAATAT
45529099 TAAT
1 TAAT
45529103 TTTCTAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 6 0.19
11 19 0.61
12 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:45529100 original size:30 final size:30
Alignment explanation
Indices: 45529066--45529127 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
45529056 AATAAAATAT
*
45529066 TAATAAATATCTTATTAAAT-ATTAATAAAA
1 TAATAAATATCTAATTAAATAATT-ATAAAA
* *
45529096 TAATAATTTTCTAATTAAATAATTATAAAA
1 TAATAAATATCTAATTAAATAATTATAAAA
45529126 TA
1 TA
45529128 TCATCAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
TAATAAATATCTAATTAAATAATTATAAAA
Found at i:45530607 original size:18 final size:18
Alignment explanation
Indices: 45530580--45530672 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
45530570 TACGACCGTT
45530580 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
45530598 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
45530616 TACGATACTATTCACGTA
1 TACGGTACTATTCACGTA
*
45530634 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
45530652 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
45530670 TAC
1 TAC
45530673 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:45530632 original size:36 final size:36
Alignment explanation
Indices: 45530580--45530672 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
45530570 TACGACCGTT
45530580 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
45530616 TACGATACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
45530652 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
45530673 AGTAGTTGGG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:45541929 original size:14 final size:15
Alignment explanation
Indices: 45541910--45541939 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45541900 ATGAAAGTTA
45541910 TAGATA-ATATATTT
1 TAGATATATATATTT
45541924 TAGATATATATATTT
1 TAGATATATATATTT
45541939 T
1 T
45541940 GAAGTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TAGATATATATATTT
Found at i:45542140 original size:23 final size:24
Alignment explanation
Indices: 45542096--45542167 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
45542086 CCTCGGTCTC
* **
45542096 TCTTAAAATGAAAATTTTTTAATT
1 TCTTGAAATGAATTTTTTTTAATT
45542120 TCTTGAAAT-AATTTTTTTTAATT
1 TCTTGAAATGAATTTTTTTTAATT
45542143 TCTTGAAATGAATTTTTTTTAATT
1 TCTTGAAATGAATTTTTTTTAATT
45542167 T
1 T
45542168 AGACCCCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 21 0.48
24 23 0.52
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (24 bp):
TCTTGAAATGAATTTTTTTTAATT
Found at i:45547271 original size:4 final size:4
Alignment explanation
Indices: 45547264--45547292 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
45547254 GTGTGTGCGT
45547264 GTGA GTGA GTGA GTGA GTGA GTGA GTGA G
1 GTGA GTGA GTGA GTGA GTGA GTGA GTGA G
45547293 GGAAATGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (4 bp):
GTGA
Found at i:45551694 original size:253 final size:254
Alignment explanation
Indices: 45551245--45551753 Score: 921
Period size: 253 Copynumber: 2.0 Consensus size: 254
45551235 GAACATAGGC
* *
45551245 CATAGGTATTCTTCATTCTTCAGCTACGTTATTTGGACCTGGATCAGGTTTCTGATATGGGTATG
1 CATAGGTATTCTTCATTCTTCAGCAACGTTATATGGACCTGGATCAGGTTTCTGATATGGGTATG
*
45551310 AATTTAAGGGTCAGATTCTTCTTTTTCTTAAAGTTGTGGAAACTCAAGTGATTTAGAAACTGTCC
66 AATTTAAGGGTCAGATTCTTCTTTTTCTTAAACTTGTGGAAACTCAAGTGATTTAGAAACTGTCC
* *
45551375 TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTGTCGTTAATGT
131 TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTATAGTTAATGT
*
45551440 TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCCCGATATTATTTGTTATATGAT
196 TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCCCGATATTATATGTTATATGAT
*
45551499 CATAGGTATTCTTCATTCTTCAGCAATGTTATATGGACCTGGATCAGGTTTCTGATATGGGTATG
1 CATAGGTATTCTTCATTCTTCAGCAACGTTATATGGACCTGGATCAGGTTTCTGATATGGGTATG
*
45551564 AATTTAAGGGTCAGATTCTT-TTTTTCTTAAACTTGTGGAAATTCAAGTGATTTAGAAACTGTCC
66 AATTTAAGGGTCAGATTCTTCTTTTTCTTAAACTTGTGGAAACTCAAGTGATTTAGAAACTGTCC
45551628 TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTATAGTTAATGT
131 TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTATAGTTAATGT
**
45551693 TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCTTGATATTATATGTTATATGAT
196 TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCCCGATATTATATGTTATATGAT
45551752 CA
1 CA
45551754 ATTGAAAGCC
Statistics
Matches: 245, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
253 163 0.67
254 82 0.33
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (254 bp):
CATAGGTATTCTTCATTCTTCAGCAACGTTATATGGACCTGGATCAGGTTTCTGATATGGGTATG
AATTTAAGGGTCAGATTCTTCTTTTTCTTAAACTTGTGGAAACTCAAGTGATTTAGAAACTGTCC
TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTATAGTTAATGT
TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCCCGATATTATATGTTATATGAT
Found at i:45551841 original size:22 final size:22
Alignment explanation
Indices: 45551816--45551857 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
45551806 GGCCAGTCAA
45551816 TTTTCCTCTACATTCTTTTCTT
1 TTTTCCTCTACATTCTTTTCTT
* * *
45551838 TTTTTCTCTTCTTTCTTTTC
1 TTTTCCTCTACATTCTTTTC
45551858 CTCCTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTCCTCTACATTCTTTTCTT
Found at i:45551849 original size:13 final size:13
Alignment explanation
Indices: 45551828--45551882 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
45551818 TTCCTCTACA
*
45551828 TTCTTTTCTTTTT
1 TTCTCTTCTTTTT
45551841 TTCTCTTCTTTCTT
1 TTCTCTTCTTT-TT
*
45551855 TTC-CTCCTTTTAT
1 TTCTCTTCTTTT-T
*
45551868 TTCTTTTCTTTTT
1 TTCTCTTCTTTTT
45551881 TT
1 TT
45551883 TTTTTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 1 0.03
13 23 0.66
14 11 0.31
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCTCTTCTTTTT
Found at i:45551873 original size:9 final size:9
Alignment explanation
Indices: 45551832--45551882 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
45551822 TCTACATTCT
45551832 TTTCTTTT-
1 TTTCTTTTC
*
45551840 TTTCTCTTC
1 TTTCTTTTC
45551849 TTTCTTTTC
1 TTTCTTTTC
* * *
45551858 CTCCTTTTA
1 TTTCTTTTC
45551867 TTTCTTTTC
1 TTTCTTTTC
45551876 TTT-TTTT
1 TTTCTTTT
45551883 TTTTTAAATT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
8 11 0.32
9 23 0.68
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:45553843 original size:2 final size:2
Alignment explanation
Indices: 45553836--45553860 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45553826 TTATATGAGA
45553836 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
45553861 TTGAAAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:45559435 original size:16 final size:16
Alignment explanation
Indices: 45559413--45559481 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
45559403 TTTGGTTCGC
45559413 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
45559429 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
45559445 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
45559462 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
45559478 TGTA
1 TGTA
45559482 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:45559459 original size:33 final size:32
Alignment explanation
Indices: 45559413--45559481 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
45559403 TTTGGTTCGC
45559413 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
45559445 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
45559478 TGTA
1 TGTA
45559482 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:45559546 original size:44 final size:45
Alignment explanation
Indices: 45559462--45559552 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
45559452 GGATTAGAGG
* * *
45559462 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
45559507 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
45559551 TG
1 TG
45559553 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:45559738 original size:18 final size:17
Alignment explanation
Indices: 45559717--45559751 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45559707 TTATTATTAA
*
45559717 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
45559735 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
45559752 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:45559811 original size:61 final size:61
Alignment explanation
Indices: 45559745--45560052 Score: 221
Period size: 61 Copynumber: 5.1 Consensus size: 61
45559735 ATATAATTTA
* * *
45559745 ATAAAATTCTTAATAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATTATAATATATGATACT
* * * * * * * *
45559806 GTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTT--T--AATTAAAATATATGAT-TT
1 ATAAAATTCTTAA-TAA-TTAA-TATTCTTATATGA-ATTTACTAAAATTATAATATATGATACT
*
45559864 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATTATAATATATGATACT
* * * * * ** * *
45559926 ATAAAA-T-ATAAT--TTGAAATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TT
1 ATAAAATTCTTAATAATT--AAT-ATTCTTATATGAATTTACTAAAATTATAATATATGATACT
* *
45559984 AATAAAATTCTTAAT-ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACT
1 -ATAAAATTCTTAATAATT-AATATTCTTATATGAATTTACTAAAATTATAATATATGATACT
45560046 ATAAAAT
1 ATAAAAT
45560053 ATAATTTAAA
Statistics
Matches: 187, Mismatches: 39, Indels: 42
0.70 0.15 0.16
Matches are distributed among these distances:
57 14 0.07
58 5 0.03
59 58 0.31
60 24 0.13
61 65 0.35
62 8 0.04
63 13 0.07
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATTATAATATATGATACT
Found at i:45559858 original size:18 final size:17
Alignment explanation
Indices: 45559835--45559871 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
45559825 AATTATTATT
45559835 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
45559851 AAATATATGATTTAATA
1 AAATATATGATTTAATA
45559868 AAAT
1 AAAT
45559872 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:45559915 original size:120 final size:120
Alignment explanation
Indices: 45559695--45560088 Score: 655
Period size: 120 Copynumber: 3.3 Consensus size: 120
45559685 ATTTAATCAT
*
45559695 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
* * * *
45559760 ATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATA
65 ATAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
*
45559816 AATTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAA
* *
45559881 TCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
45559936 ATTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
* *
45560000 TTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
65 ATAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* *
45560056 ATTTAAAATAATTATTATTAAATATAATTTAAT
1 ATTTAACATAATTATTATTAAATATATTTTAAT
45560089 ATTTTTTCTA
Statistics
Matches: 258, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
119 2 0.01
120 251 0.97
121 5 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAA
TAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
Found at i:45559978 original size:18 final size:17
Alignment explanation
Indices: 45559955--45559991 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
45559945 AATTATTATT
45559955 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
45559971 AAATATATGATTTAATA
1 AAATATATGATTTAATA
45559988 AAAT
1 AAAT
45559992 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:45567512 original size:19 final size:18
Alignment explanation
Indices: 45567461--45567516 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
45567451 TGAAAATAAA
45567461 TATAATTG-TAATAATTT
1 TATAATTGTTAATAATTT
*
45567478 T-TAATCAT-TTATTAATTT
1 TATAAT--TGTTAATAATTT
45567496 TATAATTGTTAAATAATTT
1 TATAATTGTT-AATAATTT
45567515 TA
1 TA
45567517 AAAATTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 4 0.13
17 2 0.06
18 12 0.39
19 13 0.42
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
TATAATTGTTAATAATTT
Found at i:45567654 original size:21 final size:21
Alignment explanation
Indices: 45567630--45567680 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
45567620 CGCTGTTTCT
* *
45567630 AATCTCACTGCTACAATACCC
1 AATCTCACCGCTACAATAACC
* *
45567651 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAATAACC
45567672 AATCTCACC
1 AATCTCACC
45567681 ACCACCGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.37, G:0.06, T:0.24
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:45578929 original size:18 final size:17
Alignment explanation
Indices: 45578896--45578929 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
45578886 TTATACAATG
*
45578896 TAATTTTATTTTTATAT
1 TAATTTTATCTTTATAT
45578913 TAATTTATATCTTTATA
1 TAATTT-TATCTTTATA
45578930 ATTTTTAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTTTATCTTTATAT
Found at i:45588966 original size:30 final size:30
Alignment explanation
Indices: 45588920--45589015 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
45588910 TTTTATTATG
*
45588920 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
45588951 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
45588981 CTATTATTTGATACCTATATCTTTGA-TTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
45589010 TCAATA
1 CCAATA
45589016 AATATAGATA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.10
30 45 0.78
31 7 0.12
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.45
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:45588975 original size:15 final size:15
Alignment explanation
Indices: 45588930--45589007 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
45588920 CCAATATCTC
45588930 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
45588945 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
45588960 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
45588975 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
*
45588990 GATACCTATATCTTT
1 GATACCCATATCTTT
45589005 GAT
1 GAT
45589008 TTTCAATAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
14 9 0.20
15 29 0.63
16 8 0.17
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.46
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:45593092 original size:18 final size:18
Alignment explanation
Indices: 45593069--45593125 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
45593059 CCCAACTACT
*
45593069 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
45593087 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
45593105 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
45593123 GTA
1 GTA
45593126 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:45594134 original size:43 final size:44
Alignment explanation
Indices: 45594073--45594156 Score: 143
Period size: 43 Copynumber: 1.9 Consensus size: 44
45594063 CTTGGATCGG
*
45594073 AGAAGCGAACAATGAATAGATCGA-CCCCGAATCCGGTAAGAAA
1 AGAAGCGAACAATGAATAGATCGACCCCCGAATCAGGTAAGAAA
*
45594116 AGAAGTGAACAATGAATAGATCGACCCCCGAATCAGGTAAG
1 AGAAGCGAACAATGAATAGATCGACCCCCGAATCAGGTAAG
45594157 TAAACCCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 23 0.61
44 15 0.39
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (44 bp):
AGAAGCGAACAATGAATAGATCGACCCCCGAATCAGGTAAGAAA
Found at i:45594410 original size:16 final size:16
Alignment explanation
Indices: 45594389--45594422 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
45594379 TGTTTTTCTA
45594389 TTGTTTTCACTTG-CTG
1 TTGTTTTC-CTTGTCTG
45594405 TTGTTTTCCTTGTCTG
1 TTGTTTTCCTTGTCTG
45594421 TT
1 TT
45594423 TGCAGGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.03, C:0.18, G:0.18, T:0.62
Consensus pattern (16 bp):
TTGTTTTCCTTGTCTG
Found at i:45594852 original size:27 final size:27
Alignment explanation
Indices: 45594822--45594888 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
45594812 TTGTCACATT
45594822 TCACTTTGCCATATTTGGCACACTTTA
1 TCACTTTGCCATATTTGGCACACTTTA
*
45594849 TCACTTTGCCATGTTTGGCACACTTTA
1 TCACTTTGCCATATTTGGCACACTTTA
45594876 TCACTTTGCCATA
1 TCACTTTGCCATA
45594889 GTTCAACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (27 bp):
TCACTTTGCCATATTTGGCACACTTTA
Found at i:45596642 original size:61 final size:60
Alignment explanation
Indices: 45596538--45596658 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 60
45596528 ATCAATTTTC
* *
45596538 CTGCTTATTTCATGCCCTTGCCATCCAGCCCAAATAGCCTTGGGT-TTATTTGCCTTTTAA
1 CTGCTGATTTCATGCCCTTGCCATCCAGCCCAAATAGCCTTGGGTCTAATTT-CCTTTTAA
* *
45596598 CTGCTGATTTCATGCCTCTTGCCGTCCAGCCCAAA-A-CATTTTGGGTCTAATTTCCTTTTAA
1 CTGCTGATTTCATGCC-CTTGCCATCCAGCCCAAATAGC--CTTGGGTCTAATTTCCTTTTAA
45596659 AACCCTCTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
59 1 0.02
60 16 0.30
61 31 0.58
62 5 0.09
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (60 bp):
CTGCTGATTTCATGCCCTTGCCATCCAGCCCAAATAGCCTTGGGTCTAATTTCCTTTTAA
Found at i:45602216 original size:18 final size:18
Alignment explanation
Indices: 45602133--45602228 Score: 77
Period size: 18 Copynumber: 5.4 Consensus size: 18
45602123 ATCTTTATTG
* * *
45602133 TTCAGTATTAGTCAGTCA
1 TTCAGTAGTAGTCATTTA
* * *
45602151 -TCAGTATTAATCAGTTA
1 TTCAGTAGTAGTCATTTA
*
45602168 TTCAGTAGTAATCATTTA
1 TTCAGTAGTAGTCATTTA
** *
45602186 TTCAGTAACAGTCGTTTA
1 TTCAGTAGTAGTCATTTA
* *
45602204 TTCAGTGGTAGTCAATTA
1 TTCAGTAGTAGTCATTTA
45602222 TTCAGTA
1 TTCAGTA
45602229 CCTTTATTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
17 15 0.24
18 48 0.76
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (18 bp):
TTCAGTAGTAGTCATTTA
Found at i:45602610 original size:16 final size:15
Alignment explanation
Indices: 45602570--45602654 Score: 80
Period size: 19 Copynumber: 5.0 Consensus size: 15
45602560 TTCAATCAGT
45602570 ATATATTTCAACTAATCA
1 ATATATTTCAA-T--TCA
45602588 GATATATTCTCAATTCA
1 -ATATATT-TCAATTCA
45602605 ATATATTTCAATTAATCA
1 ATATATTTCAA-T--TCA
45602623 GATATATTCTCAATTCA
1 -ATATATT-TCAATTCA
45602640 ATATATTTCAATTCA
1 ATATATTTCAATTCA
45602655 TTTTATATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.20
16 15 0.25
17 6 0.10
18 3 0.05
19 16 0.27
20 8 0.13
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.42
Consensus pattern (15 bp):
ATATATTTCAATTCA
Found at i:45602637 original size:20 final size:19
Alignment explanation
Indices: 45602563--45602652 Score: 88
Period size: 16 Copynumber: 5.0 Consensus size: 19
45602553 TTTAGTTTTC
*
45602563 AATCAGTATATATTTCAACT
1 AATCAG-ATATATTTCAATT
45602583 AATCAGATATATTCTCAA-T
1 AATCAGATATATT-TCAATT
45602602 --TCA-ATATATTTCAATT
1 AATCAGATATATTTCAATT
45602618 AATCAGATATATTCTCAA-T
1 AATCAGATATATT-TCAATT
45602637 --TCA-ATATATTTCAATT
1 AATCAGATATATTTCAATT
45602653 CATTTTATAT
Statistics
Matches: 63, Mismatches: 0, Indels: 18
0.78 0.00 0.22
Matches are distributed among these distances:
15 8 0.13
16 16 0.25
17 6 0.10
18 3 0.05
19 16 0.25
20 14 0.22
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.42
Consensus pattern (19 bp):
AATCAGATATATTTCAATT
Found at i:45602651 original size:35 final size:35
Alignment explanation
Indices: 45602570--45602652 Score: 157
Period size: 35 Copynumber: 2.4 Consensus size: 35
45602560 TTCAATCAGT
*
45602570 ATATATTTCAACTAATCAGATATATTCTCAATTCA
1 ATATATTTCAATTAATCAGATATATTCTCAATTCA
45602605 ATATATTTCAATTAATCAGATATATTCTCAATTCA
1 ATATATTTCAATTAATCAGATATATTCTCAATTCA
45602640 ATATATTTCAATT
1 ATATATTTCAATT
45602653 CATTTTATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (35 bp):
ATATATTTCAATTAATCAGATATATTCTCAATTCA
Found at i:45603074 original size:19 final size:20
Alignment explanation
Indices: 45603040--45603084 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
45603030 AATTTTCCCT
45603040 TTTCTCCCTTTCTTTTCTTTC
1 TTTCTCCC-TTCTTTTCTTTC
45603061 TTTCTCCC-TCTTTTCTTTC
1 TTTCTCCCTTCTTTTCTTTC
*
45603080 ATTCT
1 TTTCT
45603085 ATTCTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.65
21 8 0.35
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTCCCTTCTTTTCTTTC
Found at i:45604990 original size:12 final size:12
Alignment explanation
Indices: 45604963--45604996 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
45604953 GGTTCAACCA
45604963 ATTTAA-TATTT
1 ATTTAATTATTT
*
45604974 TTTTAATTATTT
1 ATTTAATTATTT
45604986 ATTTAATTATT
1 ATTTAATTATT
45604997 GTTGGTCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTAATTATTT
Found at i:45609120 original size:31 final size:31
Alignment explanation
Indices: 45609082--45609155 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
45609072 TTATGTCTCA
*
45609082 ATTTTTTAAATTATTTAATGAT-ATTTTAATT
1 ATTTTTTAAATTATTGAATGATAATTTTAA-T
* * *
45609113 ATTTTTTATATTATTGATTTATAATTTTAAT
1 ATTTTTTAAATTATTGAATGATAATTTTAAT
*
45609144 ATTTTTTTAATT
1 ATTTTTTAAATT
45609156 TAAATTTAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 29 0.81
32 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (31 bp):
ATTTTTTAAATTATTGAATGATAATTTTAAT
Found at i:45613319 original size:22 final size:20
Alignment explanation
Indices: 45613276--45613314 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
45613266 CAATTTAAAA
45613276 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
45613296 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
45613315 ATGTAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:45614787 original size:6 final size:6
Alignment explanation
Indices: 45614776--45614801 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45614766 TTACATTAAC
45614776 CATGTG CATGTG CATGTG CATGTG CA
1 CATGTG CATGTG CATGTG CATGTG CA
45614802 AGACAGGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (6 bp):
CATGTG
Found at i:45622007 original size:93 final size:93
Alignment explanation
Indices: 45621897--45622253 Score: 660
Period size: 93 Copynumber: 3.8 Consensus size: 93
45621887 GCCCCTAAGT
* * * * * *
45621897 GAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
45621962 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
45621990 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
45622055 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
45622083 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
45622148 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
45622176 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
45622241 CGAGTTCGGATGC
66 CGAGTTCGGATGC
45622254 TCAACCATCC
Statistics
Matches: 258, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 258 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:45622057 original size:46 final size:46
Alignment explanation
Indices: 45621892--45622250 Score: 385
Period size: 46 Copynumber: 7.7 Consensus size: 46
45621882 AACCCGCCCC
* * * * *
45621892 TAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
45621938 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
45621986 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* *
45622031 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
45622079 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* *
45622124 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
45622172 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
45622217 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
45622251 TGCTCAACCA
Statistics
Matches: 262, Mismatches: 30, Indels: 42
0.78 0.09 0.13
Matches are distributed among these distances:
43 18 0.07
44 6 0.02
45 6 0.02
46 117 0.45
47 87 0.33
48 6 0.02
49 6 0.02
50 16 0.06
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:45622269 original size:46 final size:46
Alignment explanation
Indices: 45621942--45622262 Score: 219
Period size: 47 Copynumber: 6.9 Consensus size: 46
45621932 CATCCATAAA
45621942 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCTCAG
* * * *
45621989 CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCA--TAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCTCAG
45622035 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCTCAG
* * * *
45622082 CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCA--TAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCTCAG
45622128 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCTCAG
* * * *
45622175 CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCA--TAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCTCAG
45622221 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
45622263 CTAGTGACAT
Statistics
Matches: 216, Mismatches: 23, Indels: 71
0.70 0.07 0.23
Matches are distributed among these distances:
43 2 0.01
44 13 0.06
45 7 0.03
46 88 0.41
47 90 0.42
48 4 0.02
49 9 0.04
50 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTCAG
Found at i:45627173 original size:40 final size:39
Alignment explanation
Indices: 45627113--45627223 Score: 141
Period size: 40 Copynumber: 2.8 Consensus size: 39
45627103 TTGAGAATAT
* *
45627113 AAAGTGGATAGGATTCGTTCCTGATTCACTATAATACCTC
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATA-ATC
** *
45627153 AAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAATT
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAATC
* * *
45627192 TAAGTGAATAGGATTTATTCCTGATTCACTAT
1 AAAGTGGATAGGATTTGTTCCTGATTCACTAT
45627224 GGTAACTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 30 0.48
40 33 0.52
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (39 bp):
AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAATC
Found at i:45627213 original size:39 final size:39
Alignment explanation
Indices: 45627114--45627234 Score: 143
Period size: 39 Copynumber: 3.1 Consensus size: 39
45627104 TGAGAATATA
* ** ** * *
45627114 AAGTGGATAGGATTCGTTCCTGATTCACTATAATACCTCA
1 AAGTGAATAGGATTTATTCCTGATTCACTATGGTAACT-T
* * *
45627154 AAGTGGATAGGATTTGTTCCTGATTCACTATGGTAATTT
1 AAGTGAATAGGATTTATTCCTGATTCACTATGGTAACTT
45627193 AAGTGAATAGGATTTATTCCTGATTCACTATGGTAACTT
1 AAGTGAATAGGATTTATTCCTGATTCACTATGGTAACTT
45627232 AAG
1 AAG
45627235 GCGGATAGGA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 39 0.54
40 33 0.46
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (39 bp):
AAGTGAATAGGATTTATTCCTGATTCACTATGGTAACTT
Found at i:45627254 original size:39 final size:38
Alignment explanation
Indices: 45627158--45627254 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 38
45627148 ACCTCAAAGT
* * *
45627158 GGATAGGATTTGTTCCTGATTCACTATGGTAATTTAAGT
1 GGATAGGATTTG-ACCTGATTCACTATGGTAACTTAAGC
*
45627197 GAATAGGATTT-ATTCCTGATTCACTATGGTAACTTAAGGC
1 GGATAGGATTTGA--CCTGATTCACTATGGTAACTTAA-GC
45627237 GGATAGGATTTGACCTGA
1 GGATAGGATTTGACCTGA
45627255 AAAGGTAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
39 37 0.76
40 11 0.22
41 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (38 bp):
GGATAGGATTTGACCTGATTCACTATGGTAACTTAAGC
Found at i:45627303 original size:78 final size:77
Alignment explanation
Indices: 45627213--45627433 Score: 325
Period size: 78 Copynumber: 2.8 Consensus size: 77
45627203 GATTTATTCC
* *
45627213 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
1 TGATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
*
45627278 TTTAAATGATATA
66 -TTAAACGATATA
* *
45627291 TGATTCATTATGGTAACCTAAGGTGGATAGGATTTGACCTGAAAAGGGTAATCCTGATTCGCTAG
1 TGATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAA-GGTAATCCTGATTCGCTAC
*
45627356 ATTACACGATATA
65 ATTAAACGATATA
* * * * *
45627369 TGATTCCTTATGATAACTTAAGGTGGGTAGGATTTGACTTGAAAAGGTAATCCTGATTCACTACA
1 TGATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
45627434 ATTACATAAG
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
77 18 0.14
78 92 0.71
79 19 0.15
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (77 bp):
TGATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
TTAAACGATATA
Found at i:45628913 original size:27 final size:26
Alignment explanation
Indices: 45628883--45628937 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
45628873 GTTTTATTTT
*
45628883 ATGTTTTATTAATACATATTTAATTAC
1 ATGTTTTATTAATACAT-TATAATTAC
*
45628910 ATGTTTTATTAGTACATTATAATTAC
1 ATGTTTTATTAATACATTATAATTAC
45628936 AT
1 AT
45628938 CTTTATAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.51
Consensus pattern (26 bp):
ATGTTTTATTAATACATTATAATTAC
Found at i:45630261 original size:19 final size:20
Alignment explanation
Indices: 45630239--45630282 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
45630229 TTTAGATTTT
*
45630239 TTTTAAAATTTTATAAA-TA
1 TTTTAAAATTTTAAAAATTA
*
45630258 TTTT-TAATTTTAAAAATTA
1 TTTTAAAATTTTAAAAATTA
45630277 TTTTAA
1 TTTTAA
45630283 TTTTTTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAAATTTTAAAAATTA
Found at i:45630268 original size:18 final size:18
Alignment explanation
Indices: 45630245--45630286 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
45630235 TTTTTTTTAA
*
45630245 AATTTTATAAA-TATTTTT
1 AATTTTAAAAATTA-TTTT
45630263 AATTTTAAAAATTATTTT
1 AATTTTAAAAATTATTTT
45630281 AATTTT
1 AATTTT
45630287 TTTTGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTTTAAAAATTATTTT
Found at i:45631180 original size:11 final size:11
Alignment explanation
Indices: 45631166--45631210 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
45631156 AGATAAATAT
45631166 TATTTTATTAA
1 TATTTTATTAA
*
45631177 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
45631190 TATTTTATTAT
1 TATTTTATTAA
45631201 TATTTTATTA
1 TATTTTATTA
45631211 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:45633248 original size:46 final size:46
Alignment explanation
Indices: 45633203--45633483 Score: 316
Period size: 46 Copynumber: 6.2 Consensus size: 46
45633193 ATGAAATGTG
* * * **
45633203 TAAGACCATGGTTGAAAGATACCATGACAACATGATATAAAATGTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
* **
45633249 TAAGACCATAGTTGAAAGATACCATGGCAATGTGACATGAAAA-GAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAA
* **
45633295 TAAGACCATGGTTGAAAGATACCGTGGCAACATGAC-GGGAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
* *
45633340 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
* * * *
45633386 AAAGATCATGGTCGAAAGATACCATGGCAACATGACAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
* * * * * * *
45633432 TAAGACCATAGTTGAAAGACACTATGGCATCATGTC-GAAGATAAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
45633477 TAAGACC
1 TAAGACC
45633484 GTGGATGGGG
Statistics
Matches: 199, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
44 3 0.02
45 51 0.26
46 141 0.71
47 4 0.02
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
Found at i:45633396 original size:91 final size:91
Alignment explanation
Indices: 45633204--45633465 Score: 326
Period size: 91 Copynumber: 2.9 Consensus size: 91
45633194 TGAAATGTGT
* ** *
45633204 AAGACCATGGTTGAAAGATACCATGACAACATGATATAAAATGTGTAAGACCATAGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACCATGGCAACATGA-CGAAAATGAGTAAGACCATAGTTGAAAGAT
** * *
45633269 ACCATGGCAATGTGACATGAAAAGAAT
65 ACCATGGCAACATGACAGGAAAAGAAA
* ** * *
45633296 AAGACCATGGTTGAAAGATACCGTGGCAACATGACGGGAATGAATAAGACCATGGTTGAAAGATA
1 AAGACCATGGTTGAAAGATACCATGGCAACATGACGAAAATGAGTAAGACCATAGTTGAAAGATA
* *
45633361 CCATGGCAACATGACGGGAAATGAAA
66 CCATGGCAACATGACAGGAAAAGAAA
* * *
45633387 AAGATCATGGTCGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGAC
1 AAGACCATGGTTGAAAGATACCATGGCAACATGAC-GAAAATGAGTAAGACCATAGTTGAAAGAT
* *
45633452 ACTATGGCATCATG
65 ACCATGGCAACATG
45633466 TCGAAGATAA
Statistics
Matches: 144, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
91 76 0.53
92 68 0.47
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (91 bp):
AAGACCATGGTTGAAAGATACCATGGCAACATGACGAAAATGAGTAAGACCATAGTTGAAAGATA
CCATGGCAACATGACAGGAAAAGAAA
Found at i:45633449 original size:137 final size:137
Alignment explanation
Indices: 45633203--45633450 Score: 345
Period size: 137 Copynumber: 1.8 Consensus size: 137
45633193 ATGAAATGTG
* * *** *
45633203 TAAGACCATGGTTGAAAGATACCATGACAACATGATATAAAATGTGTAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGACAACATGACAGAAAATGAAAAAGACCATAGTCGAAAGA
** *
45633268 TACCATGGCAATGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCGTGGCAACATGACGG
66 TACCATGGCAACATGACATGAAAAGAATAAGACCATAGTTGAAAGATACCGTGGCAACATGACGG
45633333 GAATGAA
131 GAATGAA
* * * * *
45633340 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAAAAAGATCATGGTCGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGACAACATGACAGAAAATGAAAAAGACCATAGTCGAAAGA
*
45633405 TACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
66 TACCATGGCAACATGACATGAAAA-GAATAAGACCATAGTTGAAAGA
45633451 CACTATGGCA
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
136 5 0.05
137 90 0.95
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (137 bp):
TAAGACCATGGTTGAAAGATACCATGACAACATGACAGAAAATGAAAAAGACCATAGTCGAAAGA
TACCATGGCAACATGACATGAAAAGAATAAGACCATAGTTGAAAGATACCGTGGCAACATGACGG
GAATGAA
Found at i:45633479 original size:137 final size:137
Alignment explanation
Indices: 45633203--45633483 Score: 332
Period size: 137 Copynumber: 2.1 Consensus size: 137
45633193 ATGAAATGTG
* * *** *
45633203 TAAGACCATGGTTGAAAGATACCATGACAACATGATATAAAATGTGTAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGACAACATGACAGAAAATGAAAAAGACCATAGTCGAAAGA
** * * * *
45633268 TACCATGGCAATGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCGTGGCAACATGACGG
66 TACCATGGCAACATGACATGAAAAGAATAAGACCATAGTTGAAAGACACCATGGCAACATGACGA
*
45633333 GAATGAA
131 GAATAAA
* * * * *
45633340 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAAAAAGATCATGGTCGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGACAACATGACAGAAAATGAAAAAGACCATAGTCGAAAGA
* * * *
45633405 TACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATGTCG
66 TACCATGGCAACATGACATGAAAA-GAATAAGACCATAGTTGAAAGACACCATGGCAACATGACG
45633469 A-AGATAAA
130 AGA-ATAAA
45633477 TAAGACC
1 TAAGACC
45633484 GTGGATGGGG
Statistics
Matches: 120, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
136 6 0.05
137 114 0.95
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (137 bp):
TAAGACCATGGTTGAAAGATACCATGACAACATGACAGAAAATGAAAAAGACCATAGTCGAAAGA
TACCATGGCAACATGACATGAAAAGAATAAGACCATAGTTGAAAGACACCATGGCAACATGACGA
GAATAAA
Found at i:45636297 original size:14 final size:15
Alignment explanation
Indices: 45636278--45636311 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
45636268 GCATTTTCTT
*
45636278 AATATTTTATTAA-A
1 AATATTTTAATAATA
45636292 AATATTTTAATAATA
1 AATATTTTAATAATA
45636307 AATAT
1 AATAT
45636312 ACATTACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:45646578 original size:51 final size:50
Alignment explanation
Indices: 45646502--45646598 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 50
45646492 ATCCTGGGTC
*
45646502 CAAATTCTCGTTAACCTTGTATATATTTGTTTGGTTGATTAATATANGATT
1 CAAATTCTCGTTAACCTCGTATATATTTGTTTGGTTGATTAATATA-GATT
45646553 CAAATTCTCGTTAACCTCGTATATATTTGTTTGGTTGATTAATATA
1 CAAATTCTCGTTAACCTCGTATATATTTGTTTGGTTGATTAATATA
45646599 AAAGCCTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.46
Consensus pattern (50 bp):
CAAATTCTCGTTAACCTCGTATATATTTGTTTGGTTGATTAATATAGATT
Found at i:45648581 original size:31 final size:29
Alignment explanation
Indices: 45648541--45648601 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
45648531 TTAATGGAGT
*
45648541 TAAAAAGTTCAGCTACCTATTTGAGATAAA
1 TAAAAAGTTCAGCTACCCATTTGAGA-AAA
*
45648571 TAAAAGAGTTCAGGTACCCATTTGAGAAAA
1 TAAAA-AGTTCAGCTACCCATTTGAGAAAA
45648601 T
1 T
45648602 GGGAAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (29 bp):
TAAAAAGTTCAGCTACCCATTTGAGAAAA
Found at i:45667240 original size:3 final size:3
Alignment explanation
Indices: 45667232--45667271 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
45667222 NNNNNNNNNN
45667232 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45667272 GTAAAATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:45668196 original size:26 final size:27
Alignment explanation
Indices: 45668160--45668221 Score: 117
Period size: 26 Copynumber: 2.3 Consensus size: 27
45668150 AAATTTCCTT
45668160 TTTTTTATTCCATTACCAACTTT-CCC
1 TTTTTTATTCCATTACCAACTTTCCCC
45668186 TTTTTTATTCCATTACCAACTTTCCCC
1 TTTTTTATTCCATTACCAACTTTCCCC
45668213 TTTTTTATT
1 TTTTTTATT
45668222 TTTTATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 23 0.66
27 12 0.34
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTTTATTCCATTACCAACTTTCCCC
Found at i:45670742 original size:25 final size:25
Alignment explanation
Indices: 45670683--45670742 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
45670673 TTTCCACTTG
* * *
45670683 ATTTGAAAACATTATTTTGTTTTAC
1 ATTTAAAAATATTATTTTATTTTAC
*
45670708 TTTTAAAAATATTATTTTATTTTA-
1 ATTTAAAAATATTATTTTATTTTAC
45670732 ATTTAATAAAT
1 ATTTAA-AAAT
45670743 TTTCTCATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (25 bp):
ATTTAAAAATATTATTTTATTTTAC
Found at i:45675349 original size:21 final size:21
Alignment explanation
Indices: 45675325--45675376 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
45675315 CAAATATATA
*
45675325 AAATCAATTCAATAAAAAAAC
1 AAATAAATTCAATAAAAAAAC
* * *
45675346 AAATAAATTTAATATAAAAAT
1 AAATAAATTCAATAAAAAAAC
45675367 AAATTAAATT
1 AAA-TAAATT
45675377 AAAATCAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAAATTCAATAAAAAAAC
Found at i:45675379 original size:16 final size:17
Alignment explanation
Indices: 45675346--45675380 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
45675336 ATAAAAAAAC
*
45675346 AAATAAATTTAATATAA
1 AAATAAATTAAATATAA
45675363 AAATAAATTAAAT-TAA
1 AAATAAATTAAATATAA
45675379 AA
1 AA
45675381 TCAATCCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAAATTAAATATAA
Found at i:45679251 original size:2 final size:2
Alignment explanation
Indices: 45679244--45679286 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
45679234 TTTGTGGTTT
45679244 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
45679286 G
1 G
45679287 GGGAAATTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:45683264 original size:21 final size:21
Alignment explanation
Indices: 45683240--45683287 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
45683230 TGCTTGCTGC
* *
45683240 TGCTGCTGTTGCATTAGT-TGA
1 TGCTGCTGCTGCA-TAATCTGA
*
45683261 TGCTTCTGCTGCATAATCTGA
1 TGCTGCTGCTGCATAATCTGA
45683282 TGCTGC
1 TGCTGC
45683288 ATCTGCCGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (21 bp):
TGCTGCTGCTGCATAATCTGA
Done.