Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000885.1 Hibiscus syriacus cultivar Beakdansim tig00001728_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1639497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1432814 original size:19 final size:18
Alignment explanation
Indices: 1432790--1432825 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1432780 CAACACAAGC
1432790 CTAACGATCAGACATTGAT
1 CTAACGATCAGA-ATTGAT
*
1432809 CTAACGGTCAGAATTGA
1 CTAACGATCAGAATTGA
1432826 AGACCTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (18 bp):
CTAACGATCAGAATTGAT
Found at i:1436916 original size:22 final size:22
Alignment explanation
Indices: 1436891--1436932 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1436881 ATTTATCATG
1436891 TAAAACATTTAACACTTATTCT
1 TAAAACATTTAACACTTATTCT
1436913 TAAAACATTTAACACTTATT
1 TAAAACATTTAACACTTATT
1436933 ATTCTCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAACATTTAACACTTATTCT
Found at i:1438282 original size:20 final size:19
Alignment explanation
Indices: 1438239--1438283 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1438229 CAAAATAATC
* *
1438239 CAATTTCACATTCTAACAT
1 CAATTTCACAATCAAACAT
1438258 CAATTTCAACAATCAAACAT
1 CAATTTC-ACAATCAAACAT
*
1438278 TAATTT
1 CAATTT
1438284 AAAGCATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTTCACAATCAAACAT
Found at i:1444492 original size:30 final size:29
Alignment explanation
Indices: 1444457--1444565 Score: 110
Period size: 30 Copynumber: 3.7 Consensus size: 29
1444447 ATATACGACG
*
1444457 AGTGTCCTTACACACCATAGTGTTGTAATG
1 AGTGTCCTTACACACCATAGT-TTGTAATA
** * *
1444487 AGTGTCCTTACACATTACAGTTATGTATTA
1 AGTGTCCTTACACACCATAGTT-TGTAATA
* * *
1444517 AGTGTCCTTACACACTATAGTACTGTACTA
1 AGTGTCCTTACACACCATAGT-TTGTAATA
*
1444547 AATGTCCTTACACACCATA
1 AGTGTCCTTACACACCATA
1444566 ATACCATATG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 1 0.02
30 65 0.98
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (29 bp):
AGTGTCCTTACACACCATAGTTTGTAATA
Found at i:1448166 original size:18 final size:18
Alignment explanation
Indices: 1448143--1448181 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1448133 GCTTGATCAA
* *
1448143 CTTCATTGTGTTCTTCAT
1 CTTCATAGTCTTCTTCAT
*
1448161 CTTCATAGTCTTCTTCCT
1 CTTCATAGTCTTCTTCAT
1448179 CTT
1 CTT
1448182 TCCTTGGGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.28, G:0.08, T:0.54
Consensus pattern (18 bp):
CTTCATAGTCTTCTTCAT
Found at i:1459330 original size:89 final size:83
Alignment explanation
Indices: 1459154--1459509 Score: 383
Period size: 83 Copynumber: 4.2 Consensus size: 83
1459144 ATTAAGTTTG
* * * * * * *
1459154 ATCTATGGTGGCGTTTTCTCAACAAACGTCGCAACAAAATTTGTACTTTAGCGGCGTTTT-ATAC
1 ATCTATAGTGGCGTTTTTTCAACAAACGCCGCAA-AATATTTATACTTTAGCGGCATTTTCGTAC
*
1459218 AAACACCGCAATAGGTGTA
65 AAACGCCGCAATAGGTGTA
* * * *
1459237 ATCTATAGTGGCATTTTTTCAACAAACGTCACAAAATATTTATACTTTAGCGGCGTTTGTGCGTT
1 ATCTATAGTGGCGTTTTTTCAACAAACGCCGCAAAATATTTATACTTTAGCGGCATTT-T-C---
*
1459302 TGTACAAACGCCGCAATAGGTGTC
61 -GTACAAACGCCGCAATAGGTGTA
* *
1459326 ATCTATAGTGGCGTTTTTTCAACAAACGCCGCAAAATATTTCTACTTGAGCGGCATTTTCGTACA
1 ATCTATAGTGGCGTTTTTTCAACAAACGCCGCAAAATATTTATACTTTAGCGGCATTTTCGTACA
* * *
1459391 AATGACGCAATAGATGTA
66 AACGCCGCAATAGGTGTA
* ** * **
1459409 ATCTATAGTGGCGTTTTTTCAACAAACACCGCAAAATATTTATACTTTAGCTACGTTTTTTTACA
1 ATCTATAGTGGCGTTTTTTCAACAAACGCCGCAAAATATTTATACTTTAGCGGCATTTTCGTACA
**
1459474 AACGCCGCAATAACTGTA
66 AACGCCGCAATAGGTGTA
* *
1459492 TTCTATAGTGAC-TTTTTT
1 ATCTATAGTGGCGTTTTTT
1459510 AAGTAAACGC
Statistics
Matches: 233, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
82 28 0.12
83 131 0.56
87 1 0.00
88 1 0.00
89 72 0.31
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (83 bp):
ATCTATAGTGGCGTTTTTTCAACAAACGCCGCAAAATATTTATACTTTAGCGGCATTTTCGTACA
AACGCCGCAATAGGTGTA
Found at i:1459353 original size:42 final size:42
Alignment explanation
Indices: 1459216--1459509 Score: 124
Period size: 42 Copynumber: 7.0 Consensus size: 42
1459206 GGCGTTTTAT
* * *
1459216 ACAAACACCGCAATAGGTGTAATCTATAGTGGCATTTTTTCA
1 ACAAACGCCGCAATAGATGTAATCTATAGTGGCGTTTTTTCA
* * * * * * * **
1459258 ACAAACGTCACAAAATAT-TTATACTTTAGCGGCGTTTGTGCGTTTGT
1 ACAAACGCCGCAATAGATGTAAT-CTATAGTGGCG-TT-T---TTTCA
* *
1459305 ACAAACGCCGCAATAGGTGTCATCTATAGTGGCGTTTTTTCA
1 ACAAACGCCGCAATAGATGTAATCTATAGTGGCGTTTTTTCA
* * ** *
1459347 ACAAACGCCGCAA-A-ATAT-TTCTACT--TGAGCGGCATTTTCGT
1 ACAAACGCCGCAATAGATGTAATCTA-TAGTG-GC-GTTTTTTC-A
* *
1459388 ACAAATGACGCAATAGATGTAATCTATAGTGGCGTTTTTTCA
1 ACAAACGCCGCAATAGATGTAATCTATAGTGGCGTTTTTTCA
* * * * * * *
1459430 ACAAACACCGCAAAATAT-TTATACTTTAGCT-ACGTTTTTT-T
1 ACAAACGCCGCAATAGATGTAAT-CTATAG-TGGCGTTTTTTCA
* *
1459471 ACAAACGCCGCAATA-ACTGTATTCTATAGTGAC-TTTTTT
1 ACAAACGCCGCAATAGA-TGTAATCTATAGTGGCGTTTTTT
1459510 AAGTAAACGC
Statistics
Matches: 182, Mismatches: 49, Indels: 44
0.66 0.18 0.16
Matches are distributed among these distances:
38 2 0.01
39 6 0.03
40 17 0.09
41 39 0.21
42 65 0.36
43 13 0.07
44 7 0.04
45 3 0.02
46 2 0.01
47 25 0.14
48 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (42 bp):
ACAAACGCCGCAATAGATGTAATCTATAGTGGCGTTTTTTCA
Found at i:1467975 original size:21 final size:21
Alignment explanation
Indices: 1467905--1467980 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
1467895 AGGGAAACAG
* * *
1467905 AGAGAGCAGCAGCAGAAGCAC
1 AGAGAGAAGCAGCGGTAGCAC
*
1467926 AGAGAGAGGCAGCGGTAGCAC
1 AGAGAGAAGCAGCGGTAGCAC
*
1467947 AGAGAGAAGCAGTGGTAGCAC
1 AGAGAGAAGCAGCGGTAGCAC
*
1467968 AGAGAGAAACAGC
1 AGAGAGAAGCAGC
1467981 ATATCAGCAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.41, C:0.18, G:0.37, T:0.04
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGTAGCAC
Found at i:1468475 original size:42 final size:43
Alignment explanation
Indices: 1468358--1468501 Score: 149
Period size: 38 Copynumber: 3.5 Consensus size: 43
1468348 GTTTGTAACA
* * *
1468358 AAAAATGCCGCTATATACCAGACCTTTTGCGGCATTT-T-TAG
1 AAAAATGCCGCTATATACCACACCTTTTGCGACGTTTATATAG
*
1468399 ---AATGCCGCTATATACCAGACCTTTTGCGACGTTTATAT-G
1 AAAAATGCCGCTATATACCACACCTTTTGCGACGTTTATATAG
* **
1468438 AAAAATGCCGCTATATATCACA-CTTTTAGCGGTGTTTATATCAG
1 AAAAATGCCGCTATATACCACACCTTTT-GCGACGTTTATAT-AG
*
1468482 AAAAATGCCGTTATATACCA
1 AAAAATGCCGCTATATACCA
1468502 GACATTTCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
38 32 0.37
39 2 0.02
40 1 0.01
41 5 0.06
42 28 0.32
44 19 0.22
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (43 bp):
AAAAATGCCGCTATATACCACACCTTTTGCGACGTTTATATAG
Found at i:1470786 original size:32 final size:31
Alignment explanation
Indices: 1470748--1470817 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
1470738 AATCTGTTAC
**
1470748 GCATTATATAAATGTGATACTAGCTCTACTGT
1 GCATTATATAAATGCCATACTA-CTCTACTGT
* * *
1470780 GGATTATTTAAATGCCATACTACTCTATTGT
1 GCATTATATAAATGCCATACTACTCTACTGT
1470811 GCATTAT
1 GCATTAT
1470818 TTGAATGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (31 bp):
GCATTATATAAATGCCATACTACTCTACTGT
Found at i:1481225 original size:17 final size:17
Alignment explanation
Indices: 1481203--1481248 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
1481193 CCTATGGTCA
*
1481203 AGTATCGATACCCCTAT
1 AGTATCGGTACCCCTAT
1481220 AGTATCGGTACCCCTAT
1 AGTATCGGTACCCCTAT
1481237 AGTATCGGTACC
1 AGTATCGGTACC
1481249 AAAAATGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (17 bp):
AGTATCGGTACCCCTAT
Found at i:1482145 original size:17 final size:18
Alignment explanation
Indices: 1482123--1482174 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
1482113 GGGTATTACA
1482123 CTTTCTTTTT-ACTTTTC
1 CTTTCTTTTTCACTTTTC
1482140 CTTTCTTTTTGCACTTTTC
1 CTTTCTTTTT-CACTTTTC
* **
1482159 TTTTCGCTTTCACTTT
1 CTTTCTTTTTCACTTT
1482175 GTTTTGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 14 0.47
ACGTcount: A:0.06, C:0.25, G:0.04, T:0.65
Consensus pattern (18 bp):
CTTTCTTTTTCACTTTTC
Found at i:1483243 original size:17 final size:15
Alignment explanation
Indices: 1483223--1483252 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1483213 TATTGTATTC
1483223 TTATTATAT-ATATA
1 TTATTATATAATATA
1483237 TTATTATATAATATA
1 TTATTATATAATATA
1483252 T
1 T
1483253 AGCAGTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATATAATATA
Found at i:1483338 original size:18 final size:17
Alignment explanation
Indices: 1483315--1483353 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1483305 AATATATAAT
1483315 AATAATAATATAAATATA
1 AATAATAATAT-AATATA
*
1483333 AATAATACTATAATATA
1 AATAATAATATAATATA
1483350 AATA
1 AATA
1483354 TTATATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATATAATATA
Found at i:1483370 original size:3 final size:3
Alignment explanation
Indices: 1483352--1483403 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
1483342 ATAATATAAA
1483352 TAT TA- TAT TA- TAT TAT TA- TAT TA- TAT T-T ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
1483393 TAT TAT TAT TA
1 TAT TAT TAT TA
1483404 CTTTTAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 9 0.21
3 33 0.77
4 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1483383 original size:11 final size:13
Alignment explanation
Indices: 1483352--1483401 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
1483342 ATAATATAAA
1483352 TATTATATTATAT
1 TATTATATTATAT
1483365 TATTATATTATA-
1 TATTATATTATAT
1483377 T-TTATATTATTAT
1 TATTATATTA-TAT
1483390 TATTATTATTAT
1 TATTA-TATTAT
1483402 TACTTTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
11 8 0.24
12 3 0.09
13 13 0.39
14 4 0.12
15 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATATTATAT
Found at i:1488535 original size:59 final size:59
Alignment explanation
Indices: 1488436--1488563 Score: 175
Period size: 59 Copynumber: 2.2 Consensus size: 59
1488426 CAACAGGCTG
* * *
1488436 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTATAGATGGTGGACACGACCTTATGTGT
* ** * *
1488495 CATATTCGGGACTGTACTTAAGTATACCTAGTATAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTATAGATGGTGGACACGACCTTATGTGT
*
1488554 CATACTCGGG
1 CATATTCGGG
1488564 TTAGCACTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTATAGATGGTGGACACGACCTTATGTGT
Found at i:1488769 original size:45 final size:45
Alignment explanation
Indices: 1488680--1488806 Score: 229
Period size: 45 Copynumber: 2.8 Consensus size: 45
1488670 GTAAGCATGC
*
1488680 AAATAAGCTTGCGAGCTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1488724 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
1488769 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTAT
1488807 GTTGATACGA
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
44 24 0.30
45 56 0.70
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1495101 original size:34 final size:34
Alignment explanation
Indices: 1495042--1495108 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1495032 TTCTTGAGAG
*
1495042 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTCA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTCA
1495076 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
1495109 AATTACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTCA
Found at i:1496164 original size:33 final size:33
Alignment explanation
Indices: 1496127--1496194 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
1496117 CAAGAAGAAT
*
1496127 TTAAAGTGCTACAACTGTGGGAAGAATGGTCAC
1 TTAAAGTGCTACAACTGTGGGAAGAAGGGTCAC
1496160 TTAAAGTGCTACAACTGTGGGAAGAAGGGTCAC
1 TTAAAGTGCTACAACTGTGGGAAGAAGGGTCAC
1496193 TT
1 TT
1496195 GAAGAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (33 bp):
TTAAAGTGCTACAACTGTGGGAAGAAGGGTCAC
Found at i:1514134 original size:3 final size:3
Alignment explanation
Indices: 1514126--1514166 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
1514116 GGGCCTGTAA
1514126 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT A
1514167 TTTTTTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1516246 original size:32 final size:32
Alignment explanation
Indices: 1516205--1516276 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
1516195 TTCGCATCAG
* *
1516205 GATGTTGAATCCCCAAAGATGCCCCAATATTT
1 GATGTTGAATCCCCAAAAATGCCCCAACATTT
*
1516237 GATGTTGAATCTCCAAAAATGCCCCAACATTT
1 GATGTTGAATCCCCAAAAATGCCCCAACATTT
1516269 GATGTTGA
1 GATGTTGA
1516277 TCAAAGATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAAATGCCCCAACATTT
Found at i:1517353 original size:12 final size:11
Alignment explanation
Indices: 1517338--1517402 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 11
1517328 TTTTCCTTTA
1517338 TTTTTGTTTCTC
1 TTTTT-TTTCTC
1517350 TTTTTTATTTTCTC
1 --TTTT-TTTTCTC
1517364 TTTCTTTTT-TCC
1 TTT-TTTTTCT-C
1517376 TTTCTTTTTCTC
1 TTT-TTTTTCTC
1517388 TTTTTTTT-TC
1 TTTTTTTTCTC
1517398 TTTTT
1 TTTTT
1517403 CTCTTTTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 7 0.15
11 6 0.13
12 21 0.45
13 2 0.04
14 10 0.21
15 1 0.02
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:1517369 original size:18 final size:18
Alignment explanation
Indices: 1517313--1517410 Score: 85
Period size: 18 Copynumber: 5.4 Consensus size: 18
1517303 ATATGTCTTG
*
1517313 TCTTTTTTCTTCATTTTT-
1 TCTTTTTTTTTC-TTTTTC
* * *
1517331 TCCTTTATTTT-TGTTTC
1 TCTTTTTTTTTCTTTTTC
*
1517348 TCTTTTTTATTTTCTCTTTC
1 TC-TTTTT-TTTTCTTTTTC
*
1517368 T-TTTTTCCTTTCTTTTTC
1 TCTTTTT-TTTTCTTTTTC
1517386 TCTTTTTTTTTCTTTTTC
1 TCTTTTTTTTTCTTTTTC
1517404 TCTTTTT
1 TCTTTTT
1517411 GTTCTGATTA
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
16 4 0.06
17 2 0.03
18 43 0.67
19 9 0.14
20 6 0.09
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (18 bp):
TCTTTTTTTTTCTTTTTC
Found at i:1517396 original size:42 final size:42
Alignment explanation
Indices: 1517313--1517408 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 42
1517303 ATATGTCTTG
*
1517313 TCTTTTT-TC-TTCATTTTTTCCTTTATTTTTGTTTCTCTTTT
1 TCTTTTTCTCTTTC-TTTTTTCCTTTATTTTTCTTTCTCTTTT
* *
1517354 T-TATTTTCTCTTTCTTTTTTCCTTTCTTTTTCTCTT-TTTTTT
1 TCT-TTTTCTCTTTCTTTTTTCCTTTATTTTTCT-TTCTCTTTT
1517396 TCTTTTTCTCTTT
1 TCTTTTTCTCTTT
1517409 TTGTTCTGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
40 1 0.02
41 5 0.11
42 35 0.74
43 6 0.13
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (42 bp):
TCTTTTTCTCTTTCTTTTTTCCTTTATTTTTCTTTCTCTTTT
Found at i:1517595 original size:2 final size:2
Alignment explanation
Indices: 1517588--1517619 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1517578 ACAACAAGGG
*
1517588 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1517620 GGACAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1520447 original size:10 final size:9
Alignment explanation
Indices: 1520430--1520468 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1520420 ATCAAAGGGG
1520430 AAAAAATAA
1 AAAAAATAA
1520439 AATAAAATAA
1 AA-AAAATAA
*
1520449 AAAAACTAA
1 AAAAAATAA
*
1520458 AAAAATTAA
1 AAAAAATAA
1520467 AA
1 AA
1520469 TTTTAAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1520489 original size:14 final size:14
Alignment explanation
Indices: 1520433--1520509 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 14
1520423 AAAGGGGAAA
*
1520433 AAATAAAATAAAAT
1 AAATAAAATAAAAG
1520447 AAA-AAAACTAAAA-
1 AAATAAAA-TAAAAG
1520460 AAATTAAAATTTTAAAAG
1 AAA-TAAAA---TAAAAG
* *
1520478 TAATAAAATAAATG
1 AAATAAAATAAAAG
*
1520492 AAATAAAAAAAGAAG
1 AAATAAAATAA-AAG
1520507 AAA
1 AAA
1520510 CCTGCGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
13 7 0.14
14 22 0.44
15 9 0.18
17 10 0.20
18 2 0.04
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAG
Found at i:1521501 original size:15 final size:15
Alignment explanation
Indices: 1521481--1521509 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1521471 AAAAAAAGTT
1521481 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
1521496 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
1521510 CGGTCGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:1522649 original size:19 final size:17
Alignment explanation
Indices: 1522625--1522715 Score: 75
Period size: 17 Copynumber: 5.4 Consensus size: 17
1522615 TTATGCGCAT
1522625 GTGGGTAGTGGTGGATTA
1 GTGGGTAGTGGTGGA-TA
1522643 GGTGGGTAGTGGTGGATA
1 -GTGGGTAGTGGTGGATA
*
1522661 GTGGGTA-AGGTAGG-T-
1 GTGGGTAGTGGT-GGATA
* **
1522676 -TGGATTAGTTAT-GATA
1 GTGG-GTAGTGGTGGATA
1522692 GTGGGTAGTGGTGGATA
1 GTGGGTAGTGGTGGATA
1522709 GTGGGTA
1 GTGGGTA
1522716 TGAACATGGG
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 10 0.18
17 23 0.40
18 2 0.04
19 15 0.26
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.32
Consensus pattern (17 bp):
GTGGGTAGTGGTGGATA
Found at i:1526339 original size:32 final size:32
Alignment explanation
Indices: 1526298--1526377 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
1526288 GGCCAGATGC
*
1526298 TAGTCAGGTTTACATTAAGATAATACACATTA
1 TAGTCAGGTTTACATTAAGATAATACACAATA
* * *
1526330 TAGTCAGGTTTACATTCAGATAATGCATAATA
1 TAGTCAGGTTTACATTAAGATAATACACAATA
* *
1526362 AAGTCAGGTTTGCATT
1 TAGTCAGGTTTACATT
1526378 TAGGTAATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (32 bp):
TAGTCAGGTTTACATTAAGATAATACACAATA
Found at i:1526386 original size:32 final size:32
Alignment explanation
Indices: 1526299--1526386 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 32
1526289 GCCAGATGCT
* * *
1526299 AGTCAGGTTTACATTAAGATAATACACATTAT
1 AGTCAGGTTTACATTAAGATAATGCACAATAA
* *
1526331 AGTCAGGTTTACATTCAGATAATGCATAATAA
1 AGTCAGGTTTACATTAAGATAATGCACAATAA
* * *
1526363 AGTCAGGTTTGCATTTAGGTAATG
1 AGTCAGGTTTACATTAAGATAATG
1526387 AACATGAGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (32 bp):
AGTCAGGTTTACATTAAGATAATGCACAATAA
Found at i:1527023 original size:250 final size:250
Alignment explanation
Indices: 1526582--1527089 Score: 1009
Period size: 250 Copynumber: 2.0 Consensus size: 250
1526572 ACATACTGCT
1526582 TGTGTTTATGGAACTCTTAATGTTGGTCTAGATTAGTGAATATACTACTAGGATTTGTAAGCTTA
1 TGTGTTTATGGAACTCTTAATGTTGGTCTAGATTAGTGAATATACTACTAGGATTTGTAAGCTTA
1526647 ACGTTCATATGTTTTCTAGATTGGGCAGCTCTTGGAGCACCATCGCAGCAGGACTTCAGCATCTC
66 ACGTTCATATGTTTTCTAGATTGGGCAGCTCTTGGAGCACCATCGCAGCAGGACTTCAGCATCTC
1526712 TTTCAGAGTATTGTACCATAGCTTTAGTGGGCATATGTATTCATAGAACCTTGCTCATGTATTTA
131 TTTCAGAGTATTGTACCATAGCTTTAGTGGGCATATGTATTCATAGAACCTTGCTCATGTATTTA
1526777 GATTCATAAGAAAAAGTTTGTAATATTTTGATTTAAGCTATGTATCATGTAGTTC
196 GATTCATAAGAAAAAGTTTGTAATATTTTGATTTAAGCTATGTATCATGTAGTTC
1526832 TGTGTTTATGGAACTCTTAATGTTGGTCTAGATTAGTGAATATACTACTAGGATTTGTAAGCTTA
1 TGTGTTTATGGAACTCTTAATGTTGGTCTAGATTAGTGAATATACTACTAGGATTTGTAAGCTTA
1526897 ACGTTCATATGTTTTCTAGATTGGGCAGCTCTTGGAGCACCATCGCAGCAGGACTTCAGCATCTC
66 ACGTTCATATGTTTTCTAGATTGGGCAGCTCTTGGAGCACCATCGCAGCAGGACTTCAGCATCTC
1526962 TTTCAGAGTATTGTACCATAGCTTTAGTGGGCATATGTATTCATAGAACCTTGCTCATGTATTTA
131 TTTCAGAGTATTGTACCATAGCTTTAGTGGGCATATGTATTCATAGAACCTTGCTCATGTATTTA
1527027 GATTCATAAGAAAAAGTTTGTAATATTTTGATTTAAGCTATGTATCATGTAGTTC
196 GATTCATAAGAAAAAGTTTGTAATATTTTGATTTAAGCTATGTATCATGTAGTTC
1527082 TG-GTTTAT
1 TGTGTTTAT
1527090 AAAATGTTTT
Statistics
Matches: 258, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
249 6 0.02
250 252 0.98
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (250 bp):
TGTGTTTATGGAACTCTTAATGTTGGTCTAGATTAGTGAATATACTACTAGGATTTGTAAGCTTA
ACGTTCATATGTTTTCTAGATTGGGCAGCTCTTGGAGCACCATCGCAGCAGGACTTCAGCATCTC
TTTCAGAGTATTGTACCATAGCTTTAGTGGGCATATGTATTCATAGAACCTTGCTCATGTATTTA
GATTCATAAGAAAAAGTTTGTAATATTTTGATTTAAGCTATGTATCATGTAGTTC
Found at i:1536358 original size:21 final size:20
Alignment explanation
Indices: 1536321--1536383 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
1536311 CCGTTAGACA
*
1536321 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
1536341 GGGGGAATCTGTTCCCCCTGG
1 GGGGGAATCTGTACCCCCT-G
1536362 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
1536382 GG
1 GG
1536384 CAATCTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 20 0.51
21 19 0.49
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.19
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:1549018 original size:23 final size:22
Alignment explanation
Indices: 1548981--1549026 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1548971 ACCAATACTA
*
1548981 TATATAGTATCGATACTACTTAG
1 TATATAATATCGATACT-CTTAG
*
1549004 TATATAATATTGATACTCTTAG
1 TATATAATATCGATACTCTTAG
1549026 T
1 T
1549027 GATGGTACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATATAATATCGATACTCTTAG
Found at i:1559410 original size:138 final size:138
Alignment explanation
Indices: 1559165--1559418 Score: 366
Period size: 138 Copynumber: 1.8 Consensus size: 138
1559155 CCGAAATGAA
** *
1559165 AATTCACAAACTCATTATGAATTTCATGGATGCACACATAGTGTCGAAAGTAAACACAATACTGA
1 AATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTCAAAAGTAAACACAATACTGA
*
1559230 TACGAAAATGCACCGTTATGCATTAAACAAAATAGATCGATAACTTTTATACATAATTGTATATA
66 TACGAAAATGCACCGTTATGCATTAAACAAAATAGATCGATAACGTTTATACATAATTGTATATA
1559295 GAAATGGT
131 GAAATGGT
** * * * * *
1559303 AATTCACAAACTCATTATGAATACCAT-GATTGCACATTTATTGTCAAAAGTACACATAGTACTT
1 AATTCACAAACTCATTATGAATACCATGGA-TGCACACATAGTGTCAAAAGTAAACACAATACTG
* * *
1559367 ATACGAAAATGCACTGTTATGCATTAAACAAAATCGATTGATAACGTTTATA
65 ATACGAAAATGCACCGTTATGCATTAAACAAAATAGATCGATAACGTTTATA
1559419 AACAATTTAT
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
137 2 0.02
138 99 0.98
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (138 bp):
AATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTCAAAAGTAAACACAATACTGA
TACGAAAATGCACCGTTATGCATTAAACAAAATAGATCGATAACGTTTATACATAATTGTATATA
GAAATGGT
Found at i:1562557 original size:28 final size:28
Alignment explanation
Indices: 1562517--1562604 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 28
1562507 CCCATTTAAG
*
1562517 ACATATCATCTTGTACTTAATCTTTGTA
1 ACATGTCATCTTGTACTTAATCTTTGTA
* * *
1562545 ACATGTCATCTTGCACATAA-CATTTATA
1 ACATGTCATCTTGTACTTAATC-TTTGTA
*
1562573 ATATGTCATCTTGTACTTAATCTTTGTA
1 ACATGTCATCTTGTACTTAATCTTTGTA
1562601 ACAT
1 ACAT
1562605 ATAGAATCAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.02
28 47 0.96
29 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (28 bp):
ACATGTCATCTTGTACTTAATCTTTGTA
Found at i:1562630 original size:56 final size:55
Alignment explanation
Indices: 1562522--1562631 Score: 132
Period size: 56 Copynumber: 2.0 Consensus size: 55
1562512 TTAAGACATA
* * * *
1562522 TCATCTTGTACTTAATCTTTGTAACATGTCATCTTGCACATAACATTTATAATATG
1 TCATCTTGTACTTAATCTTTGTAACATATAATCATGCACATAACA-TCATAATATG
**
1562578 TCATCTTGTACTTAATCTTTGTAACATATAGAATCATGCATTTAACA-CATAATA
1 TCATCTTGTACTTAATCTTTGTAACATAT--AATCATGCACATAACATCATAATA
1562632 ATATATCACA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 34 0.74
58 12 0.26
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (55 bp):
TCATCTTGTACTTAATCTTTGTAACATATAATCATGCACATAACATCATAATATG
Found at i:1562847 original size:21 final size:21
Alignment explanation
Indices: 1562823--1562969 Score: 159
Period size: 21 Copynumber: 7.0 Consensus size: 21
1562813 AGATGACTTG
* *
1562823 TATGTCCTGAAAGACCTCATA
1 TATGTCCCGAAGGACCTCATA
* *** *
1562844 TATGTCCCAAAGGATGACATG
1 TATGTCCCGAAGGACCTCATA
* * **
1562865 TATATCCCGATGGACCTTGTA
1 TATGTCCCGAAGGACCTCATA
*
1562886 TATGTCCCGAAGGACCTCGTA
1 TATGTCCCGAAGGACCTCATA
1562907 TATGTCCCGAAGGACCTCATA
1 TATGTCCCGAAGGACCTCATA
* *
1562928 TATGTCCTGAAGGACCTCGTA
1 TATGTCCCGAAGGACCTCATA
*
1562949 TATGTCCCGAAGGACCACATA
1 TATGTCCCGAAGGACCTCATA
1562970 GAACCCTCGA
Statistics
Matches: 101, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 101 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (21 bp):
TATGTCCCGAAGGACCTCATA
Found at i:1562860 original size:42 final size:42
Alignment explanation
Indices: 1562789--1562934 Score: 132
Period size: 42 Copynumber: 3.5 Consensus size: 42
1562779 AAATTATCCT
* * * * *
1562789 GAAGGATCTCATATATGTTACGAAA-GATGACTTGTATGTCCT
1 GAAGGACCTCATATATG-TCCCAAAGGATGACATGTATGTCCC
* *
1562831 GAAAGACCTCATATATGTCCCAAAGGATGACATGTATATCCC
1 GAAGGACCTCATATATGTCCCAAAGGATGACATGTATGTCCC
* ** * *** * *
1562873 GATGGACCTTGTATATGTCCCGAAGGACCTCGTATATGTCCC
1 GAAGGACCTCATATATGTCCCAAAGGATGACATGTATGTCCC
1562915 GAAGGACCTCATATATGTCC
1 GAAGGACCTCATATATGTCC
1562935 TGAAGGACCT
Statistics
Matches: 82, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
41 5 0.06
42 77 0.94
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (42 bp):
GAAGGACCTCATATATGTCCCAAAGGATGACATGTATGTCCC
Found at i:1562943 original size:63 final size:63
Alignment explanation
Indices: 1562823--1562969 Score: 177
Period size: 63 Copynumber: 2.3 Consensus size: 63
1562813 AGATGACTTG
* * ** * * *
1562823 TATGTCCTGAAAGACCTCATATATGTCCCAAAGGATGACATGTATATCCCGATGGACCTTGTA
1 TATGTCCCGAAGGACCTCATATATGTCCCAAAGGACCACATATATATCCCGAAGGACCTCGTA
* * * * *
1562886 TATGTCCCGAAGGACCTCGTATATGTCCCGAAGGACCTCATATATGTCCTGAAGGACCTCGTA
1 TATGTCCCGAAGGACCTCATATATGTCCCAAAGGACCACATATATATCCCGAAGGACCTCGTA
*
1562949 TATGTCCCGAAGGACCACATA
1 TATGTCCCGAAGGACCTCATA
1562970 GAACCCTCGA
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (63 bp):
TATGTCCCGAAGGACCTCATATATGTCCCAAAGGACCACATATATATCCCGAAGGACCTCGTA
Found at i:1563155 original size:33 final size:33
Alignment explanation
Indices: 1563102--1563204 Score: 145
Period size: 33 Copynumber: 3.1 Consensus size: 33
1563092 ATCATGTAGC
* *
1563102 TTGTATAACATTATTGTATGATCTCATAGATCA
1 TTGTGTAACATTCTTGTATGATCTCATAGATCA
* *
1563135 TTGTGTAACATTCTTATATGAGT-TCATAGATCC
1 TTGTGTAACATTCTTGTATGA-TCTCATAGATCA
*
1563168 TTGTGTAACATTCTTGTATGATCTCATAGATCT
1 TTGTGTAACATTCTTGTATGATCTCATAGATCA
1563201 TTGT
1 TTGT
1563205 CATATAACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.02
33 60 0.97
34 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (33 bp):
TTGTGTAACATTCTTGTATGATCTCATAGATCA
Found at i:1564543 original size:29 final size:31
Alignment explanation
Indices: 1564493--1564554 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
1564483 ATTTTGGTCC
* *
1564493 CTAAACATTTTCAAAGTTTATACTTTGATCA
1 CTAAACATTTACAAAGTTTATAATTTGATCA
*
1564524 CTAAAC-TTTACAAA-TTTATAATTTGGTCA
1 CTAAACATTTACAAAGTTTATAATTTGATCA
1564553 CT
1 CT
1564555 CACTAAATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
30 7 0.25
31 6 0.21
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (31 bp):
CTAAACATTTACAAAGTTTATAATTTGATCA
Found at i:1567331 original size:30 final size:30
Alignment explanation
Indices: 1567297--1567358 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1567287 ATAAAGATTT
1567297 GGACCAATTT-ATAATTTTGAAAAAGTTATG
1 GGACCAATTTGATAATTTTG-AAAAGTTATG
*
1567327 GGACCATTTTGATAATTTTGAAAAGTTATG
1 GGACCAATTTGATAATTTTGAAAAGTTATG
1567357 GG
1 GG
1567359 TTTGATGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 21 0.70
31 9 0.30
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (30 bp):
GGACCAATTTGATAATTTTGAAAAGTTATG
Found at i:1569117 original size:18 final size:18
Alignment explanation
Indices: 1569084--1569144 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
1569074 ACTTGAAAAT
1569084 AATCTGAAATTAAGTTATG
1 AATCTGAAA-TAAGTTATG
1569103 AATCTGAAATAAGTTATG
1 AATCTGAAATAAGTTATG
* * * *
1569121 AGTCCAGAAACAAGTTCTG
1 AAT-CTGAAATAAGTTATG
1569140 AATCT
1 AATCT
1569145 AAGAATGAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 12 0.34
19 23 0.66
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (18 bp):
AATCTGAAATAAGTTATG
Found at i:1569775 original size:3 final size:3
Alignment explanation
Indices: 1569767--1569794 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1569757 TTTTTGCCCC
1569767 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1569795 CTTAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1571118 original size:53 final size:54
Alignment explanation
Indices: 1571056--1571164 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
1571046 TTTAATACGT
*
1571056 TAATTATTATTCTTCATTTTATC-TTTATTTAATTTTAATTACATTAATATATA
1 TAATTATTATTCTTCATTTTATCTTTTATTTAATTTTAATCACATTAATATATA
* *
1571109 TAATTATTATTCTTCATTTTATCTTTTTTTTAATTTTAGTCACATTAATATATA
1 TAATTATTATTCTTCATTTTATCTTTTATTTAATTTTAATCACATTAATATATA
1571163 TA
1 TA
1571165 TATATATATG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 23 0.44
54 29 0.56
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (54 bp):
TAATTATTATTCTTCATTTTATCTTTTATTTAATTTTAATCACATTAATATATA
Found at i:1585174 original size:134 final size:133
Alignment explanation
Indices: 1584942--1588396 Score: 4074
Period size: 134 Copynumber: 25.9 Consensus size: 133
1584932 TAACCAGTTG
* * * *
1584942 TCCCCAGTAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTTATTACTTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * *
1585007 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTATGAGCGCTATCAATATTAGATAACCA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCGC-GTCAACACTAGATAACCA
*
1585072 ACCA
130 GCCA
* *
1585076 TCCCCAGCAGAGTGGAACCTTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCGCGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * *
1585141 GAGTCGTGTCATCCACTGACCAGATCTCTTCATCACGTAGGAACAGCGTCAACATTAGATAACCA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACCA
* *
1585206 GTCG
130 GCCA
* * * * * **
1585210 TCTCCA-TAGAGTAGAACCATGTTATTATCATTCCTAAAGATAACCAGAACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* *
1585274 GA-TCCGTGTCATCCACTGACCAGATCTTCTCATCACGTAGGAGCAGCGTCAACATTAGATAACC
66 GAGT-CGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACC
1585338 AGCCA
129 AGCCA
* * * *
1585343 T-CCCAGCAAAGTGGAATCGTGTTATCATCATTCCTAAAGATGGCCAGAGCTCTTCATCATGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * ** *
1585407 GA-ACTGTGTCATCCACTGACCAGATCTCCTCATCACATAGGAGCAGTATCAACATTAGATAACC
66 GAGTC-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACC
*
1585471 AACCA
129 AGCCA
** *
1585476 TCAACAGCAGAGTGGAACCGTG-T-T-ATCATTCCTAAAGATGGCCAGAACTCTTCATAACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * * * *
1585538 GAGTCGTGTCATGCATTGAACAGATCTCCTCATCACGTAGGAGCAACGTCAACATTAGATAACTA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACCA
* *
1585603 GTCG
130 GCCA
* *
1585607 TCCCCAGCAGAGTGGAACTGTGTTATCATCATTCCTAAAGATGACCAGAACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * *
1585672 GAGTCGCGTCATCCACTGACCAGATCTCTTCATCACGTAGGAGCAGCGTCAACACAAGATAACCA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACCA
1585737 GCCA
130 GCCA
* * * *
1585741 TCCCCA-AATGAGTGGAATCATGTTATCATCATTCTTAAAGATGGCCAAGAACTCTTCATCACGT
1 TCCCCAGCA-GAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCC-AGAACTCTTCATCACGT
* *
1585805 ATGAG-CAGTGTCAACC-CCGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGATAA
64 ATGAGTC-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAA
1585868 CCAGCCA
127 CCAGCCA
* * * *
1585875 TTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGTCCAAAACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
*
1585940 AAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTTA-GAGCAGCGTCAACACTAGATAACC
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACG-TAGGAGC-GCGTCAACACTAGATAACC
*
1586004 AGCCG
129 AGCCA
* ** *
1586009 TCCCGAGCAGTCTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGAACTCTTCATCACGTA
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCC-AGAACTCTTCATCACGTA
* * * * *
1586074 TGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGC-CATGTCAACTC-AGATAAA
65 TGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCGC--GTCAACACTAGATAAC
** *
1586137 CAATCG
128 CAGCCA
* *
1586143 TCCCCATCAGAGTGGAACCGTGTTATCATCATTCCTAAAGAGGGCCA-AACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * *
1586207 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGAAGCATCAACACTAGATAACAA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAG-CGCGTCAACACTAGATAACCA
*
1586272 GCCG
130 GCCA
* * * *
1586276 TCCCCAGCAGAGTGGAACCGTGTTATTATAATTTCTAAAGATGGCCAAAACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * * ** *
1586341 GAGAT-ATGTCATCCATTGACTAGATCTCCTCATTACGTAGGAGCAAAGTCAACACTGGATAACC
66 GAG-TCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACC
1586405 AGCCA
129 AGCCA
* * *
1586410 TCCCCAGTAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGCCAATAACTCTTCATCACGTA
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCC-AGAACTCTTCATCACGTA
* *
1586475 TGAG-CAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCAACACTAGATAAC
65 TGAGTC-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAG-CGCGTCAACACTAGATAAC
* *
1586539 CAACTA
128 CAGCCA
* * * * * * *
1586545 TTCCCAGTAGAGTGGAACCATGTTATCATCATTCCTAAATATGGCCAGAACTCTTCGTCGCCTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * *
1586610 GAGTCGTATCATCCACTGACCAGATATCCTAATCACGTAAGAGCAGCGTCAACACTAGATAACCA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACCA
*
1586675 GTCA
130 GCCA
* * * *
1586679 TCTCGAGCAGACTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGAACTCTTCATCACGTA
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCC-AGAACTCTTCATCACGTA
* * * *
1586744 TGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGC-CATGTCAACTC-AGATAAC
65 TGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCGC--GTCAACACTAGATAAC
***
1586807 CAGTTG
128 CAGCCA
*
1586813 TCCCCAGCAGACTGGAACCGTGTTATCATCATTCCTAAAGATGGCCA-AACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * *
1586877 GAGTCATGTCATCCACTGACCAGATCTCCTCATCATGTAGGAGAAGCGTCAACACTAGATAACAA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAG-CGCGTCAACACTAGATAACCA
1586942 G-CA
130 GCCA
* * * *
1586945 TCCCCAGCAGAGTGGAACCGTGTTATTATAATTTCTAAAGATGGCCAAAACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * * *
1587010 GAGAT-GTGTCATCCACTGACCAGGTCTGCTCATTATGTAGGAGCGACGTCAACACTGGATAACC
66 GAG-TCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCG-CGTCAACACTAGATAACC
* *
1587074 AGTCG
129 AGCCA
* * *
1587079 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGTCAATAACTCTTCATCACGTA
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGG-CCAGAACTCTTCATCACGTA
* *
1587144 TGAG-CAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCAACACTAGATAAC
65 TGAGTC-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAG-CGCGTCAACACTAGATAAC
*
1587208 CAACCA
128 CAGCCA
* * * * *
1587214 TTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGACCAGAACTCTTCATCTCCTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * *
1587279 GAGTTGTGTCATCCACTGACCAGATCTCCTCATCACATAAGAGCAGCGTCAACATTAGATAACCA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACCA
*
1587344 GTCA
130 GCCA
* * **
1587348 TCCCGAGCAGACTGGAACTATGTT-TCATCATTCCTAAAGATGGCCAAGAACTCTTCATCACGTA
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCC-AGAACTCTTCATCACGTA
* * * * * *
1587412 TGAGTAGTGGCATCCCCCGACCAGATCTCCTCATCACGTTGGAGC-CATGTCAACTC-AGATAAC
65 TGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCGC--GTCAACACTAGATAAC
* *
1587475 CAGTCG
128 CAGCCA
* *
1587481 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTTCTAAAGATGGTCA-AACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * *
1587545 GAGTCGTG---T-CA-TGAACTGATCTCCTCATCACGTA-GAGCAGCGTCAACACTAGATAACAA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACCA
*
1587604 GCCG
130 GCCA
* * * * * *
1587608 TCCCCAGCAGAGTGGAACCGTGTTATTATAATTCTTAAAGATGGCTAGAACTCTTAATGACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * *
1587673 GAGTTGTGTCATCCACTGACCAAATCTCCTCATCACGTAGGAGTAGCGTCAATACTAGATAACCA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAG-CGCGTCAACACTAGATAACCA
*
1587738 GCCG
130 GCCA
* * * * * *
1587742 TCCCCAGCGGATTGGAACCGTGTTATCATCATTTCTAAAAATGGCCAATAACTCTTCATCACATA
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCC-AGAACTCTTCATCACGTA
* * * *
1587807 TGAG-CAGTCTCATCC-CCGACCAGATCTCCTAATCACGTAGGAGCTGCGTTAACACTAGATAAC
65 TGAGTC-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAAC
* *
1587870 CAGTCG
128 CAGCCA
* * *** *
1587876 TCCCCAACAGAGTGAAATTATGTTATCATCATTCCTAAGGATGGCCAGAACTCTTCATCACGTAT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* * * * *
1587941 GAGCCGTGTCATCCACTAACCAGATCTCCTTATCATGTAGGAGCAGTGTCAACACTAGATAACCA
66 GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGC-GCGTCAACACTAGATAACCA
*
1588006 GCCG
130 GCCA
* *
1588010 TCCCCAGCACAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCA-ATATCTCTTCATCACGT
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGA-A-CTCTTCATCACGT
* * * *
1588074 ATGAG-CAGTGTCATCCCCCGACCAGATCTCCTCATCACGTTGGAGCCGTGTCAAC-CTCAGATA
64 ATGAGTC-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAG-CGCGTCAACACT-AGATA
**
1588137 ACCAGGAA
126 ACCAGCCA
* * *
1588145 T-CCCAGCAGAGTGGAACCGTTTTATAATCATTCCTAAAGATGGACAAGAACTCTTCATCACGTA
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGG-CCAGAACTCTTCATCACGTA
* * * * * * *
1588209 TGAGTAGTGTCATCCCCCGACCATATCTCCTCATCACGTAGGAGCCGTGTTAACTC-AGATAACC
65 TGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAG-CGCGTCAACACTAGATAACC
*
1588273 CGCCA
129 AGCCA
*
1588278 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGACAAGAACTCTTCATCACGTA
1 TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGG-CCAGAACTCTTCATCACGTA
* * * *
1588343 TGAG-CAGTGTCATCCCCCGACCGGATCTCCTCATCACGTAGGAGCCGTGTCAAC
65 TGAGTC-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAG-CGCGTCAAC
1588397 TGTTAGAGTA
Statistics
Matches: 2859, Mismatches: 383, Indels: 158
0.84 0.11 0.05
Matches are distributed among these distances:
126 11 0.00
127 71 0.02
128 24 0.01
129 1 0.00
131 110 0.04
132 204 0.07
133 506 0.18
134 1442 0.50
135 485 0.17
136 5 0.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (133 bp):
TCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
GAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCGCGTCAACACTAGATAACCAG
CCA
Found at i:1586368 original size:669 final size:668
Alignment explanation
Indices: 1584941--1588396 Score: 4616
Period size: 669 Copynumber: 5.2 Consensus size: 668
1584931 ATAACCAGTT
* * * * * *
1584941 GTCCCCAGTAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAGAACTCTTTATTACTTA
1 GTCCCCAGCAGAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCAAAACTCTTCATCACGTA
* * * *
1585006 TGAG-TCGTGTCATCCACTGACCAGATCTCCTCATCACGTATGAGC-GCTATCAATATTAGATAA
66 TGAGAT-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCAGC-GTCAACACTAGATAA
* * * * *
1585069 CCAACCATCCCCAGCAGAGTGGAACCTTGTTATCATCATTCCTAAAGATGGCC-AGAACTCTTCA
129 CCAGCCATCCCCA-AAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGCCAATAACTCTTCA
* * * * * *
1585133 TCGCGTATGAGTC-GTGTCATCCACTGACCAGATCTCTTCATCACGTAGGAACAGCGTCAACATT
193 TCACGTATGAG-CAGTGTCA-CCCCCGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACT
* * * * * *
1585197 AGATAACCAGTC-GTCTCCA-TAGAGTAGAACCATGTTATTATCATTCCTAAAGATAACCAGAAC
256 AGATAACCAGCCATTC-CCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGACCAGAAC
*
1585260 TCTTCATCACGTATGA-TCCGTGTCATCCACTGACCAGATCTTCTCATCACG-TAGGAGCAGCGT
320 TCTTCATCACGTATGAGT-CGTGTCATCCACTGACCAGATCTCCTCATCACGTTA-GAGCAGCGT
* * *
1585323 CAACATTAGATAACCAGCCATCCC-AGCAAAGTGGAA-TCGTGTTATCATCATTCCTAAAGATGG
383 CAACACTAGATAACCAGCCATCCCGAGCAGACTGGAACT-GTGTTATCATCATTCCTAAAGATGG
* * * * * *
1585386 CC-AGAGCTCTTCATCATGTATGAACT-GTGTCATCCACTGACCAGATCTCCTCATCACATAGGA
447 CCAAGAACTCTTCATCACGTATG-AGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGA
* * ** * **
1585449 G-CAGTATCAACATTAGATAACCAACCATCAACAGCAGAGTGGAACCGTG-T-T-ATCATTCCTA
511 GCCA-TGTCAAC-TCAGATAACCAGTCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTA
* * * *
1585510 AAGATGGCCAGAACTCTTCATAACGTATGAGTCGTGTCATGCATTGAACAGATCTCCTCATCACG
574 AAGATGGCCA-AACTCTTCATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACG
* * *
1585575 TAGGAGCAA-CGTCAACATTAGATAACTAGTC
638 TAGGAG-AAGCGTCAACACTAGATAACAAGCC
* * * *
1585606 GTCCCCAGCAGAGTGGAACTGTGTTATCATCATTCCTAAAGATGACCAGAACTCTTCATCACGTA
1 GTCCCCAGCAGAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCAAAACTCTTCATCACGTA
* * *
1585671 TGAG-TCGCGTCATCCACTGACCAGATCTCTTCATCACGTAGGAGCAGCGTCAACACAAGATAAC
66 TGAGAT-GTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGATAAC
* * * * *
1585735 CAGCCATCCCCAAATGAGTGGAATCATGTTATCATCATTCTTAAAGATGGCCAAGAACTCTTCAT
130 CAGCCATCCCCAAA-GAGTGGAACCGTGTTATCATCATTCCTAAAAATGGCCAATAACTCTTCAT
*
1585800 CACGTATGAGCAGTGTCAACCCCGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGA
194 CACGTATGAGCAGTGTCACCCCCGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGA
* *
1585865 TAACCAGCCATTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGTCCAAAACTCTT
259 TAACCAGCCATTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGACCAGAACTCTT
*
1585930 CATCACGTATAAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTTAGAGCAGCGTCAACAC
324 CATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTTAGAGCAGCGTCAACAC
* *
1585995 TAGATAACCAGCCGTCCCGAGCAGTCTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGAA
389 TAGATAACCAGCCATCCCGAGCAGACTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGAA
1586060 CTCTTCATCACGTATGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTC
454 CTCTTCATCACGTATGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTC
* * * *
1586125 AACTCAGATAAACAATCGTCCCCATCAGAGTGGAACCGTGTTATCATCATTCCTAAAGAGGGCCA
519 AACTCAGATAACCAGTCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCA
*
1586190 AACTCTTCATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGAAGCA
584 AACTCTTCATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGAAGCG
1586255 TCAACACTAGATAACAAGCC
649 TCAACACTAGATAACAAGCC
* *
1586275 GTCCCCAGCAGAGTGGAACCGTGTTATTATAATTTCTAAAGATGGCCAAAACTCTTCATCACGTA
1 GTCCCCAGCAGAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCAAAACTCTTCATCACGTA
* * * * ** *
1586340 TGAGATATGTCATCCATTGACTAGATCTCCTCATTACGTAGGAGCAAAGTCAACACTGGATAACC
66 TGAGATGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGATAACC
*
1586405 AGCCATCCCCAGTAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGCCAATAACTCTTCATC
131 AGCCATCCCCA-AAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGCCAATAACTCTTCATC
*
1586470 ACGTATGAGCAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCAACACTAGA
195 ACGTATGAGCAGTGTCA-CCCCCGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGA
* * * * *
1586535 TAACCAACTATTCCCAGTAGAGTGGAACCATGTTATCATCATTCCTAAATATGGCCAGAACTCTT
259 TAACCAGCCATTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGACCAGAACTCTT
* * * * * * *
1586600 CGTCGCCTATGAGTCGTATCATCCACTGACCAGATATCCTAATCACGTAAGAGCAGCGTCAACAC
324 CATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTTAGAGCAGCGTCAACAC
* *
1586665 TAGATAACCAGTCATCTCGAGCAGACTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGAA
389 TAGATAACCAGCCATCCCGAGCAGACTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGAA
1586730 CTCTTCATCACGTATGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTC
454 CTCTTCATCACGTATGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTC
* *
1586795 AACTCAGATAACCAGTTGTCCCCAGCAGACTGGAACCGTGTTATCATCATTCCTAAAGATGGCCA
519 AACTCAGATAACCAGTCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCA
* *
1586860 AACTCTTCATCACGTATGAGTCATGTCATCCACTGACCAGATCTCCTCATCATGTAGGAGAAGCG
584 AACTCTTCATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGAAGCG
1586925 TCAACACTAGATAACAAG-C
649 TCAACACTAGATAACAAGCC
* * *
1586944 ATCCCCAGCAGAGTGGAACCGTGTTATTATAATTTCTAAAGATGGCCAAAACTCTTCATCACGTA
1 GTCCCCAGCAGAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCAAAACTCTTCATCACGTA
* * * * *
1587009 TGAGATGTGTCATCCACTGACCAGGTCTGCTCATTATGTAGGAGC-GACGTCAACACTGGATAAC
66 TGAGATGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCAG-CGTCAACACTAGATAAC
* * * *
1587073 CAGTCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGTCAATAACTCTTCAT
130 CAGCCATCCCCA-AAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGCCAATAACTCTTCAT
*
1587138 CACGTATGAGCAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCAACACTAG
194 CACGTATGAGCAGTGTCA-CCCCCGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAG
*
1587203 ATAACCAACCATTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGACCAGAACTCT
258 ATAACCAGCCATTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGACCAGAACTCT
* * * * *
1587268 TCATCTCCTATGAGTTGTGTCATCCACTGACCAGATCTCCTCATCACATAAGAGCAGCGTCAACA
323 TCATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTTAGAGCAGCGTCAACA
* * *
1587333 TTAGATAACCAGTCATCCCGAGCAGACTGGAACTATGTT-TCATCATTCCTAAAGATGGCCAAGA
388 CTAGATAACCAGCCATCCCGAGCAGACTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGA
* *
1587397 ACTCTTCATCACGTATGAGTAGTGGCATCCCCCGACCAGATCTCCTCATCACGTTGGAGCCATGT
453 ACTCTTCATCACGTATGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGT
* *
1587462 CAACTCAGATAACCAGTCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTTCTAAAGATGGTC
518 CAACTCAGATAACCAGTCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCC
* * *
1587527 AAACTCTTCATCACGTATGAGTCGTG---T-CA-TGAACTGATCTCCTCATCACGTA-GAGCAGC
583 AAACTCTTCATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGAAGC
1587586 GTCAACACTAGATAACAAGCC
648 GTCAACACTAGATAACAAGCC
* * * * * *
1587607 GTCCCCAGCAGAGTGGAACCGTGTTATTATAATTCTTAAAGATGGCTAGAACTCTTAATGACGTA
1 GTCCCCAGCAGAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCAAAACTCTTCATCACGTA
* * * *
1587672 TGAGTTGTGTCATCCACTGACCAAATCTCCTCATCACGTAGGAGTAGCGTCAATACTAGATAACC
66 TGAGATGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGATAACC
* ** * *
1587737 AGCCGTCCCCAGCGGATTGGAACCGTGTTATCATCATTTCTAAAAATGGCCAATAACTCTTCATC
131 AGCCATCCCCA-AAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGCCAATAACTCTTCATC
* * * * * *
1587802 ACATATGAGCAGTCTCATCCCCGACCAGATCTCCTAATCACGTAGGAGCTGCGTTAACACTAGAT
195 ACGTATGAGCAGTGTCACCCCCGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGAT
* * * * * ** * *
1587867 AACCAGTCGTCCCCAACAGAGTGAAATTATGTTATCATCATTCCTAAGGATGGCCAGAACTCTTC
260 AACCAGCCATTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGACCAGAACTCTTC
* * * * *
1587932 ATCACGTATGAGCCGTGTCATCCACTAACCAGATCTCCTTATCATG-TAGGAGCAGTGTCAACAC
325 ATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTTA-GAGCAGCGTCAACAC
* * * * * * * *
1587996 TAGATAACCAGCCGTCCCCAGCACAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCAATAT
389 TAGATAACCAGCCATCCCGAGCAGACTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGAA
* * *
1588061 CTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAGATCTCCTCATCACGTTGGAGCCGTGTC
454 CTCTTCATCACGTATGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTC
*** * *
1588126 AACCTCAGATAACCAGGAAT-CCCAGCAGAGTGGAACCGTTTTATAATCATTCCTAAAGATGGAC
519 AA-CTCAGATAACCAGTCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGG-C
* * * * * **
1588190 AAGAACTCTTCATCACGTATGAGTAGTGTCATCCCCCGACCATATCTCCTCATCACGTAGGAGCC
582 CA-AACTCTTCATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGAA
* * * **
1588255 GTGTTAACTC-AGATAACCCGCC
646 GCGTCAACACTAGATAACAAGCC
* * *
1588277 ATCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGACAAGAACTCTTCATCACGT
1 GTCCCCAGCAGAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCAA-AACTCTTCATCACGT
* * * * *
1588342 ATGAGCA-GTGTCATCCCCCGACCGGATCTCCTCATCACGTAGGAGCCGTGTCAAC
65 ATGAG-ATGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAAC
1588397 TGTTAGAGTA
Statistics
Matches: 2504, Mismatches: 251, Indels: 66
0.89 0.09 0.02
Matches are distributed among these distances:
661 1 0.00
662 206 0.08
663 334 0.13
664 19 0.01
665 236 0.09
666 147 0.06
667 71 0.03
668 238 0.10
669 665 0.27
670 518 0.21
671 69 0.03
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (668 bp):
GTCCCCAGCAGAGTGGAACCGTGTTATCATAATTCCTAAAGATGGCCAAAACTCTTCATCACGTA
TGAGATGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGATAACC
AGCCATCCCCAAAGAGTGGAACCGTGTTATCATCATTCCTAAAAATGGCCAATAACTCTTCATCA
CGTATGAGCAGTGTCACCCCCGACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACACTAGATA
ACCAGCCATTCCCAGCAGAGTGGAACCATGTTATCATCATTCCTAAAGATGACCAGAACTCTTCA
TCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTTAGAGCAGCGTCAACACTA
GATAACCAGCCATCCCGAGCAGACTGGAACTGTGTTATCATCATTCCTAAAGATGGCCAAGAACT
CTTCATCACGTATGAGTAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGTCAA
CTCAGATAACCAGTCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAAA
CTCTTCATCACGTATGAGTCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAGAAGCGTC
AACACTAGATAACAAGCC
Found at i:1589489 original size:90 final size:90
Alignment explanation
Indices: 1589368--1589543 Score: 307
Period size: 90 Copynumber: 2.0 Consensus size: 90
1589358 TAATCCCAAA
* * *
1589368 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
1589433 TAGGTTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
1589458 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
1589523 TAGGGTAACTTGGCTATAAAA
66 TAGGGTAACTTGGATATAAAA
1589544 TGGTGTGTTA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:1590063 original size:133 final size:131
Alignment explanation
Indices: 1589860--1590223 Score: 364
Period size: 133 Copynumber: 2.7 Consensus size: 131
1589850 GGTCCCAACA
*
1589860 TCAACTCAGATAACCAGCCATCCCCAACAGAGTATAACCGTTTATCATCATTCCTAAAGATGACC
1 TCAACTCAGATAACCAGCCATCCCCAACAGAGTAGAACCGTTTATCATCATTCCTAAAGATGACC
*
1589925 AAGAACTCTTCATCACGTTTGAG-CAGTGTCATTTCC-CGACCAGATCTCCTCATCACATAGGAG
66 AAGAACTCTTCATCACGTATGAGTC-GTGTCA--TCCACGACCAGATCTCCTCATCACATA-GAG
1589988 CCGTG
127 CCGTG
*** * * *
1589993 TCAACTCAGATAACCAGTTGTCCCCAACAGAGTAGAACTGTGTTATCATCCTTCCTAAAGATGGC
1 TCAACTCAGATAACCAGCCATCCCCAACAGAGTAGAACCGT-TTATCATCATTCCTAAAGATGAC
* * * *
1590058 C-AGAACTCTTCATCGCGTATGAGTCGTGTCATCCATTGTCCAGATCTCCTCATCACGTAGAGCC
65 CAAGAACTCTTCATCACGTATGAGTCGTGTCATCCA-CGACCAGATCTCCTCATCACATAGAGCC
1590122 GTG
129 GTG
* * ** ** * * * **
1590125 TCACCTTAGATAACCA-AAACTCTACATCA-CGTATGAGCCGTGTTATCA-CCCTCCTTAAAGAT
1 TCAACTCAGATAACCAGCCA-TCCCCAACAGAGTA-GAACCGT-TTATCATCATTCC-TAAAGAT
*
1590187 AACCAAGAACTCTTCATCACGTATGAG-CAGTGTCATC
62 GACCAAGAACTCTTCATCACGTATGAGTC-GTGTCATC
1590224 TTCAGCAACA
Statistics
Matches: 195, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
131 11 0.06
132 50 0.26
133 111 0.57
134 23 0.12
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (131 bp):
TCAACTCAGATAACCAGCCATCCCCAACAGAGTAGAACCGTTTATCATCATTCCTAAAGATGACC
AAGAACTCTTCATCACGTATGAGTCGTGTCATCCACGACCAGATCTCCTCATCACATAGAGCCGT
G
Found at i:1591565 original size:29 final size:30
Alignment explanation
Indices: 1591496--1591554 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1591486 CAATTTAAGG
* *
1591496 CAAAATGGTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
1591526 CAAAATGTTTTTGGACTT-AATTAAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
1591555 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:1591665 original size:21 final size:21
Alignment explanation
Indices: 1591634--1591731 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
1591624 AGGGTGTCAA
1591634 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
* * *
1591655 GGTGTATCCATGCATCCCTGT
1 AGTGCATCCATGCATCCCTGC
1591676 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCATCCCTG--C
* *
1591697 TAGTGCATCGATGCAT-CATGC
1 -AGTGCATCCATGCATCCCTGC
1591718 AGTGCATCCATGCA
1 AGTGCATCCATGCA
1591732 CTCAAACACC
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.20
21 31 0.48
22 13 0.20
23 3 0.05
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:1591703 original size:22 final size:20
Alignment explanation
Indices: 1591675--1591732 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
1591665 TGCATCCCTG
*
1591675 TAGTGCATCCATGCACCTGCAC
1 TAGTGCATCCATGCACATG--C
*
1591697 TAGTGCATCGATGCATCATGC
1 TAGTGCATCCATGCA-CATGC
1591718 -AGTGCATCCATGCAC
1 TAGTGCATCCATGCAC
1591733 TCAAACACCG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 1 0.03
22 14 0.44
23 3 0.09
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (20 bp):
TAGTGCATCCATGCACATGC
Found at i:1591820 original size:20 final size:20
Alignment explanation
Indices: 1591757--1591828 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1591747 CAATTAGTGT
* **
1591757 ATCGATGCATCCTTCTGTGC
1 ATCGATGCATCCTGCCATGC
* ** *
1591777 ATCGATGTATCAAGGCCATAC
1 ATCGATGCATC-CTGCCATGC
1591798 ATCGATGCATCCTGCCATGC
1 ATCGATGCATCCTGCCATGC
*
1591818 ATCCATGCATC
1 ATCGATGCATC
1591829 AAGGCTGCAA
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.28
Consensus pattern (20 bp):
ATCGATGCATCCTGCCATGC
Found at i:1591850 original size:10 final size:10
Alignment explanation
Indices: 1591831--1591865 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1591821 CATGCATCAA
1591831 GGCT-GCAAC
1 GGCTAGCAAC
1591840 GGCTAGCAAC
1 GGCTAGCAAC
*
1591850 GGCTAGTAAC
1 GGCTAGCAAC
1591860 GGCTAG
1 GGCTAG
1591866 TTTATTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.14
Consensus pattern (10 bp):
GGCTAGCAAC
Found at i:1592242 original size:34 final size:32
Alignment explanation
Indices: 1592203--1592272 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1592193 TTTTGTAAAG
* *
1592203 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1592237 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1592269 GGGA
1 GGGA
1592273 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1593280 original size:9 final size:9
Alignment explanation
Indices: 1593268--1593292 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1593258 GAAAGGGAAG
1593268 AGAAGAAAA
1 AGAAGAAAA
1593277 AGAAGAAAA
1 AGAAGAAAA
1593286 AGAAGAA
1 AGAAGAA
1593293 GGAGGAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:1595093 original size:34 final size:30
Alignment explanation
Indices: 1595055--1595123 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 30
1595045 TTGATATAAC
1595055 AATTTAAGGCAAAATGGTTTTTGGACATGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGAC-TGAATTG
*
1595089 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTGAATTG
1595118 AATTTA
1 AATTTA
1595124 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 11 0.33
30 10 0.30
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTGAATTG
Found at i:1595134 original size:29 final size:30
Alignment explanation
Indices: 1595064--1595123 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1595054 CAATTTAAGG
1595064 CAAAATGGTTTTTGGACATGAATTGAATTTA
1 CAAAAT-GTTTTTGGACATGAATTGAATTTA
*
1595095 CAAAATGTTTTTGGAC-TTAATTGAATTTA
1 CAAAATGTTTTTGGACATGAATTGAATTTA
1595124 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 12 0.43
30 10 0.36
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACATGAATTGAATTTA
Found at i:1595230 original size:21 final size:20
Alignment explanation
Indices: 1595203--1595300 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 20
1595193 AGGGTGTCAA
1595203 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCAT-CCTGC
*
1595224 GGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCAT-CCTGC
1595245 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCATCCTG--C
* *
1595266 TAGTGCATCGATGCATCATGC
1 -AGTGCATCCATGCATCCTGC
1595287 AGTGCATCCATGCA
1 AGTGCATCCATGCA
1595301 CTCAAACACC
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 35 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCATCCTGC
Found at i:1595370 original size:41 final size:41
Alignment explanation
Indices: 1595323--1595402 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
1595313 ATGCAATTAG
* ** * *
1595323 TGCATCGATGCATCCTTCTGTGCATCGATGTATCAAGGCCA
1 TGCATCGATGCATCCTGCCATGCATCCATGCATCAAGGCCA
1595364 TGCATCGATGCATCCTGCCATGCATCCATGCATCAAGGC
1 TGCATCGATGCATCCTGCCATGCATCCATGCATCAAGGC
1595403 TGCAACGGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (41 bp):
TGCATCGATGCATCCTGCCATGCATCCATGCATCAAGGCCA
Found at i:1595385 original size:20 final size:20
Alignment explanation
Indices: 1595323--1595397 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
1595313 ATGCAATTAG
* **
1595323 TGCATCGATGCATCCTTCTG
1 TGCATCGATGCATCCTGCCA
* **
1595343 TGCATCGATGTATCAAGGCCA
1 TGCATCGATGCATC-CTGCCA
1595364 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCATCCTGCCA
*
1595384 TGCATCCATGCATC
1 TGCATCGATGCATC
1595398 AAGGCTGCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCCA
Found at i:1595788 original size:34 final size:32
Alignment explanation
Indices: 1595748--1595817 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1595738 TTTTGTAAAG
* *
1595748 GGGAAAGGTTCTAGTTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
1595782 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1595814 GGGA
1 GGGA
1595818 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
Found at i:1606290 original size:41 final size:41
Alignment explanation
Indices: 1606245--1606335 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
1606235 TATTAGATTG
1606245 ATGATATATTAGTAAAATAGTATAAAAAGGATTTAATATTA
1 ATGATATATTAGTAAAATAGTATAAAAAGGATTTAATATTA
1606286 ATGATATATTAGTAAAATAGTATAAAAAGGATTTAATATTA
1 ATGATATATTAGTAAAATAGTATAAAAAGGATTTAATATTA
1606327 ATGATATAT
1 ATGATATAT
1606336 AATTCGTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (41 bp):
ATGATATATTAGTAAAATAGTATAAAAAGGATTTAATATTA
Found at i:1619795 original size:23 final size:22
Alignment explanation
Indices: 1619763--1619823 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
1619753 AGAACCCGTG
1619763 GGGGGTATCGATTCCCCTTCAAA
1 GGGGGTATCGATTCCCCTTC-AA
* *
1619786 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTTCAA
*
1619808 GGGGGTATCAATTCCC
1 GGGGGTATCGATTCCC
1619824 TCTGCCCTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTTCAA
Found at i:1623980 original size:48 final size:44
Alignment explanation
Indices: 1623872--1623990 Score: 139
Period size: 48 Copynumber: 2.6 Consensus size: 44
1623862 GTAACCATAC
*
1623872 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAA
* * * * *
1623916 AAAAAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATT-GAAA
*
1623964 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
1623991 AAGGTAAGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
44 21 0.34
45 2 0.03
46 2 0.03
47 13 0.21
48 24 0.39
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (44 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAA
Done.