Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007909.1 Hibiscus syriacus cultivar Beakdansim tig00110303_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: 3382237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 17
Found at i:1350241 original size:7 final size:7
Alignment explanation
Indices: 1350229--1350262 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1350219 ATCATGGTCG
1350229 AATTTTT
1 AATTTTT
1350236 AATTTTT
1 AATTTTT
*
1350243 AA-TTTA
1 AATTTTT
1350249 AATTTTT
1 AATTTTT
1350256 AATTTTT
1 AATTTTT
1350263 GTAATTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:1350254 original size:13 final size:13
Alignment explanation
Indices: 1350236--1350260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1350226 TCGAATTTTT
1350236 AATTTTTAATTTA
1 AATTTTTAATTTA
1350249 AATTTTTAATTT
1 AATTTTTAATTT
1350261 TTGTAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTAATTTA
Found at i:1355275 original size:15 final size:16
Alignment explanation
Indices: 1355243--1355275 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1355233 TAAATCTTTC
1355243 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
1355259 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
1355274 TT
1 TT
1355276 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:1356047 original size:16 final size:17
Alignment explanation
Indices: 1356020--1356054 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1356010 TATCGCCGAC
1356020 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
1356037 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
1356053 CG
1 CG
1356055 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:1357773 original size:31 final size:32
Alignment explanation
Indices: 1357737--1357813 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 32
1357727 TCAAAATACA
1357737 TAAGATATGGTCATC-TTCATTTTTATTTAAT
1 TAAGATATGGTCATCTTTCATTTTTATTTAAT
* *
1357768 TAAGATATGATCA-CTTTCGTTTTTATTTAAT
1 TAAGATATGGTCATCTTTCATTTTTATTTAAT
**
1357799 TAAGACGTGGTCATC
1 TAAGATATGGTCATC
1357814 ACGGATTAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.47
Consensus pattern (32 bp):
TAAGATATGGTCATCTTTCATTTTTATTTAAT
Found at i:1362467 original size:15 final size:15
Alignment explanation
Indices: 1362447--1362483 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1362437 AATTTAGCCC
**
1362447 GCGGGTTTTGACGGT
1 GCGGGTTTAAACGGT
1362462 GCGGGTTTAAACGGT
1 GCGGGTTTAAACGGT
1362477 GCGGGTT
1 GCGGGTT
1362484 AAAAAGCCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.46, T:0.30
Consensus pattern (15 bp):
GCGGGTTTAAACGGT
Found at i:1369850 original size:22 final size:22
Alignment explanation
Indices: 1369825--1369868 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1369815 ATTTTTATAA
* *
1369825 ATAA-TTTAATTTTTAAATAATT
1 ATAACTTT-ATTTTAAAAAAATT
1369847 ATAACTTTATTTTAAAAAAATT
1 ATAACTTTATTTTAAAAAAATT
1369869 TGAATTCTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAACTTTATTTTAAAAAAATT
Found at i:1370312 original size:26 final size:25
Alignment explanation
Indices: 1370283--1370339 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
1370273 ATTATCAAGC
*
1370283 ATAATAACATATTAGGTAGCGCTTAT
1 ATAATAA-ATAATAGGTAGCGCTTAT
*
1370309 ATAAT--GTAATAGGTAGCGCTTAT
1 ATAATAAATAATAGGTAGCGCTTAT
1370332 ATAATAAA
1 ATAATAAA
1370340 ATAGGCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 21 0.81
26 5 0.19
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (25 bp):
ATAATAAATAATAGGTAGCGCTTAT
Found at i:1370342 original size:23 final size:23
Alignment explanation
Indices: 1370295--1370344 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1370285 AATAACATAT
**
1370295 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
1370318 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
1370341 TAGG
1 TAGG
1370345 CATTTAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:1370365 original size:53 final size:53
Alignment explanation
Indices: 1370306--1370414 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
1370296 AGGTAGCGCT
*
1370306 TATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGCATTTAATCGGTAA
1 TATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGCATTTAACCGGTAA
*
1370359 TATATAATGTAATAGGTGGCGCTTATATAATAAAATAGGCATTTAACCGGTAA
1 TATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGCATTTAACCGGTAA
1370412 TAT
1 TAT
1370415 TATTAAGTAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.34
Consensus pattern (53 bp):
TATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGCATTTAACCGGTAA
Found at i:1370747 original size:232 final size:235
Alignment explanation
Indices: 1370341--1370808 Score: 906
Period size: 232 Copynumber: 2.0 Consensus size: 235
1370331 TATAATAAAA
*
1370341 TAGGCATTTAATCGGTAATATATAATGTAATAGGTGGCGCTTATATAATAAAATAGGCATTTAAC
1 TAGGCATTTAATCGGTAATATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGCATTTAAC
1370406 CGGTAATATTATTAAGTACAATAACATATTAGGCAGTGCTTATATAATGTAATAGGTAGCACTTA
66 CGGTAATATTATTAAGTACAATAACATATTAGGCAGTGCTTATATAATGTAATAGGTAGCACTTA
1370471 TATTGACCTATTTTATAAGTAAATCGGTATATATATACCGGTAACATTATAAATTTAACTATTAC
131 TATTGACCTATTTTATAAGTAAATCGGTATATATATACCGGTAACATTATAAATTTAACTATTAC
1370536 ATTATAA-T-TCGGTTTCGAT-TTTTTTGGATCGATACTT
196 ATTATAATTATCGGTTTCGATATTTTTTGGATCGATACTT
1370573 TAGGCATTTAATCGGTAATATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGCATTTAAC
1 TAGGCATTTAATCGGTAATATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGCATTTAAC
1370638 CGGTAATATTATTAAGTACAATAACATATTAGGCAGTGCTTATATAATGTAATAGGTAGCACTTA
66 CGGTAATATTATTAAGTACAATAACATATTAGGCAGTGCTTATATAATGTAATAGGTAGCACTTA
1370703 TATTGACCTATTTTATAAGTAAATCGGTATATATATACCGGTAACATTATAAATTTAACTATTAC
131 TATTGACCTATTTTATAAGTAAATCGGTATATATATACCGGTAACATTATAAATTTAACTATTAC
1370768 ATTATAATTATCGGTTTCGATATTTTTTGGATCGATACTT
196 ATTATAATTATCGGTTTCGATATTTTTTGGATCGATACTT
1370808 T
1 T
1370809 TTATAAATGT
Statistics
Matches: 232, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
232 201 0.87
233 1 0.00
234 11 0.05
235 19 0.08
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (235 bp):
TAGGCATTTAATCGGTAATATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGCATTTAAC
CGGTAATATTATTAAGTACAATAACATATTAGGCAGTGCTTATATAATGTAATAGGTAGCACTTA
TATTGACCTATTTTATAAGTAAATCGGTATATATATACCGGTAACATTATAAATTTAACTATTAC
ATTATAATTATCGGTTTCGATATTTTTTGGATCGATACTT
Found at i:1371152 original size:182 final size:182
Alignment explanation
Indices: 1370840--1371859 Score: 1712
Period size: 182 Copynumber: 5.6 Consensus size: 182
1370830 TGTGTTCACC
** * * *
1370840 TTTTGTCATTTATAAACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
1370905 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAATTGTCG
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
*
1370969 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
1371022 TTTTGTCATTTCGAGATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
** *
1371087 TTTATAAAGTATCGTTACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* *
1371152 TACTTATAATAAATTATCGACACTTTCAACATAACCTGTAGCGTTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * *
1371204 TTTTGTCATTTCGAGACCGGTTTTGCCATATTATTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
1371269 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
1371334 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
1371386 TTTTGTCATTTCGAGATCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACA-T
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
1371450 TTTATAAATTATCGACACGTTATTGACGCTATAACTTCTTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
* *
1371512 ATACTTATAATAAATTATCGACACTATCAACATAACCGGTAGCG-TTTACTTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
1371564 TTTTGTCATTTCGAGACTGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
1371629 TTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
1371693 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
1371745 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
1371810 TTTATAAAGTATCGACACTTTATTGACGATATAACTTCTTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAA
1371860 AAAGGTAAAA
Statistics
Matches: 785, Mismatches: 45, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
177 2 0.00
178 87 0.11
179 80 0.10
180 46 0.06
181 158 0.20
182 412 0.52
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:1372414 original size:20 final size:19
Alignment explanation
Indices: 1372368--1372414 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1372358 TCCGGTATCA
*
1372368 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
1372387 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
1372408 TTTTACC
1 TTTTACC
1372415 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:1372686 original size:181 final size:181
Alignment explanation
Indices: 1372335--1372808 Score: 662
Period size: 182 Copynumber: 2.6 Consensus size: 181
1372325 CGTACTTACG
* * * * *
1372335 AAAGTATCGACAATTTTAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTCGATACCG-TTT
* *
1372400 TATCATATTTTTACCTGTTATATCGTTGTTTGATCGATACATTTTTTTAAAGTATCGACACTTTA
65 TATCATATTTTTACCTGTTATATCGTTG-TTGATCGATACATTTTTTGAAAGTATCAACACTTTA
* *
1372465 TAGGCGCTAAAATTACTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
129 TAGGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * *
1372517 AAAGTTTCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTGGATACCAGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTCGATACC-GTTT
*
1372582 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCAACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCAACACTTTAT
**
1372647 AGGCGCTAAAACTACTTCTCTTTTAAATTAATGAAGTGTCGATCCTTATATT
130 AGGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * * *
1372699 AAAGTACCGACACTTTAAATATATTCGATACCGCTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTCGATAC-CGTTT
* * * *
1372764 TGTCATAGTTTTACATGTTATATCGTTGTGGATCGATACATTTTT
65 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTT
1372809 AATTTGGATC
Statistics
Matches: 259, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
181 80 0.31
182 178 0.69
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTCGATACCGTTTT
ATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCAACACTTTATA
GGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
Found at i:1373499 original size:19 final size:19
Alignment explanation
Indices: 1373475--1373511 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1373465 ATGACCAACA
*
1373475 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1373494 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1373512 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1373608 original size:21 final size:21
Alignment explanation
Indices: 1373584--1373633 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1373574 ACTATCGCAA
1373584 TGCGATAGTCCAAATTCGCGT
1 TGCGATAGTCCAAATTCGCGT
** *
1373605 TGCGATAGTCCGTATTGGCGT
1 TGCGATAGTCCAAATTCGCGT
1373626 TGCGATAG
1 TGCGATAG
1373634 ACTGTTCACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (21 bp):
TGCGATAGTCCAAATTCGCGT
Found at i:1373648 original size:20 final size:21
Alignment explanation
Indices: 1373623--1373663 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
1373613 TCCGTATTGG
1373623 CGTTGCGATAG-ACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
1373643 CGTTGCGATAGCACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
1373664 ATTGCGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (21 bp):
CGTTGCGATAGCACTGTTCAC
Found at i:1373668 original size:20 final size:20
Alignment explanation
Indices: 1373625--1373670 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1373615 CGTATTGGCG
*
1373625 TTGCGATAGACTGTTCACCG
1 TTGCGATAGACTGTTCACCA
1373645 TTGCGATAGCACTGTTCA-CA
1 TTGCGATAG-ACTGTTCACCA
1373665 TTGCGA
1 TTGCGA
1373671 ATTTACGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (20 bp):
TTGCGATAGACTGTTCACCA
Found at i:1373934 original size:22 final size:22
Alignment explanation
Indices: 1373909--1373954 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1373899 AAAATTTACA
* *
1373909 AAAACAAGATAAAAATTTGTAC
1 AAAACAAGATAAAAACTTGAAC
*
1373931 AAAATAAGATAAAAACTTGAAC
1 AAAACAAGATAAAAACTTGAAC
1373953 AA
1 AA
1373955 TTTTTGTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (22 bp):
AAAACAAGATAAAAACTTGAAC
Found at i:1374249 original size:15 final size:16
Alignment explanation
Indices: 1374224--1374253 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1374214 TAATTTAGAA
1374224 TTTATATTTATTTAAT
1 TTTATATTTATTTAAT
1374240 TTTATA-TTATTTAA
1 TTTATATTTATTTAA
1374254 AATTTAGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATATTTATTTAAT
Found at i:1374259 original size:16 final size:17
Alignment explanation
Indices: 1374216--1374259 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1374206 ATCATAAATA
*
1374216 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
1374233 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
1374248 ATTTAAAATTTA
1 ATTTAAAATTTA
1374260 GAGTTTATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.26
16 13 0.57
17 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:1374441 original size:20 final size:20
Alignment explanation
Indices: 1374416--1374463 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1374406 TATCGTAAAT
1374416 TCGCAATATGAACAGTGCTA
1 TCGCAATATGAACAGTGCTA
**
1374436 TCGCAACGGTGAACAGTGCTA
1 TCGCAA-TATGAACAGTGCTA
*
1374457 TCACAAT
1 TCGCAAT
1374464 GATTTTGGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATATGAACAGTGCTA
Found at i:1374566 original size:20 final size:19
Alignment explanation
Indices: 1374543--1374588 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1374533 GAAAACTTAT
* *
1374543 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1374563 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1374582 TTGCGAT
1 TTGCGAT
1374589 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1374578 original size:19 final size:19
Alignment explanation
Indices: 1374554--1374590 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1374544 TGCGATACTG
*
1374554 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1374573 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1374591 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1379928 original size:18 final size:20
Alignment explanation
Indices: 1379905--1379954 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1379895 AGCCAAATTT
*
1379905 GTATCGATACTCATGG-A-A
1 GTATCGATACTCAAGGAAGA
1379923 GTATCGATAC-CAAGGATAGA
1 GTATCGATACTCAAGGA-AGA
1379943 GTATCGATACTC
1 GTATCGATACTC
1379955 CTCAATAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.15
18 10 0.37
19 1 0.04
20 11 0.41
21 1 0.04
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (20 bp):
GTATCGATACTCAAGGAAGA
Found at i:1393759 original size:18 final size:18
Alignment explanation
Indices: 1393738--1393777 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1393728 TCGTAAACAA
1393738 TTTTATCTTAATAAATTT
1 TTTTATCTTAATAAATTT
*
1393756 TTTT-TCTTAATTAATTT
1 TTTTATCTTAATAAATTT
1393773 TTTTA
1 TTTTA
1393778 AAGTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATCTTAATAAATTT
Found at i:1393784 original size:26 final size:26
Alignment explanation
Indices: 1393755--1393811 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1393745 TTAATAAATT
*
1393755 TTTTTTCTTAATTAATTTTTTTAAAG
1 TTTTTTCTTAATTAATTTTTTTAAAA
1393781 TTTTTTCTTAATTAATTTTTTTAAAA
1 TTTTTTCTTAATTAATTTTTTTAAAA
1393807 TTTTT
1 TTTTT
1393812 AGCGGGTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTTTCTTAATTAATTTTTTTAAAA
Found at i:1396794 original size:2 final size:2
Alignment explanation
Indices: 1396787--1396811 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1396777 AGCTCACTGT
1396787 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1396812 GGATAATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1399932 original size:68 final size:69
Alignment explanation
Indices: 1399854--1399991 Score: 242
Period size: 68 Copynumber: 2.0 Consensus size: 69
1399844 GCGGAGGCTA
*
1399854 AAACTGAAACTTAATTATGTAACGAGTAATAACAGAT-ATAAATGATTCAGAAAAGAATAAGTTT
1 AAACTGAAACTTAACTATGTAACGAGTAATAACAGATGATAAATGATTCAGAAAAGAATAAGTTT
1399918 TCTG
66 TCTG
* *
1399922 AAACTGAAACTTAACTATGTAATGAGTAATAACAGATGATAAATGATTCAGAAAAGAATAATTTT
1 AAACTGAAACTTAACTATGTAACGAGTAATAACAGATGATAAATGATTCAGAAAAGAATAAGTTT
1399987 TCTG
66 TCTG
1399991 A
1 A
1399992 CAAGTATAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 35 0.53
69 31 0.47
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (69 bp):
AAACTGAAACTTAACTATGTAACGAGTAATAACAGATGATAAATGATTCAGAAAAGAATAAGTTT
TCTG
Found at i:1410746 original size:2 final size:2
Alignment explanation
Indices: 1410739--1410763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1410729 ATTTATAGTG
1410739 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1410764 TGGTTCAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1413591 original size:24 final size:24
Alignment explanation
Indices: 1413563--1413608 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1413553 AACTGTCGCG
*
1413563 TAGAATTTGCACTGAAGTGCCACA
1 TAGAATATGCACTGAAGTGCCACA
*
1413587 TAGAATATGCACTGATGTGCCA
1 TAGAATATGCACTGAAGTGCCA
1413609 TATATATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (24 bp):
TAGAATATGCACTGAAGTGCCACA
Found at i:1413664 original size:24 final size:23
Alignment explanation
Indices: 1413640--1413685 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1413630 CGCGTAAAAT
1413640 TTATCCCGAAGGACCACATAGAA
1 TTATCCCGAAGGACCACATAGAA
* *
1413663 TTGTCCCGAAGGACCGCATAGAA
1 TTATCCCGAAGGACCACATAGAA
1413686 CCCTCGACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
TTATCCCGAAGGACCACATAGAA
Found at i:1413751 original size:19 final size:19
Alignment explanation
Indices: 1413722--1413772 Score: 93
Period size: 19 Copynumber: 2.6 Consensus size: 19
1413712 ACCTCTAATT
1413722 CTTATAACATATACTTTGGG
1 CTTA-AACATATACTTTGGG
1413742 CTTAAACATATACTTTGGG
1 CTTAAACATATACTTTGGG
1413761 CTTAAACATATA
1 CTTAAACATATA
1413773 ATTATTTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 27 0.87
20 4 0.13
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (19 bp):
CTTAAACATATACTTTGGG
Found at i:1417263 original size:20 final size:19
Alignment explanation
Indices: 1417151--1417264 Score: 68
Period size: 20 Copynumber: 5.6 Consensus size: 19
1417141 AAATGACCAA
* *
1417151 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGC-AATTT
* * *
1417171 CAATTTCGCAACACAGTTT
1 CAAATTCGCAACGCAATTT
1417190 CCAAATTCGCAACGCGAATTT
1 -CAAATTCGCAACGC-AATTT
* * *
1417211 CCCAAATTCGTAACTCATTTT
1 --CAAATTCGCAACGCAATTT
*
1417232 CTGCAA-TCGCAACGCAAATTT
1 C--AAATTCGCAACGC-AATTT
1417253 CAAATTCGCAAC
1 CAAATTCGCAAC
1417265 TCGATTTCTT
Statistics
Matches: 71, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
19 5 0.07
20 38 0.54
21 15 0.21
22 13 0.18
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.25
Consensus pattern (19 bp):
CAAATTCGCAACGCAATTT
Found at i:1417360 original size:20 final size:20
Alignment explanation
Indices: 1417257--1417392 Score: 84
Period size: 20 Copynumber: 6.8 Consensus size: 20
1417247 AAATTTCAAA
*
1417257 TTCGCAACTCG-A-TTTCTT
1 TTCGCAACACGAATTTTCTT
**
1417275 TCTCGCAATGCGAA-TTTCTTT
1 T-TCGCAACACGAATTTTC-TT
*
1417296 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGAA-TTTTCTT
* *
1417316 TTCGCAACAAG-ATTTTCTAA
1 TTCGCAACACGAATTTTCT-T
* *
1417336 ATCGCAACACGAATTTTGTT
1 TTCGCAACACGAATTTTCTT
* * ***
1417356 TTCGCAACTCGATTTTTGAA
1 TTCGCAACACGAATTTTCTT
1417376 TTCGCAACACGAATTTT
1 TTCGCAACACGAATTTT
1417393 AATTTAACAA
Statistics
Matches: 91, Mismatches: 19, Indels: 14
0.73 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 15 0.16
20 63 0.69
21 12 0.13
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (20 bp):
TTCGCAACACGAATTTTCTT
Found at i:1417392 original size:40 final size:40
Alignment explanation
Indices: 1417296--1417392 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 40
1417286 GAATTTCTTT
*
1417296 TTCGCAACAC-AAGTTTCCTTTTCGCAACAAGATTTTCTAA
1 TTCGCAACACGAA-TTTTCTTTTCGCAACAAGATTTTCTAA
* * **
1417336 ATCGCAACACGAATTTTGTTTTCGCAACTCGATTTT-TGAA
1 TTCGCAACACGAATTTTCTTTTCGCAACAAGATTTTCT-AA
1417376 TTCGCAACACGAATTTT
1 TTCGCAACACGAATTTT
1417393 AATTTAACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.02
40 46 0.94
41 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (40 bp):
TTCGCAACACGAATTTTCTTTTCGCAACAAGATTTTCTAA
Found at i:1417599 original size:16 final size:15
Alignment explanation
Indices: 1417564--1417602 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1417554 TCCCCATCTC
*
1417564 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1417579 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1417595 TAATTTTT
1 TAATTTTT
1417603 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1418220 original size:12 final size:12
Alignment explanation
Indices: 1418199--1418232 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1418189 ACCACATTTC
*
1418199 CAATACCAAACA
1 CAATATCAAACA
1418211 CAATATCAAACA
1 CAATATCAAACA
*
1418223 CAATCTCAAA
1 CAATATCAAA
1418233 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1418410 original size:24 final size:24
Alignment explanation
Indices: 1418353--1418399 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1418343 AGTCAGTATT
1418353 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
1418377 CGAAATTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
1418400 TCGGATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:1420667 original size:12 final size:12
Alignment explanation
Indices: 1420652--1420686 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1420642 AGGAAATCAA
1420652 AATCACAATCGC
1 AATCACAATCGC
* *
1420664 AATCAAAATCCC
1 AATCACAATCGC
1420676 AATCACAATCG
1 AATCACAATCG
1420687 GCTTCACCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.46, C:0.31, G:0.06, T:0.17
Consensus pattern (12 bp):
AATCACAATCGC
Found at i:1420669 original size:18 final size:18
Alignment explanation
Indices: 1420646--1420685 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1420636 AGCAAAAGGA
*
1420646 AATCAAAATCACAATCGC
1 AATCAAAATCACAATCAC
*
1420664 AATCAAAATCCCAATCAC
1 AATCAAAATCACAATCAC
1420682 AATC
1 AATC
1420686 GGCTTCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.30, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCACAATCAC
Found at i:1422431 original size:21 final size:21
Alignment explanation
Indices: 1422390--1422485 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
1422380 GTGAATCGGG
1422390 CTCTTGAACGATG-G-GGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1422409 CTCTTGAACGATGAGATGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1422430 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1422451 CTCTTGAGCGAT-AGGAGGGGC
1 CTCTTGAACGATGA-GAGGGGC
*
1422472 CTCTTGAATGATGA
1 CTCTTGAACGATGA
1422486 TAGGTGAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.20
20 1 0.02
21 51 0.77
22 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1422794 original size:21 final size:21
Alignment explanation
Indices: 1422770--1422821 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1422760 TGAAACAATC
* *
1422770 TCACGTAGAGCGGTTACCTCA
1 TCACGTAGAGCAGATACCTCA
* *
1422791 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGCAGATACCTCA
*
1422812 CCACGTAGAG
1 TCACGTAGAG
1422822 AACCATTGTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (21 bp):
TCACGTAGAGCAGATACCTCA
Found at i:1422880 original size:21 final size:22
Alignment explanation
Indices: 1422830--1422945 Score: 73
Period size: 21 Copynumber: 5.5 Consensus size: 22
1422820 AGAACCATTG
* * *
1422830 TCATCGCGTAAAACATC-TACC
1 TCATCACGTAAAGCACCGTACC
1422851 TCA-CTACGTAAAG-ACCGTACC
1 TCATC-ACGTAAAGCACCGTACC
* * * **
1422872 TCATCACGTCATGCACCAT-TG
1 TCATCACGTAAAGCACCGTACC
*
1422893 TCATCACGTAAAGTACCG-ACC
1 TCATCACGTAAAGCACCGTACC
* *
1422914 TCATCACGCAAAGCACTG-ACC
1 TCATCACGTAAAGCACCGTACC
*
1422935 TTATCACGTAA
1 TCATCACGTAA
1422946 CTCCCCTAAC
Statistics
Matches: 71, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.04
21 63 0.89
22 5 0.07
ACGTcount: A:0.32, C:0.33, G:0.13, T:0.22
Consensus pattern (22 bp):
TCATCACGTAAAGCACCGTACC
Found at i:1423135 original size:42 final size:42
Alignment explanation
Indices: 1423060--1423164 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
1423050 GTGATGGAAT
* * * *
1423060 AGGTGATGACTCTCGGTGTGGAGGTGTATAATCGGCCCGATC
1 AGGTGATGGCTCTCGATGTGGAGCTGTAGAATCGGCCCGATC
* *
1423102 AGGTGATGGCTCTCGATGTTGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGATGTGGAGCTGTAGAATCGGCCCGATC
*
1423144 AGGTGATGGCTCTCGAAGTGG
1 AGGTGATGGCTCTCGATGTGG
1423165 GGGGTGCTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.27
Consensus pattern (42 bp):
AGGTGATGGCTCTCGATGTGGAGCTGTAGAATCGGCCCGATC
Found at i:1424664 original size:20 final size:20
Alignment explanation
Indices: 1424641--1424717 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
1424631 TTTGAAACTT
* *
1424641 AAATTCGAAACACGAAAATG
1 AAATTCGCAACGCGAAAATG
1424661 AAATTCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
*
1424681 AAAATCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
* *
1424701 AAAATCGCAACGTGAAA
1 AAATTCGCAACGCGAAA
1424718 CTAAAATCGC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.13
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:1427338 original size:23 final size:21
Alignment explanation
Indices: 1427294--1427340 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1427284 GCATGATTAA
*
1427294 TGATTTTCTTGAATTTTTGAT
1 TGATTTCCTTGAATTTTTGAT
*
1427315 TGATTTCCTATGAGTTTATTGAT
1 TGATTTCCT-TGAATTT-TTGAT
1427338 TGA
1 TGA
1427341 CATGTATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 8 0.36
ACGTcount: A:0.21, C:0.06, G:0.17, T:0.55
Consensus pattern (21 bp):
TGATTTCCTTGAATTTTTGAT
Found at i:1427755 original size:20 final size:20
Alignment explanation
Indices: 1427732--1427781 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1427722 AGTTTTCAAA
1427732 AAAAAAAAAGAAAAAAAAGG
1 AAAAAAAAAGAAAAAAAAGG
** * *
1427752 AAAAACGAAGAAGAAAAATG
1 AAAAAAAAAGAAAAAAAAGG
1427772 AAAACAAAAA
1 AAAA-AAAAA
1427782 AAATAAGTTG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAAAAGG
Found at i:1431992 original size:25 final size:25
Alignment explanation
Indices: 1431907--1432193 Score: 370
Period size: 24 Copynumber: 11.6 Consensus size: 25
1431897 TATTTTATAT
1431907 TATTCTACGAGGCACTTTGTGTGCA
1 TATTCTACGAGGCACTTTGTGTGCA
*
1431932 -ATTCTATGAGGCACTTTGTGTGCA
1 TATTCTACGAGGCACTTTGTGTGCA
1431956 -ATTCTACGAGGCA-TTCTGTGTGCA
1 TATTCTACGAGGCACTT-TGTGTGCA
* *
1431980 TATTCTACAAGGCACTTTGTGTGTA
1 TATTCTACGAGGCACTTTGTGTGCA
*
1432005 -ATTCTACGAGACACTTTGTGTGCA
1 TATTCTACGAGGCACTTTGTGTGCA
* *
1432029 TATTCTACGAGACACTGTGTGTGCA
1 TATTCTACGAGGCACTTTGTGTGCA
1432054 -ATTCTACGAGGCACTTTGTGTGCA
1 TATTCTACGAGGCACTTTGTGTGCA
* *
1432078 TATTCTATGAGGTACTTTGTGTGCACA
1 TATTCTACGAGGCACTTTGTGTG--CA
*
1432105 TATTATACGAGGCACTTTGTGTGCA
1 TATTCTACGAGGCACTTTGTGTGCA
*
1432130 -ATTCTACGAGGCATTTTGTGTGCA
1 TATTCTACGAGGCACTTTGTGTGCA
* * * *
1432154 TATTCTAAGAGGCACATTGTGCGTA
1 TATTCTACGAGGCACTTTGTGTGCA
*
1432179 TATTCTACGTGGCAC
1 TATTCTACGAGGCAC
1432194 ATTGGTTCTG
Statistics
Matches: 230, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.01
24 108 0.47
25 96 0.42
26 2 0.01
27 22 0.10
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (25 bp):
TATTCTACGAGGCACTTTGTGTGCA
Found at i:1432008 original size:49 final size:49
Alignment explanation
Indices: 1431908--1432193 Score: 371
Period size: 49 Copynumber: 5.8 Consensus size: 49
1431898 ATTTTATATT
*
1431908 ATTCTACGAGGCACTTTGTGTGCA-ATTCTATGAGGCACTTTGTGTGCA
1 ATTCTACGAGGCACTTTGTGTGCATATTCTACGAGGCACTTTGTGTGCA
* *
1431956 ATTCTACGAGGCA-TTCTGTGTGCATATTCTACAAGGCACTTTGTGTGTA
1 ATTCTACGAGGCACTT-TGTGTGCATATTCTACGAGGCACTTTGTGTGCA
* * *
1432005 ATTCTACGAGACACTTTGTGTGCATATTCTACGAGACACTGTGTGTGCA
1 ATTCTACGAGGCACTTTGTGTGCATATTCTACGAGGCACTTTGTGTGCA
* *
1432054 ATTCTACGAGGCACTTTGTGTGCATATTCTATGAGGTACTTTGTGTGCACA
1 ATTCTACGAGGCACTTTGTGTGCATATTCTACGAGGCACTTTGTGTG--CA
* *
1432105 TATTATACGAGGCACTTTGTGTGCA-ATTCTACGAGGCATTTTGTGTGCA
1 -ATTCTACGAGGCACTTTGTGTGCATATTCTACGAGGCACTTTGTGTGCA
* * * * *
1432154 TATTCTAAGAGGCACATTGTGCGTATATTCTACGTGGCAC
1 -ATTCTACGAGGCACTTTGTGTGCATATTCTACGAGGCAC
1432194 ATTGGTTCTG
Statistics
Matches: 207, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
47 2 0.01
48 21 0.10
49 126 0.61
50 14 0.07
51 21 0.10
52 23 0.11
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (49 bp):
ATTCTACGAGGCACTTTGTGTGCATATTCTACGAGGCACTTTGTGTGCA
Found at i:1432510 original size:17 final size:17
Alignment explanation
Indices: 1432488--1432540 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
1432478 TGCTATTAAT
1432488 TTTTATTTTTATTTATA
1 TTTTATTTTTATTTATA
1432505 TTTTA-TTTTATTTTATA
1 TTTTATTTTTA-TTTATA
*
1432522 TTTTATTATTATTT-TA
1 TTTTATTTTTATTTATA
1432538 TTT
1 TTT
1432541 ATGTTATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 10 0.30
17 19 0.58
18 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTATTTATA
Found at i:1432511 original size:5 final size:5
Alignment explanation
Indices: 1432488--1432540 Score: 61
Period size: 6 Copynumber: 9.6 Consensus size: 5
1432478 TGCTATTAAT
1432488 TTTTA TTTTTA TTTATA TTTTA TTTTA TTTTATA TTTTA TTATTA TTTTA
1 TTTTA -TTTTA TTT-TA TTTTA TTTTA -TTT-TA TTTTA TT-TTA TTTTA
1432538 TTT
1 TTT
1432541 ATGTTATTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 20 0.47
6 21 0.49
7 2 0.05
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:1432526 original size:28 final size:27
Alignment explanation
Indices: 1432488--1432548 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
1432478 TGCTATTAAT
1432488 TTTTATTTTTATT-TATATTTTATTTTA
1 TTTTATTTTTATTAT-TATTTTATTTTA
1432515 TTTTATATTTTATTATTATTTTA-TTTA
1 TTTTAT-TTTTATTATTATTTTATTTTA
*
1432542 TGTTATT
1 TTTTATT
1432549 AATAATAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.48
28 14 0.45
29 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTTATTTTTATTATTATTTTATTTTA
Found at i:1432542 original size:12 final size:11
Alignment explanation
Indices: 1432488--1432540 Score: 72
Period size: 11 Copynumber: 4.7 Consensus size: 11
1432478 TGCTATTAAT
1432488 TTTTATTTTTA
1 TTTTATTTTTA
1432499 -TTTATATTTTA
1 TTTTAT-TTTTA
1432510 TTTTATTTTATA
1 TTTTATTTT-TA
*
1432522 TTTTATTATTA
1 TTTTATTTTTA
1432533 TTTTATTT
1 TTTTATTT
1432541 ATGTTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 5 0.14
11 17 0.46
12 15 0.41
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1433356 original size:17 final size:18
Alignment explanation
Indices: 1433330--1433364 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1433320 TCTTTAGGAT
1433330 ATTTTATTTTAT-TTTAA
1 ATTTTATTTTATCTTTAA
*
1433347 ATTTTCTTTTATCTTTAA
1 ATTTTATTTTATCTTTAA
1433365 GAAGATTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTATTTTATCTTTAA
Found at i:1439057 original size:24 final size:24
Alignment explanation
Indices: 1439028--1439084 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
1439018 TCATGAACAA
* *
1439028 GCTCATTTAGAAGCTCGTTTATAT
1 GCTCATTTACAAGCTCGTTTATAG
* ** *
1439052 GTTCATGAACATGCTCGTTTATAG
1 GCTCATTTACAAGCTCGTTTATAG
1439076 GCTCATTTA
1 GCTCATTTA
1439085 ATTTTTTATA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (24 bp):
GCTCATTTACAAGCTCGTTTATAG
Found at i:1443212 original size:29 final size:29
Alignment explanation
Indices: 1443170--1443228 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1443160 ATTTTCACTT
1443170 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1443199 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1443228 A
1 A
1443229 TCAATTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1445064 original size:15 final size:15
Alignment explanation
Indices: 1445037--1445144 Score: 180
Period size: 15 Copynumber: 7.2 Consensus size: 15
1445027 CGTAGGACTC
1445037 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
1445052 CTACGTCCTGAAGGA
1 CTACATCCCGAAGGA
1445067 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1445082 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1445097 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1445112 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1445127 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
1445142 CTA
1 CTA
1445145 TTATACCCTC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 85 1.00
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:1445073 original size:30 final size:30
Alignment explanation
Indices: 1445037--1445144 Score: 207
Period size: 30 Copynumber: 3.6 Consensus size: 30
1445027 CGTAGGACTC
*
1445037 CTACATCCCGAAGGACTACGTCCTGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
1445067 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
1445097 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
1445127 CTACATCCCGAAGGACTA
1 CTACATCCCGAAGGACTA
1445145 TTATACCCTC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:1445271 original size:29 final size:29
Alignment explanation
Indices: 1445229--1445302 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
1445219 TTTCATATGT
1445229 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1445257 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1445286 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
1445303 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1445358 original size:24 final size:24
Alignment explanation
Indices: 1445318--1445364 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1445308 TATCATGTTC
* *
1445318 TCATATCACAGGTCATATTACATA
1 TCATATCACAAGTCATATCACATA
1445342 TCATATCACATAG-CATATCACAT
1 TCATATCACA-AGTCATATCACAT
1445365 GAACATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (24 bp):
TCATATCACAAGTCATATCACATA
Found at i:1445364 original size:12 final size:12
Alignment explanation
Indices: 1445331--1445364 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1445321 TATCACAGGT
* *
1445331 CATATTACATAT
1 CATATCACATAG
1445343 CATATCACATAG
1 CATATCACATAG
1445355 CATATCACAT
1 CATATCACAT
1445365 GAACATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (12 bp):
CATATCACATAG
Found at i:1445781 original size:64 final size:63
Alignment explanation
Indices: 1445673--1445897 Score: 206
Period size: 64 Copynumber: 3.5 Consensus size: 63
1445663 TAATGAAGGT
* * * ** * * ** *
1445673 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGT-GTCACTATTAATAGG
* *
1445737 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATAGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTGTCACTATTAATAGG
* * *
1445801 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAAATA
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-GTCACTATT--AATA
1445865 -G
62 GG
**
1445866 -TGCATCGATGCACTACCAATGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
1445898 ATTCATATAA
Statistics
Matches: 138, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
63 3 0.02
64 127 0.92
65 4 0.03
66 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTGTCACTATTAATAGG
Found at i:1451639 original size:15 final size:15
Alignment explanation
Indices: 1451616--1451738 Score: 201
Period size: 15 Copynumber: 8.2 Consensus size: 15
1451606 CGTAGGACTC
1451616 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1451631 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1451646 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1451661 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
*
1451676 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1451691 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1451706 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
*
1451721 CTACATTCCGAAGGA
1 CTACATCCCGAAGGA
1451736 CTA
1 CTA
1451739 TTATACCCTC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 101 1.00
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:1451865 original size:29 final size:29
Alignment explanation
Indices: 1451823--1451896 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
1451813 TTTCATATGT
1451823 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1451851 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1451880 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
1451897 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1451952 original size:24 final size:24
Alignment explanation
Indices: 1451912--1451958 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1451902 TATCATGTTC
* *
1451912 TCATATCACAGGTCATATTACATA
1 TCATATCACAAGTCATATCACATA
1451936 TCATATCACATAG-CATATCACAT
1 TCATATCACA-AGTCATATCACAT
1451959 GAACATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (24 bp):
TCATATCACAAGTCATATCACATA
Found at i:1451958 original size:12 final size:12
Alignment explanation
Indices: 1451925--1451958 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1451915 TATCACAGGT
* *
1451925 CATATTACATAT
1 CATATCACATAG
1451937 CATATCACATAG
1 CATATCACATAG
1451949 CATATCACAT
1 CATATCACAT
1451959 GAACATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (12 bp):
CATATCACATAG
Found at i:1452377 original size:64 final size:64
Alignment explanation
Indices: 1452269--1452445 Score: 198
Period size: 64 Copynumber: 2.8 Consensus size: 64
1452259 TAATGAAGGT
* * * ** * * **
1452269 ATGCATCGATGCACTACTGATGCATCGGTGCATC-AAAGGTATTCGATGTAGT-ATTATTGTTGG
1 ATGCATCGATACACTACTTATGCATCGATGCA-CGAATTGCATTCGATGT-GTCACTATTAATGG
1452332 G
64 G
* *
1452333 ATGCATCGATACACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATACACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTGTCACTATTAATGGG
*
1452397 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATACACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1452446 CTTTATTTTA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
63 3 0.03
64 93 0.97
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (64 bp):
ATGCATCGATACACTACTTATGCATCGATGCACGAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:1452466 original size:64 final size:63
Alignment explanation
Indices: 1452269--1452493 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 63
1452259 TAATGAAGGT
* * * ** * * * ** *
1452269 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGT-TTCACTATTAATGAG
* * *
1452333 ATGCATCGATACACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAATGAG
* *
1452397 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAAAT-
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATT--AATG
1452460 AG
62 AG
**
1452462 -TGCATCGATGCACTACCAATGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
1452494 ATTCATATAA
Statistics
Matches: 136, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 3 0.02
64 126 0.93
65 4 0.03
66 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAATGAG
Found at i:1454775 original size:43 final size:43
Alignment explanation
Indices: 1454713--1454799 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
1454703 TAATTTGGAT
* **
1454713 TTCCTTTCCTATATATAAATTGGTTTAATTTAATCGTACCCAA
1 TTCCGTTCCTATATATAAATTAATTTAATTTAATCGTACCCAA
* * *
1454756 TTCCGTTCTTATATTTAAATTAATTTAATTTAATTGTACCCAA
1 TTCCGTTCCTATATATAAATTAATTTAATTTAATCGTACCCAA
1454799 T
1 T
1454800 ATGTTAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (43 bp):
TTCCGTTCCTATATATAAATTAATTTAATTTAATCGTACCCAA
Found at i:1455311 original size:21 final size:21
Alignment explanation
Indices: 1455287--1455330 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1455277 AGAATAAGAT
1455287 TACTATAATAGCATATTTAGA
1 TACTATAATAGCATATTTAGA
1455308 TACTATAATAGCATATTTAGA
1 TACTATAATAGCATATTTAGA
1455329 TA
1 TA
1455331 ACTCACTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (21 bp):
TACTATAATAGCATATTTAGA
Found at i:1467411 original size:16 final size:16
Alignment explanation
Indices: 1467380--1467409 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1467370 TTTTAATTTG
1467380 CTAAAATTTTATAAAT
1 CTAAAATTTTATAAAT
1467396 CTAAAATTTT-TAAA
1 CTAAAATTTTATAAA
1467410 ATTTTATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
CTAAAATTTTATAAAT
Found at i:1469120 original size:53 final size:53
Alignment explanation
Indices: 1469048--1469150 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
1469038 AACGAAATGA
*
1469048 TAATTCACAAACTCATTATGAATACCATGAATGCACACATAGTGCCGAAAAGG
1 TAATTCACAAAATCATTATGAATACCATGAATGCACACATAGTGCCGAAAAGG
* *
1469101 TAATTCACAAAATCATTATGAATACCATGGATGTACACATAGTGCCGAAA
1 TAATTCACAAAATCATTATGAATACCATGAATGCACACATAGTGCCGAAA
1469151 GTACACATAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (53 bp):
TAATTCACAAAATCATTATGAATACCATGAATGCACACATAGTGCCGAAAAGG
Found at i:1469978 original size:23 final size:24
Alignment explanation
Indices: 1469952--1470015 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
1469942 CAGCTCGTAT
1469952 AATTGCACCGAAGTGCCA-CATAG
1 AATTGCACCGAAGTGCCAGCATAG
* * * *
1469975 AATTGTATCGGAGTG-CAGCGTAG
1 AATTGCACCGAAGTGCCAGCATAG
*
1469998 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1470016 TATAATAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 2 0.06
23 28 0.88
24 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (24 bp):
AATTGCACCGAAGTGCCAGCATAG
Found at i:1470978 original size:64 final size:64
Alignment explanation
Indices: 1470869--1471012 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 64
1470859 CATCCTTAAC
* * *
1470869 GGTGCATCGATGCACTTACTTGTGCATCAGTGCACAAAATACATTCGATGTTT-TTGTATCAAAG
1 GGTGCATCGATGCACTGACTTATGCATCAGTGCACAAAATACATTCGATGTTTCTTCT-TCAAAG
* * * * *
1470933 GAGTGCATCGATGCAC-GCCTTATGCATC-GATGCACTAATTGCATTCGATGTTTCTTCTTTAAA
1 G-GTGCATCGATGCACTGACTTATGCATCAG-TGCACAAAATACATTCGATGTTTCTTCTTCAAA
1470996 G
64 G
1470997 GGTGCATCGATGCACT
1 GGTGCATCGATGCACT
1471013 TTGAATGTGC
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
63 15 0.22
64 36 0.53
65 17 0.25
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (64 bp):
GGTGCATCGATGCACTGACTTATGCATCAGTGCACAAAATACATTCGATGTTTCTTCTTCAAAG
Found at i:1472731 original size:2 final size:2
Alignment explanation
Indices: 1472724--1472785 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1472714 TAAACTATTC
1472724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1472766 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1472786 CTTTACAGCC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1475007 original size:23 final size:23
Alignment explanation
Indices: 1474981--1475049 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1474971 CACCACAGCT
*
1474981 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1475004 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
1475027 CGTAGAATTGTACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1475050 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1475157 original size:2 final size:2
Alignment explanation
Indices: 1475152--1475199 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1475142 GTTCCGAAGA
1475152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1475194 AT AT AT
1 AT AT AT
1475200 CCCGAAGGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1475350 original size:27 final size:27
Alignment explanation
Indices: 1475293--1475350 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1475283 ATGTTATCAC
*
1475293 ACTTTCACATATTCACATGTACATGTC
1 ACTTTCACATATTCACATGTACATGTA
* *
1475320 ACTTTCATATTATTCACATGT-CATTTA
1 ACTTTCACA-TATTCACATGTACATGTA
1475347 ACTT
1 ACTT
1475351 GTAACACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.43
Consensus pattern (27 bp):
ACTTTCACATATTCACATGTACATGTA
Found at i:1477555 original size:21 final size:20
Alignment explanation
Indices: 1477511--1477562 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
1477501 TTTTCAATTA
1477511 CAGTATCGATACCTCCACAT
1 CAGTATCGATACCTCCACAT
*
1477531 CAGTATCGATACTACTTCA-AT
1 CAGTATCGATAC--CTCCACAT
1477552 CAGTATCGATA
1 CAGTATCGATA
1477563 TTGTTCATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.41
21 13 0.45
22 4 0.14
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (20 bp):
CAGTATCGATACCTCCACAT
Found at i:1482368 original size:20 final size:20
Alignment explanation
Indices: 1482345--1482397 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1482335 AAGCAGCTTG
*
1482345 CGAAAAAATAGAAAAA-AATT
1 CGAAAAAATAGAAAAAGAA-A
1482365 CG-AAAAA-AGAAAAAGAAA
1 CGAAAAAATAGAAAAAGAAA
*
1482383 AGAAAAAATAGAAAA
1 CGAAAAAATAGAAAA
1482398 TTCAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 8 0.29
19 12 0.43
20 8 0.29
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (20 bp):
CGAAAAAATAGAAAAAGAAA
Found at i:1487949 original size:41 final size:41
Alignment explanation
Indices: 1487739--1487968 Score: 128
Period size: 41 Copynumber: 5.6 Consensus size: 41
1487729 CATATAAGTG
* * * * *
1487739 CTTTAGTGGTGTTTTTAAACAAATGCCACCACAGAAT-CTT
1 CTTTAGTGGCGTTTTTAAACAAACGCCACAAAAGAATAGTT
* * *
1487779 ACTTTAGTGGCGTTTCTAAACAAACACCACAAAATAATCA-TT
1 -CTTTAGTGGCGTTTTTAAACAAACGCCACAAAAGAAT-AGTT
* * ** * ** * *
1487821 CTTTAGTGACCTTTTTTAAACAAACGCCGTAATAGGGTACATA
1 CTTTAGTG-GCGTTTTTAAACAAACGCCACAAAAGAATA-GTT
* * * * ** *
1487864 CATTT--TGGTGTTTTTAGACAAACGTCACTACAA-CCTAGTA
1 C-TTTAGTGGCGTTTTTAAACAAACGCCAC-AAAAGAATAGTT
*
1487904 CTTTAGTGGCGTTTCTAAACAAACGCCACAAAAGAATAGTT
1 CTTTAGTGGCGTTTTTAAACAAACGCCACAAAAGAATAGTT
*
1487945 CTTTAGTGGTGTTTTTGAAACAAA
1 CTTTAGTGGCGTTTTT-AAACAAA
1487969 TGTTGCAATA
Statistics
Matches: 138, Mismatches: 40, Indels: 21
0.69 0.20 0.11
Matches are distributed among these distances:
39 3 0.02
40 6 0.04
41 92 0.67
42 32 0.23
43 2 0.01
44 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (41 bp):
CTTTAGTGGCGTTTTTAAACAAACGCCACAAAAGAATAGTT
Found at i:1494030 original size:12 final size:13
Alignment explanation
Indices: 1494008--1494040 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
1493998 AGATAATGAT
1494008 GGGGAAGGAGGAA
1 GGGGAAGGAGGAA
1494021 GGGG-AGGAGGAA
1 GGGGAAGGAGGAA
1494033 GGGAGAAG
1 GGG-GAAG
1494041 CAGAAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.61
13 5 0.28
14 2 0.11
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (13 bp):
GGGGAAGGAGGAA
Found at i:1496541 original size:2 final size:2
Alignment explanation
Indices: 1496534--1496558 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1496524 ACTCTGCAGT
1496534 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1496559 TAACATGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1501779 original size:170 final size:170
Alignment explanation
Indices: 1501497--1501837 Score: 673
Period size: 170 Copynumber: 2.0 Consensus size: 170
1501487 GGTAGTGGGA
1501497 TCCCACAAGCGATACCCCTTTACTCCATCAGCATACCCCAAGAATTTGCATTTCCTGGATTTTGG
1 TCCCACAAGCGATACCCCTTTACTCCATCAGCATACCCCAAGAATTTGCATTTCCTGGATTTTGG
1501562 ATCCAGCTTTGAAATTTCTTGGGCGTTGTACATCACGTACACAATACTTCCAAATACATGGAGAT
66 ATCCAGCTTTGAAATTTCTTGGGCGTTGTACATCACGTACACAATACTTCCAAATACATGGAGAT
1501627 TTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGG
131 TTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGG
1501667 TCCCACAAGCGATACCCCTTTACTCCATCAGCATACCCCAAGAATTTGCATTTCCTGGATTTTGG
1 TCCCACAAGCGATACCCCTTTACTCCATCAGCATACCCCAAGAATTTGCATTTCCTGGATTTTGG
*
1501732 ATCCAGCTTTGAAATTTCTTGGGCGTTGTACATCACGTACACAATACTTCCAAATACATGGAGGT
66 ATCCAGCTTTGAAATTTCTTGGGCGTTGTACATCACGTACACAATACTTCCAAATACATGGAGAT
1501797 TTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGG
131 TTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGG
1501837 T
1 T
1501838 GTCTTCAGCT
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 170 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (170 bp):
TCCCACAAGCGATACCCCTTTACTCCATCAGCATACCCCAAGAATTTGCATTTCCTGGATTTTGG
ATCCAGCTTTGAAATTTCTTGGGCGTTGTACATCACGTACACAATACTTCCAAATACATGGAGAT
TTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGG
Found at i:1505609 original size:60 final size:60
Alignment explanation
Indices: 1505476--1505663 Score: 164
Period size: 60 Copynumber: 3.1 Consensus size: 60
1505466 TTGCACCATG
* * * * * *
1505476 TCTCTAAACTATTATATTTACTTTAAATT-GATCCTTAAA-TTATTGATTATTTAAATTTCA
1 TCTCCAAACTATGACATTTATTTTAAATTAG-TCCTTAAACTT-TTGAATATTTCAATTTCA
* * *
1505536 TCTCTAAATTATGACTTTTATTTTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTCA
1 TCTCCAAACTATGACATTTATTTTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTCA
* * * * * ** * * *
1505596 TCTCCGAACTATGACAATCATTCTAAACTAGTCCCCAAACTTTTAAATCTTCCAATTTCA
1 TCTCCAAACTATGACATTTATTTTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTCA
*
1505656 TCCCCAAA
1 TCTCCAAA
1505664 TTCAGCCAAA
Statistics
Matches: 104, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
60 101 0.97
61 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (60 bp):
TCTCCAAACTATGACATTTATTTTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTCA
Found at i:1508254 original size:32 final size:32
Alignment explanation
Indices: 1508213--1508277 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
1508203 GACATTTTTT
*
1508213 TGAAATGAAGTGATATATCACT-AAAACGTTTC
1 TGAAATGAAGTGATATATCAATGAAAA-GTTTC
1508245 TGAAATGAAGTGATATATCAATGAAAAGTTTC
1 TGAAATGAAGTGATATATCAATGAAAAGTTTC
1508277 T
1 T
1508278 ATCACCGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 27 0.87
33 4 0.13
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (32 bp):
TGAAATGAAGTGATATATCAATGAAAAGTTTC
Found at i:1511195 original size:12 final size:12
Alignment explanation
Indices: 1511180--1511211 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1511170 ATATATGTAT
1511180 ATGTGTATGTGC
1 ATGTGTATGTGC
*
1511192 ATGTGCATGTGC
1 ATGTGTATGTGC
1511204 ATGTGTAT
1 ATGTGTAT
1511212 ATATATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.09, G:0.31, T:0.41
Consensus pattern (12 bp):
ATGTGTATGTGC
Found at i:1511649 original size:29 final size:29
Alignment explanation
Indices: 1511588--1511680 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
1511578 TGATCATAAA
* * * *
1511588 CAGAAACAGAACGAGG-ATATAATCCTATA
1 CAGAAATAAAACGAGGAAT-TAATCCCATG
1511617 CAGAAATAAAACG-GGAAATTAATCCCATG
1 CAGAAATAAAACGAGG-AATTAATCCCATG
** **
1511646 CAGAGTTAGTACGAGGAATTAATCCCATG
1 CAGAAATAAAACGAGGAATTAATCCCATG
1511675 CA-AAAT
1 CAGAAAT
1511681 CAAGACTGCA
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 4 0.08
29 43 0.84
30 4 0.08
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.19
Consensus pattern (29 bp):
CAGAAATAAAACGAGGAATTAATCCCATG
Found at i:1512325 original size:16 final size:16
Alignment explanation
Indices: 1512294--1512345 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
1512284 CGAGTCGGTT
1512294 AATGGGTCATGTCTGTC
1 AATGGGTCA-GTCTGTC
*
1512311 AATGGGTCAGTCTGTT
1 AATGGGTCAGTCTGTC
* *
1512327 AACGGGTCGAGTCGGTC
1 AATGGGTC-AGTCTGTC
1512344 AA
1 AA
1512346 CAGGTCAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (16 bp):
AATGGGTCAGTCTGTC
Found at i:1514216 original size:64 final size:64
Alignment explanation
Indices: 1514097--1514216 Score: 138
Period size: 64 Copynumber: 1.9 Consensus size: 64
1514087 TAAATTTAAA
* * *** *
1514097 AAAATCAAAGAAGGAAATATTAAATTTTAAAAAATGTTATATAAAAAATGTTAAAAGAAAAAAT
1 AAAATCAAAGAAGAAAATATTAAATTTCAAAAAATAAAATATAAAAAATGATAAAAGAAAAAAT
1514161 AAAAT-AAATGAAGAAAATATTAAATTTCAGAAAAATAAAA-ATAAAAAAAT-ATAAAA
1 AAAATCAAA-GAAGAAAATATTAAATTTCA-AAAAATAAAATAT-AAAAAATGATAAAA
1514217 AATGTTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.06
64 30 0.64
65 14 0.30
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (64 bp):
AAAATCAAAGAAGAAAATATTAAATTTCAAAAAATAAAATATAAAAAATGATAAAAGAAAAAAT
Found at i:1514281 original size:16 final size:16
Alignment explanation
Indices: 1514230--1514287 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
1514220 GTTAAAAGAG
*
1514230 AAAATAAAAATAAAAT
1 AAAATAAAAATAAAAC
* * **
1514246 TAAATAAAAA-AGTAGG
1 AAAATAAAAATA-AAAC
1514262 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
1514278 AAAATAAAAA
1 AAAATAAAAA
1514288 AAGAAGTGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:1514346 original size:24 final size:25
Alignment explanation
Indices: 1514309--1514365 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1514299 AATTTGAAAG
*
1514309 AAAATATAAGGAAA-GAAAA-ATAAT
1 AAAATA-AATGAAAGGAAAATATAAT
1514333 AATAATAAATGAAAGGAAAATATAAT
1 AA-AATAAATGAAAGGAAAATATAAT
1514359 AAAATAA
1 AAAATAA
1514366 TAAATAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 8 0.28
25 14 0.48
26 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (25 bp):
AAAATAAATGAAAGGAAAATATAAT
Found at i:1514437 original size:18 final size:18
Alignment explanation
Indices: 1514414--1514456 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1514404 TTGTTTTTTA
*
1514414 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1514432 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1514450 AAATAAA
1 AAATAAA
1514457 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1515797 original size:85 final size:85
Alignment explanation
Indices: 1515694--1516142 Score: 571
Period size: 85 Copynumber: 5.3 Consensus size: 85
1515684 CAGATATCTT
* * * * *
1515694 TTCTCGACTTAAGCTATGTTGTAAATTTGATCTGTCC-TTAAGCTGAATGTAATCGAACTCGAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATG-CCTTTGAGCTGAATGTAATCGAACTCGAAG
*
1515758 GTCTTTGCTGACAGATAGCCC
65 GTCTTTGCTGACAGATAACCC
* * * *
1515779 TTCTCGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTAAATGTAATCGAACTCAAAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTC-GAAG
*
1515844 GTCTTTG-TGGACAGGTAACCC
65 GTCTTTGCT-GACAGATAACCC
* * * *
1515865 TTCTCTCCTTGAGTTATGCTG-ATAATTTGATATGCCTTTGAGCTGAGTATAATCGAACTCGAAG
1 TTCTCGCCTTGAGCTATGCTGTA-AATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAG
* * *
1515929 GTCTTGGTTGACAGATAGCCC
65 GTCTTTGCTGACAGATAACCC
* * *
1515950 TTCTCGCCTTGAGCTATGCTATAAATTTGATATGTCTTTGAGCTGAATGTAATCGAACCCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
1516015 TCTTTTGCTGACAGATAACCC
66 TC-TTTGCTGACAGATAACCC
* *
1516036 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
* * * *
1516101 TCTTGGTTGAAAGATATCCC
66 TCTTTGCTGACAGATAACCC
* *
1516121 TTATTGCCTTGAGCTATGCTGT
1 TTCTCGCCTTGAGCTATGCTGT
1516143 CAATAGTTCC
Statistics
Matches: 317, Mismatches: 40, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
84 2 0.01
85 163 0.51
86 152 0.48
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (85 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
TCTTTGCTGACAGATAACCC
Found at i:1516002 original size:171 final size:170
Alignment explanation
Indices: 1515694--1516140 Score: 621
Period size: 171 Copynumber: 2.6 Consensus size: 170
1515684 CAGATATCTT
* * * * * * *
1515694 TTCTCGACTTAAGCTATGTTGTAAATTTGATCTGTCC-TTAAGCTGAATGTAATCGAACTCGAAG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATG-CCTTTGAGCTGAGTGTAATCGAACTCGAAG
* * * * *
1515758 GTCTTTGCTGACAGATAGCCCTTCTCGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCT
65 GTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCT
*
1515823 AAATGTAATCGAACTCAAAAGGTCTTTGTG-GACAGGTAACCC
130 AAATGTAATCGAAC-CAAAAGGTCTTT-TGCGACAGATAACCC
* *
1515865 TTCTCTCCTTGAGTTATGCTG-ATAATTTGATATGCCTTTGAGCTGAGTATAATCGAACTCGAAG
1 TTCTCGCCTTGAGTTATGCTGTA-AATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
1515929 GTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGTCTTTGAGCT
65 GTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCT
* **
1515994 GAATGTAATCGAACCCGAAGGTCTTTTGCTGACAGATAACCC
130 AAATGTAATCGAACCAAAAGGTCTTTTGC-GACAGATAACCC
1516036 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * *
1516101 TCTTGGTTGAAAGATATCCCTTATTGCCTTGAGCTATGCT
66 TCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCT
1516141 GTCAATAGTT
Statistics
Matches: 246, Mismatches: 25, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
169 2 0.01
170 13 0.05
171 230 0.93
172 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (170 bp):
TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
TCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTTGAGCTA
AATGTAATCGAACCAAAAGGTCTTTTGCGACAGATAACCC
Found at i:1520223 original size:9 final size:9
Alignment explanation
Indices: 1520201--1520347 Score: 66
Period size: 9 Copynumber: 15.4 Consensus size: 9
1520191 AAAAAATGTT
*
1520201 AAAAGAAAA
1 AAAATAAAA
1520210 AAAATAAAA
1 AAAATAAAA
* * *
1520219 TAAATGAAG
1 AAAATAAAA
**
1520228 AAAATATTA
1 AAAATAAAA
**
1520237 AATTTAAAA
1 AAAATAAAA
1520246 AAAATAAAA
1 AAAATAAAA
1520255 ATAAA-AAAA
1 A-AAATAAAA
**
1520264 ATCATGAAAA
1 AAAAT-AAAA
* *
1520274 GAGAA-AATA
1 -AAAATAAAA
1520283 AAAATAAAA
1 AAAATAAAA
1520292 TAAAATAAAA
1 -AAAATAAAA
1520302 TAAAATAAAA
1 -AAAATAAAA
1520312 AAGTGAGA-AAATA
1 AA---A-ATAAA-A
1520325 AAAATAAAA
1 AAAATAAAA
1520334 CAAAATAAAA
1 -AAAATAAAA
1520344 AAAA
1 AAAA
1520348 GAAGTGTTAA
Statistics
Matches: 103, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
8 4 0.04
9 50 0.49
10 39 0.38
11 2 0.02
12 4 0.04
13 4 0.04
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (9 bp):
AAAATAAAA
Found at i:1520253 original size:15 final size:15
Alignment explanation
Indices: 1520241--1520344 Score: 74
Period size: 16 Copynumber: 7.0 Consensus size: 15
1520231 ATATTAAATT
1520241 TAAAAAAAATAAAAA
1 TAAAAAAAATAAAAA
*
1520256 TAAAAAAAATCATGAAA
1 TAAAAAAAAT-A-AAAA
* *
1520273 -AGAGAAAATAAAAA
1 TAAAAAAAATAAAAA
1520287 TAAAATAAAAT-AAAA
1 TAAAA-AAAATAAAAA
* *
1520302 T-AAAATAA-AAAAG
1 TAAAAAAAATAAAAA
* *
1520315 T-GAGAAAATAAAAA
1 TAAAAAAAATAAAAA
1520329 TAAAACAAAATAAAAA
1 TAAAA-AAAATAAAAA
1520345 AAAGAAGTGT
Statistics
Matches: 67, Mismatches: 14, Indels: 15
0.70 0.15 0.16
Matches are distributed among these distances:
13 11 0.16
14 11 0.16
15 19 0.28
16 23 0.34
17 3 0.04
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (15 bp):
TAAAAAAAATAAAAA
Found at i:1520258 original size:42 final size:41
Alignment explanation
Indices: 1520194--1520305 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
1520184 GTTATATAAA
* * * *
1520194 AAATGTTAAAAGAAA-AAAAATAAAATAAATGAAGAAAATATT
1 AAAT-TTAAAAAAAATAAAAATAAAATAAATCAAGAAAAGA-G
* *
1520236 AAATTTAAAAAAAATAAAAATAAAAAAAATCATGAAAAGAG
1 AAATTTAAAAAAAATAAAAATAAAATAAATCAAGAAAAGAG
* *
1520277 AAAATAAAAATAAAAT-AAAATAAAATAAA
1 AAATTTAAAA-AAAATAAAAATAAAATAAA
1520306 ATAAAAAAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 29 0.49
42 30 0.51
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (41 bp):
AAATTTAAAAAAAATAAAAATAAAATAAATCAAGAAAAGAG
Found at i:1520260 original size:5 final size:5
Alignment explanation
Indices: 1520241--1520347 Score: 58
Period size: 5 Copynumber: 20.0 Consensus size: 5
1520231 ATATTAAATT
* *
1520241 TAAAA -AAAA TAAAAA TAAAA AAAATCA TGAAAA GAGAAA ATAAAAA TAAAA
1 TAAAA TAAAA T-AAAA TAAAA TAAA--A T-AAAA TA-AAA -TAAA-A TAAAA
* * *
1520292 TAAAA TAAAA TAAAA TAAAA -AAGTGA GAAAA TAAAAA TAAAA CAAAA
1 TAAAA TAAAA TAAAA TAAAA TAA--AA TAAAA T-AAAA TAAAA TAAAA
1520339 TAAAA -AAAA
1 TAAAA TAAAA
1520348 GAAGTGTTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
4 10 0.12
5 42 0.52
6 21 0.26
7 5 0.06
8 3 0.04
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.14
Consensus pattern (5 bp):
TAAAA
Found at i:1520287 original size:68 final size:66
Alignment explanation
Indices: 1520144--1520290 Score: 170
Period size: 68 Copynumber: 2.2 Consensus size: 66
1520134 AATTAAATTT
*** * * *
1520144 AAAAAAATCAAAGAAGAAAATATTAAATTTTAAAAAAAATGTTATATAAAAAATGTTAAAAGAAA
1 AAAAAAAT-AAAGAAGAAAATATTAAATTTTAAAAAAAATAAAATAAAAAAAATATGAAAAGAAA
1520209 AA
65 AA
1520211 AAATAAAATAAATGAAGAAAATATTAAA-TTTAAAAAAAATAAAAATAAAAAAAATCATGAAAAG
1 AAA-AAAATAAA-GAAGAAAATATTAAATTTTAAAAAAAAT-AAAATAAAAAAAAT-ATGAAAAG
*
1520275 AGAAA
62 AAAAA
*
1520280 ATAAAAATAAA
1 AAAAAAATAAA
1520291 ATAAAATAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
67 18 0.26
68 38 0.56
69 12 0.18
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (66 bp):
AAAAAAATAAAGAAGAAAATATTAAATTTTAAAAAAAATAAAATAAAAAAAATATGAAAAGAAAA
A
Found at i:1520307 original size:42 final size:40
Alignment explanation
Indices: 1520242--1520347 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 40
1520232 TATTAAATTT
*
1520242 AAAA-AAAATAAAAATAAAAAAAATCATGAAAA-GAGAAAATA
1 AAAATAAAAT-AAAATAAAAAAAAT-A-AAAAAGGAGAAAATA
1520283 AAAATAAAATAAAATAAAATAAAATAAAAAAGTGAGAAAATA
1 AAAATAAAATAAAATAAAA-AAAATAAAAAAG-GAGAAAATA
*
1520325 AAAATAAAACAAAATAAAAAAAA
1 AAAATAAAATAAAATAAAAAAAA
1520348 GAAGTGTTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
40 4 0.07
41 18 0.31
42 37 0.63
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (40 bp):
AAAATAAAATAAAATAAAAAAAATAAAAAAGGAGAAAATA
Found at i:1520329 original size:37 final size:36
Alignment explanation
Indices: 1520283--1520353 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 36
1520273 AGAGAAAATA
*
1520283 AAAATAAAATAAAATAAAATAAAATAAAA-AAGTGAG
1 AAAATAAAATAAAACAAAATAAAA-AAAAGAAGTGAG
1520319 AAAATAAAAATAAAACAAAATAAAAAAAAGAAGTG
1 AAAAT-AAAATAAAACAAAATAAAAAAAAGAAGTG
1520354 TTAAATTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 9 0.28
37 23 0.72
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (36 bp):
AAAATAAAATAAAACAAAATAAAAAAAAGAAGTGAG
Found at i:1520394 original size:22 final size:20
Alignment explanation
Indices: 1520369--1520416 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
1520359 TTCGAAAGAA
1520369 AATACAAGGAAAGAAAAAATAT
1 AATA-AAGGAAAG-AAAAATAT
* *
1520391 AATAAATGAAAGGAAAATAT
1 AATAAAGGAAAGAAAAATAT
1520411 AATAAA
1 AATAAA
1520417 ATAATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 7 0.29
22 4 0.17
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (20 bp):
AATAAAGGAAAGAAAAATAT
Found at i:1520401 original size:21 final size:20
Alignment explanation
Indices: 1520377--1520416 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1520367 AAAATACAAG
1520377 GAAAGAAAAAATATAATAAAT
1 GAAAG-AAAAATATAATAAAT
*
1520398 GAAAGGAAAATATAATAAA
1 GAAAGAAAAATATAATAAA
1520417 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (20 bp):
GAAAGAAAAATATAATAAAT
Found at i:1520497 original size:18 final size:19
Alignment explanation
Indices: 1520467--1520512 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1520457 AAGTTGTGTT
*
1520467 TTAAAATAAAAGATAAGAA
1 TTAAAATAAAAGAAAAGAA
*
1520486 TTAAAA-AAAAGAAAATAA
1 TTAAAATAAAAGAAAAGAA
1520504 TT-AAATAAA
1 TTAAAATAAA
1520513 TAATATAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 15 0.62
19 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
TTAAAATAAAAGAAAAGAA
Found at i:1522083 original size:20 final size:20
Alignment explanation
Indices: 1522042--1522079 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1522032 ATTTGAACAT
*
1522042 ATTTAATTGTTTCAAATGTA
1 ATTTAATTGATTCAAATGTA
*
1522062 ATTT-ATTGATTCTAATGT
1 ATTTAATTGATTCAAATGT
1522080 TAATAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (20 bp):
ATTTAATTGATTCAAATGTA
Found at i:1522990 original size:22 final size:23
Alignment explanation
Indices: 1522964--1523006 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1522954 TTATTAAAAT
1522964 TATTTGAATCAA-TTTAAATTCA
1 TATTTGAATCAATTTTAAATTCA
* *
1522986 TATTTTAATTAATTTTAAATT
1 TATTTGAATCAATTTTAAATT
1523007 TATAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTTGAATCAATTTTAAATTCA
Found at i:1523228 original size:24 final size:25
Alignment explanation
Indices: 1523177--1523239 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
1523167 AAAAATGTTT
* * *
1523177 TTTTATAATTTAA-TCTTTTAGTTT
1 TTTTATAATTTAATTATTTTAGATC
1523201 TTTTATAATTTAATTATTTTA-ATC
1 TTTTATAATTTAATTATTTTAGATC
* *
1523225 TTTTTTTATTTAATT
1 TTTTATAATTTAATT
1523240 TAGTCTTGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 27 0.82
25 6 0.18
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTTATAATTTAATTATTTTAGATC
Found at i:1524627 original size:18 final size:18
Alignment explanation
Indices: 1524604--1524638 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1524594 ACCCTTTTCA
*
1524604 AAAATGATTTTCTGGTTC
1 AAAATGATTTTATGGTTC
1524622 AAAATGATTTTATGGTT
1 AAAATGATTTTATGGTT
1524639 AAGTGTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (18 bp):
AAAATGATTTTATGGTTC
Found at i:1526423 original size:29 final size:29
Alignment explanation
Indices: 1526356--1526441 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
1526346 ATACGTGACA
* *
1526356 TTAATTAAAGAATATTTTAAATA-TATATT
1 TTAATTAAAAAATATTTTAAATACT-TATC
*
1526385 TTAATAAAAAAATATTTTAAATACTTATC
1 TTAATTAAAAAATATTTTAAATACTTATC
** *
1526414 TTGGTTAAAATAATAATTTTAAGTACTT
1 TTAATTAAAA-AAT-ATTTTAAATACTT
1526442 TGACTAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 31 0.66
30 4 0.09
31 12 0.26
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
TTAATTAAAAAATATTTTAAATACTTATC
Found at i:1527290 original size:228 final size:227
Alignment explanation
Indices: 1526850--1527297 Score: 781
Period size: 229 Copynumber: 2.0 Consensus size: 227
1526840 GTAAATTATC
* * *
1526850 TATCCTTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1526915 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
1526980 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1527045 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
1527078 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTATCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1527143 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
1527208 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATG-AACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
1527272 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
1527298 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
227 4 0.02
228 74 0.35
229 131 0.63
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1527386 original size:20 final size:19
Alignment explanation
Indices: 1527363--1527408 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1527353 AGATATACCA
1527363 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1527383 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1527403 GGTAAA
1 GGTAAA
1527409 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1527559 original size:19 final size:20
Alignment explanation
Indices: 1527528--1527573 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1527518 CGATATAACA
1527528 GGTAAAAATATGAT-AAACC
1 GGTAAAAATATGATAAAACC
1527547 GGTAATAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
1527567 GGTAAAA
1 GGTAAAA
1527574 TGATACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:1530742 original size:19 final size:19
Alignment explanation
Indices: 1530698--1530741 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1530688 AATGTCGAGT
1530698 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1530717 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1530736 T-ATTTT
1 TAATTTT
1530742 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1531569 original size:399 final size:399
Alignment explanation
Indices: 1530824--1532247 Score: 2708
Period size: 399 Copynumber: 3.6 Consensus size: 399
1530814 TTAAGGGTCA
* *
1530824 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1530889 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1530954 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1531019 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
* *
1531084 CACCCATCAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGAA
261 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
1531149 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
326 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1531214 TAAATAATG
391 TAAATAATG
*
1531223 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
*
1531288 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1531353 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
* **
1531418 TAATGTGTCGACACTAATATAGTGTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGT
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
* *
1531483 GCATCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
260 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
1531547 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
325 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
1531612 CTAAATAATG
390 CTAAATAATG
1531622 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1531687 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1531752 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
1531817 AATGTGTCGACACTAATATAGTCTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
1531882 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
261 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
1531947 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
326 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1532012 TAAATAATG
391 TAAATAATG
1532021 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1532086 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1532150 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1532215 AATGTGTCGACACTAATATAGTTTGTGTCGATA
196 AATGTGTCGACACTAATATAGTTTGTGTCGATA
1532248 CTAATTTAAA
Statistics
Matches: 1003, Mismatches: 20, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
398 333 0.33
399 478 0.48
400 192 0.19
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (399 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
TAAATAATG
Found at i:1531593 original size:199 final size:199
Alignment explanation
Indices: 1530824--1532247 Score: 2661
Period size: 200 Copynumber: 7.1 Consensus size: 199
1530814 TTAAGGGTCA
* *
1530824 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1530889 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1530954 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1531019 AATG
196 AATG
** *
1531023 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
* * *
1531088 CATCAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGAATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1531153 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1531218 TAATG
195 TAATG
*
1531223 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
*
1531288 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1531353 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1531418 TAATG
195 TAATG
*
1531423 TGTCGACACTAATATAGTGTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1531488 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1531553 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1531618 AATG
196 AATG
1531622 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1531687 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1531752 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1531817 AATG
196 AATG
* ** *
1531821 TGTCGACACTAATATAGTCTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
*
1531886 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1531951 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1532016 TAATG
195 TAATG
1532021 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
1532086 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1532150 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1532215 AATG
196 AATG
1532219 TGTCGACACTAATATAGTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1532248 CTAATTTAAA
Statistics
Matches: 1198, Mismatches: 25, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
198 140 0.12
199 474 0.40
200 584 0.49
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:1533734 original size:6 final size:6
Alignment explanation
Indices: 1533709--1533806 Score: 56
Period size: 6 Copynumber: 16.3 Consensus size: 6
1533699 ATCGGTCGCA
* * * *
1533709 GAAGAT GAAGCT GACA-AT GAAGAT GACA-AT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GA-AGAT GAAGAT GA-AGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
1533757 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
1533805 GA
1 GA
1533807 TGATCCAAAC
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
5 1 0.01
6 70 0.96
7 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1533745 original size:3 final size:3
Alignment explanation
Indices: 1533737--1533810 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
1533727 GAAGATGACA
* * * ** * *
1533737 ATG ATG ATG ATG ATG ACG ATG AAG CTG GCG ATG AAG ATG ATG ACG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
1533785 ATG ATG ATG ATG ATG AAG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
1533811 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.35, C:0.05, G:0.34, T:0.26
Consensus pattern (3 bp):
ATG
Found at i:1533758 original size:42 final size:42
Alignment explanation
Indices: 1533712--1533802 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
1533702 GGTCGCAGAA
*
1533712 GATGAAGCTGACAATGAAGATGACAATGATGATGATGATGAC
1 GATGAAGCTGACAATGAAGATGACAACGATGATGATGATGAC
* * ** *
1533754 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACAATGAAGATGACAACGATGATGATGATGAC
1533796 GATGAAG
1 GATGAAG
1533803 ATGATGATCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.08, G:0.33, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACAATGAAGATGACAACGATGATGATGATGAC
Done.