Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008184.1 Hibiscus syriacus cultivar Beakdansim tig00110785_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: 1549336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1113768 original size:21 final size:21
Alignment explanation
Indices: 1113706--1113770 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
1113696 TACATATTCA
**
1113706 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAAATCG
* * **
1113727 CAATGCGATAGTCGACTATCG
1 CATTGCGATAGTCCAAAATCG
*
1113748 CATTGCGATACTCCAAAATCG
1 CATTGCGATAGTCCAAAATCG
1113769 CA
1 CA
1113771 ACGACCGGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (21 bp):
CATTGCGATAGTCCAAAATCG
Found at i:1114384 original size:5 final size:5
Alignment explanation
Indices: 1114369--1114400 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1114359 CGCCGCCATC
*
1114369 CGTCT CATCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1114401 GGTCGTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.03, C:0.41, G:0.19, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:1121189 original size:21 final size:21
Alignment explanation
Indices: 1121155--1121194 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1121145 GTAAAACACC
*
1121155 AATAATAACATTTTCAGTAGA
1 AATAATAACATTTTAAGTAGA
**
1121176 AATAATAATGTTTTAAGTA
1 AATAATAACATTTTAAGTA
1121195 AATTTTTACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
AATAATAACATTTTAAGTAGA
Found at i:1124212 original size:22 final size:19
Alignment explanation
Indices: 1124186--1124225 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
1124176 TAACTAAAAT
1124186 ATAAATTATCATATAGAATATG
1 ATAAATT-T-ATATA-AATATG
1124208 ATAAATTTATATAAATAT
1 ATAAATTTATATAAATAT
1124226 ATTAAATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 1 0.06
22 7 0.39
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (19 bp):
ATAAATTTATATAAATATG
Found at i:1130637 original size:33 final size:33
Alignment explanation
Indices: 1130592--1130668 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
1130582 GAATAGAGAA
*
1130592 AGGAGCATGGGTGATTTAGCGCATTGCAAGGCG
1 AGGAGCACGGGTGATTTAGCGCATTGCAAGGCG
*
1130625 AGGAGCACGGGTGATTTAGTGCATTGCAAGGCG
1 AGGAGCACGGGTGATTTAGCGCATTGCAAGGCG
1130658 AGGAGCACGGG
1 AGGAGCACGGG
1130669 GACGAACAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.25, C:0.16, G:0.42, T:0.18
Consensus pattern (33 bp):
AGGAGCACGGGTGATTTAGCGCATTGCAAGGCG
Found at i:1132433 original size:13 final size:13
Alignment explanation
Indices: 1132415--1132459 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1132405 GAAACAAAAA
1132415 CAAAATGCCACTG
1 CAAAATGCCACTG
** *
1132428 CAAAATGAAAC-A
1 CAAAATGCCACTG
1132440 CAAAATGCCACTG
1 CAAAATGCCACTG
1132453 CAAAATG
1 CAAAATG
1132460 AAACTAACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.49, C:0.24, G:0.13, T:0.13
Consensus pattern (13 bp):
CAAAATGCCACTG
Found at i:1132443 original size:25 final size:25
Alignment explanation
Indices: 1132414--1132463 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1132404 TGAAACAAAA
1132414 ACAAAATGCCACTGCAAAATGAAAC
1 ACAAAATGCCACTGCAAAATGAAAC
1132439 ACAAAATGCCACTGCAAAATGAAAC
1 ACAAAATGCCACTGCAAAATGAAAC
1132464 TAACATACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (25 bp):
ACAAAATGCCACTGCAAAATGAAAC
Found at i:1134112 original size:2 final size:2
Alignment explanation
Indices: 1134107--1134141 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1134097 TAAAAAAATA
*
1134107 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1134142 AAAGTTGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1135634 original size:42 final size:42
Alignment explanation
Indices: 1135546--1135749 Score: 284
Period size: 42 Copynumber: 4.8 Consensus size: 42
1135536 TGTACACCAA
* * * *
1135546 TAAGGCTTAACTTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTG
1 TAAGGCTTACCTT-TGCACACAGCAAAGGGA-CCT-GGGAAACTG
* **
1135590 TAAGGCTTACCCTCACACACAGCAAAGGGACCTGGGAAACTG
1 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTG
1135632 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTG
1 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTG
* * *
1135674 TAAGTCTTACCTTTGCACACAACAAAGGGACCTGGAAAACTG
1 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTG
1135716 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTG
1 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTG
1135750 ATAATACTTC
Statistics
Matches: 144, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
42 118 0.82
43 12 0.08
44 14 0.10
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (42 bp):
TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTG
Found at i:1136546 original size:12 final size:12
Alignment explanation
Indices: 1136529--1136560 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1136519 TTTAATGGTC
1136529 GGTCAAAGTTCT
1 GGTCAAAGTTCT
1136541 GGTCAAAGTTCT
1 GGTCAAAGTTCT
*
1136553 GGTTAAAG
1 GGTCAAAG
1136561 GTGGTCAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.31
Consensus pattern (12 bp):
GGTCAAAGTTCT
Found at i:1136650 original size:29 final size:29
Alignment explanation
Indices: 1136585--1136739 Score: 154
Period size: 29 Copynumber: 5.4 Consensus size: 29
1136575 ATAAACCATT
* * *
1136585 TTACGAAAATAGCATCATTTTC-AAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
1136613 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
* * *
1136642 TTACTAAAATATCA--ATTTTTAAAAAACAA
1 TTACCAAAATATCACCA-TTTT-CAAAATAA
** * *
1136671 TTATGAAAATAACACCCTTTTCAAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
* * *
1136700 TTACCAGAATACCACCATTTTCCAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
1136729 TTACCAAAATA
1 TTACCAAAATA
1136740 CCATCCGGTC
Statistics
Matches: 103, Mismatches: 19, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
27 1 0.01
28 23 0.22
29 75 0.73
30 4 0.04
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (29 bp):
TTACCAAAATATCACCATTTTCAAAATAA
Found at i:1142931 original size:42 final size:42
Alignment explanation
Indices: 1142880--1143045 Score: 287
Period size: 42 Copynumber: 4.0 Consensus size: 42
1142870 GAGCCTAGGA
* *
1142880 AAACTGTAAGGCTTACCCTCGCACACAACAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
1142922 AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
* *
1142964 AAACTGTAAGGCTTACCTTAGCACACAACAAAGGGACCTGAG
1 AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
*
1143006 AAACTGTAAGGCTTACCTTTGTACACAACAAAGGGACCTG
1 AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTG
1143046 ATAATACTTC
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 118 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
Found at i:1143905 original size:29 final size:29
Alignment explanation
Indices: 1143873--1144025 Score: 92
Period size: 29 Copynumber: 5.2 Consensus size: 29
1143863 CTATTATACG
*
1143873 AAAATAGCATCATTTTCAAAATAATTATC
1 AAAATAGCATCATTTTCAAAATAATTACC
* * * * **
1143902 AAAATATCACCTTTTTCAAAATAGTTATT
1 AAAATAGCATCATTTTCAAAATAATTACC
* * ** * * ** *
1143931 AATATATCACTTTTTTTAAAAAAAAAAAACG
1 AAAATAGCA-TCATTTT-CAAAATAATTACC
1143962 AAAATAGCAT-ATTTTCAAAAATAATTACC
1 AAAATAGCATCATTTTC-AAAATAATTACC
* * * *
1143991 AGAATACCACCATTTTCGAAATAATTACC
1 AAAATAGCATCATTTTCAAAATAATTACC
1144020 AAAATA
1 AAAATA
1144026 CCACCCGGTC
Statistics
Matches: 92, Mismatches: 28, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
29 67 0.73
30 12 0.13
31 13 0.14
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATAGCATCATTTTCAAAATAATTACC
Found at i:1145886 original size:38 final size:37
Alignment explanation
Indices: 1145806--1145895 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 37
1145796 CAAATGGGTG
*
1145806 TCCCACGTGTCTTTTTCTTTTTATTTTTTTATTCATA
1 TCCCACGTGTCTTTTTCTTTTTATTTTATTATTCATA
* * *
1145843 GCCCACGTGTCATTTTAT-TTTTTAATTTTATTGTT-GTA
1 TCCCACGTGTC-TTTT-TCTTTTT-ATTTTATTATTCATA
1145881 TCCCACGTGTACTTT
1 TCCCACGTGT-CTTT
1145896 CGGTTTGGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
37 10 0.23
38 23 0.52
39 11 0.25
ACGTcount: A:0.16, C:0.19, G:0.10, T:0.56
Consensus pattern (37 bp):
TCCCACGTGTCTTTTTCTTTTTATTTTATTATTCATA
Found at i:1151202 original size:23 final size:23
Alignment explanation
Indices: 1151176--1151237 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
1151166 AATAACATAT
1151176 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
1151199 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
*
1151222 TAAGTAGCGCTTATAT
1 TAGGTAGCGCTTATAT
1151238 TGACCTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:1151589 original size:198 final size:197
Alignment explanation
Indices: 1151265--1151754 Score: 580
Period size: 198 Copynumber: 2.5 Consensus size: 197
1151255 AAATCAGTAA
* * * * * * *
1151265 ATTTAAACCAGTTACATTATAAATTGACCTATTACATTATAAATATTGGTTTTGATGTTTTCGGG
1 ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTTCGGG
* *** *
1151330 ATCGATA-TAATTTT-AAATGTATCGACACTTTATGCGTGCAACTCGTTTGTGTTTTATTTTGGA
65 ATCGATACT--TTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTTGGA
* * * *
1151393 AAAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATT-TGCTAATTAA-C
128 AAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCT-CTAATGAACC
1151456 CGATAT
192 CGATAT
* * *
1151462 ATTTTAACCGGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGATGTTTCGAGG
1 ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTCG-GG
*
1151527 ATCGATACTTTTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTGCCATTCATTTTGGAA
65 ATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTTGGAA
* * * * *
1151592 AAATGTATCGACACAAATTAAAAAAGTGTCGATACTTTATGTTGACCTATTCTCTCATGAACCCG
129 AAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGAACCCG
1151657 ATAT
194 ATAT
*
1151661 ATTTCT-ACCGGTTACATTGGAAATTTACCTATTACATTATAATTATCGGTCTCTCTGAT-TTT-
1 ATTT-TAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGT-T-TC-GATGTTTC
* *
1151723 GGGATTGATACTTGTTATAAATGTATCGACAC
62 GGGATCGATACTTTTTA-AAATGTATCGACAC
1151755 AAAATCTAAC
Statistics
Matches: 251, Mismatches: 32, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
196 9 0.04
197 56 0.22
198 95 0.38
199 80 0.32
200 3 0.01
201 5 0.02
202 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (197 bp):
ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTCGGGA
TCGATACTTTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTTGGAAAA
AAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGAACCCGAT
AT
Found at i:1157806 original size:20 final size:20
Alignment explanation
Indices: 1157762--1157820 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 20
1157752 CCCTGTGGGC
1157762 GGGAATCGGTTCCCCTTCAAAGG
1 GGGAATCGGTT-CCC-TCAAA-G
1157785 GGGAATCGGTTCCCTC-AAG
1 GGGAATCGGTTCCCTCAAAG
*
1157804 GGGAGATCGATTCCCTC
1 GGGA-ATCGGTTCCCTC
1157821 TGTACCAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.15
20 13 0.38
21 2 0.06
22 3 0.09
23 11 0.32
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (20 bp):
GGGAATCGGTTCCCTCAAAG
Found at i:1161645 original size:20 final size:20
Alignment explanation
Indices: 1161603--1161645 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1161593 TTGTTTTCAT
* *
1161603 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
1161623 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
1161643 TTT
1 TTT
1161646 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:1164837 original size:197 final size:199
Alignment explanation
Indices: 1164424--1165473 Score: 1044
Period size: 197 Copynumber: 5.1 Consensus size: 199
1164414 GTAATTTTAA
* * * * *
1164424 AAAGTATCGACACTAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAA-AACTG
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTATTTTCT--TAATAACCG
* * * * * * * *
1164488 GTAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTACAATTACGGGTTTCGATGTTTT
64 GTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * * *
1164553 TAGGATCGACACTTTTTCTAAATGTATCGACACTTTTTTGTGAACTTGTTTGGAAAATTTATTAT
129 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTAT
*
1164618 GAACAT
194 GGACAT
* * * *
1164624 AAAGTGTCAACACAAATGTATAAAGTATCGATACATTATGTATACCT-TTTT-TTAATAACCGAT
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTATTTTCTTAATAACCGGT
1164687 ATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
66 ATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* *
1164752 GGATCGACACTTGTTATAAATGTGTTGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGG
131 GGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGG
1164817 ACAT
196 ACAT
* * * *
1164821 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCGG
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTAT-TTTCTTAATAACCGG
* *
1164886 TATATTTAGACCGGTTACATTGTTATATTACCTATTACATTATAATTATGTGTTTCGATGTTTTT
65 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * * *
1164951 GGGATCGACACTTGTTATAAATGTATCAACACTTGTTATAAATGTATAGACACTTTTTTCGTG-C
130 GGGATCGACACTTGTTATAAATGTATCGACACTT-TT-T---CG--T-GA-ACTTGTTT-G-GAA
* **
1165015 ACTTGGTT-TGGAAATACATTCT
184 AATTTATTATGG----ACA---T
* *
1165037 GGACAACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATA
1 ----AA-A-GTATCGACACAAATGTATAAAGTGTCGATACATTA-TGTATACCTATTTTCT--TA
* * * * * * * *
1165101 A-AACCGGTAAATTTA-ATCTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTT
57 ATAACCGGTATATTTAGA-CCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTC
* * *
1165164 GATGTTTTTGGGATTGACACTTGATATAAATGTATCGACACTTATTT-ATGAACTTGTTTTGGTT
121 GATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTT-TTTCGTGAACTTG---T--TT
** *
1165228 GGAAAATACATTATGGACAC
180 GGAAAATTTATTATGGACAT
*
1165248 AAAGTATCGACACAAATGTATAAAGTGTCGATACTTTATGTATACCTATTTTCTT-ATAAACCGG
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTATTTTCTTAAT-AACCGG
* * *
1165312 TATATTTAGACCAGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATGTTTTT
65 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * * **
1165377 GGGATCGATACTTTTTTATAAATGTATCGACACTTTGTTCGTGCACTTGGTTTGG-AAATACATT
130 GGGATCGACAC-TTGTTATAAATGTATCGACACTTT-TTCGTGAACTT-GTTTGGAAAATTTATT
*
1165441 CTGGACA-
192 ATGGACAT
* * *
1165448 ACATGTATCGACACGAATGAATAAAG
1 A-AAGTATCGACACAAATGTATAAAG
1165474 CAAATTCATT
Statistics
Matches: 713, Mismatches: 89, Indels: 95
0.79 0.10 0.11
Matches are distributed among these distances:
196 3 0.00
197 170 0.24
198 2 0.00
199 7 0.01
200 145 0.20
201 38 0.05
202 6 0.01
203 1 0.00
204 69 0.10
205 70 0.10
206 9 0.01
207 4 0.01
208 2 0.00
209 10 0.01
210 6 0.01
211 1 0.00
213 7 0.01
214 5 0.01
215 1 0.00
216 3 0.00
217 5 0.01
218 5 0.01
220 2 0.00
221 9 0.01
222 130 0.18
223 3 0.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (199 bp):
AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTATTTTCTTAATAACCGGT
ATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGG
ACAT
Found at i:1164982 original size:21 final size:21
Alignment explanation
Indices: 1164957--1165005 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
1164947 TTTTGGGATC
1164957 GACACTTGTTATAAATGTATCA
1 GACACTTGTTATAAATGTAT-A
1164979 -ACACTTGTTATAAATGTATA
1 GACACTTGTTATAAATGTATA
1164999 GACACTT
1 GACACTT
1165006 TTTTCGTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
GACACTTGTTATAAATGTATA
Found at i:1165143 original size:222 final size:218
Alignment explanation
Indices: 1164754--1165411 Score: 732
Period size: 222 Copynumber: 3.0 Consensus size: 218
1164744 TGTTTTTGGG
* **
1164754 ATCGACACTTGTTATAAATGTGTTGACAC-TTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
1 ATCGACACTTGTTATAAATGT-ATGACACTTTTTTCGTG-ACTTGTTTGG-AAATACATTATGGA
* * *
1164818 CATA-AAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCT-TTCTT-TTTTAAT
63 CA-ACAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTATT-TTCTTATAA-
* *
1164880 AACCGGTATATTTAGACCGGTTACATTGTTATATTACCTATTACATTATAATTATGTGTTTCGAT
125 AACCGGTATATTTAGACCGGTTACATTG-TAAATTACCTATTACATTATAATTATGGGTTTCGAT
1164945 GTTTTTGGGATCGACACTTGTTATAAATGT
189 GTTTTTGGGATCGACACTTGTTATAAATGT
* *
1164975 ATCAACACTTGTTATAAATGTATAGACACTTTTTTCGTGCACTTGGTTTGGAAATACATTCTGGA
1 ATCGACACTTGTTATAAATGTAT-GACACTTTTTTCGTG-ACTT-GTTTGGAAATACATTATGGA
* * * *
1165040 CAACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAAAA
63 CAACAAGTATCGACACAAATGTATAAAGTGTCGATACATTA-TGTATACCTATTTTCTTATAAAA
* * * * * *
1165104 CCGGTAAATTTA-ATCTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTTGATG
127 CCGGTATATTTAGA-CCGGTTACATTGTAAA-TTACCTATTACATTATAATTATGGGTTTCGATG
* *
1165168 TTTTTGGGATTGACACTTGATATAAATGT
190 TTTTTGGGATCGACACTTGTTATAAATGT
*
1165197 ATCGACAC---TTAT---T-TATGA-ACTTGTTTT-G-G--TTG---GAAAATACATTATGGAC-
1 ATCGACACTTGTTATAAATGTATGACACTT-TTTTCGTGACTTGTTTGGAAATACATTATGGACA
*
1165246 ACAAAGTATCGACACAAATGTATAAAGTGTCGATACTTTATGTATACCTATTTTCTTAT-AAACC
65 AC-AAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTATTTTCTTATAAAACC
* ** *
1165310 GGTATATTTAGACCAGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATGTTT
129 GGTATATTTAGACCGGTTACATTG-TAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
1165375 TTGGGATCGATACTTTTTTATAAATGT
193 TTGGGATCGACAC-TTGTTATAAATGT
1165402 ATCGACACTT
1 ATCGACACTT
1165412 TGTTCGTGCA
Statistics
Matches: 375, Mismatches: 45, Indels: 48
0.80 0.10 0.10
Matches are distributed among these distances:
204 68 0.18
205 85 0.23
206 2 0.01
208 1 0.00
209 2 0.01
212 1 0.00
213 5 0.01
214 6 0.02
215 3 0.01
216 1 0.00
219 4 0.01
220 1 0.00
221 32 0.09
222 152 0.41
223 12 0.03
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (218 bp):
ATCGACACTTGTTATAAATGTATGACACTTTTTTCGTGACTTGTTTGGAAATACATTATGGACAA
CAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTATTTTCTTATAAAACCGG
TATATTTAGACCGGTTACATTGTAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTGTTATAAATGT
Found at i:1165376 original size:204 final size:206
Alignment explanation
Indices: 1165017--1165473 Score: 542
Period size: 205 Copynumber: 2.2 Consensus size: 206
1165007 TTTCGTGCAC
* *
1165017 TTGGTTTGGAAATACATTCTGGACAACATGTATCGACACAAATGAATAAAGTGTCGATACATATT
1 TTGGTTTGGAAATACATTATGGACAACAAGTATCGACACAAATGAATAAAGTGTCGATACATATT
**
1165082 GTAGACCTATTTTCTCATAAAACCGGTAAATTTAATCTGGTTACATTGTAAAGTGACCTATTACA
66 GTAGACCTATTTTCTCATAAAACCGGTAAATTTAATCCAGTTACATTGTAAAGTGACCTATTACA
* * * *
1165147 TTATAGTTACGGGTTTTGATGTTTTTGGGATTGACAC-TTGATATAAATGTATCGACACTTATTT
131 TTATAATTACGGGTCTCGATGTTTTTGGGATCGACACTTTGATATAAATGTATCGACACTTATTT
1165211 ATGAACTTGTT
196 ATGAACTTGTT
* *
1165222 TTGG-TTGGAAAATACATTATGGAC-ACAAAGTATCGACACAAATGTATAAAGTGTCGATAC-TT
1 TTGGTTTGG-AAATACATTATGGACAAC-AAGTATCGACACAAATGAATAAAGTGTCGATACATA
* * * * ** *
1165284 TATGTATACCTATTTTCTTAT-AAACCGGTATATTTAGA-CCAGTTACATTGTTATTTTACCTAT
64 T-TGTAGACCTATTTTCTCATAAAACCGGTAAATTTA-ATCCAGTTACATTGTAAAGTGACCTAT
* * **
1165347 TACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACTTTTTTATAAATGTATCGACACTT
127 TACATTATAATTACGGGTCTCGATGTTTTTGGGATCGACACTTTGATATAAATGTATCGACACTT
* *
1165412 -TGTTCGTGCAC-----
192 AT-TT-ATGAACTTGTT
* * *
1165423 TTGGTTTGGAAATACATTCTGGACAACATGTATCGACACGAATGAATAAAG
1 TTGGTTTGGAAATACATTATGGACAACAAGTATCGACACAAATGAATAAAG
1165474 CAAATTCATT
Statistics
Matches: 216, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
201 39 0.18
202 6 0.03
204 77 0.36
205 90 0.42
206 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (206 bp):
TTGGTTTGGAAATACATTATGGACAACAAGTATCGACACAAATGAATAAAGTGTCGATACATATT
GTAGACCTATTTTCTCATAAAACCGGTAAATTTAATCCAGTTACATTGTAAAGTGACCTATTACA
TTATAATTACGGGTCTCGATGTTTTTGGGATCGACACTTTGATATAAATGTATCGACACTTATTT
ATGAACTTGTT
Found at i:1168325 original size:15 final size:15
Alignment explanation
Indices: 1168305--1168340 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1168295 TGATTTCCTC
*
1168305 AGAAGAGCTAGGTTG
1 AGAAGAGATAGGTTG
*
1168320 AGAAGAGATGGGTTG
1 AGAAGAGATAGGTTG
1168335 AGAAGA
1 AGAAGA
1168341 TCCCAGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.42, T:0.17
Consensus pattern (15 bp):
AGAAGAGATAGGTTG
Found at i:1169029 original size:198 final size:198
Alignment explanation
Indices: 1168810--1169448 Score: 932
Period size: 198 Copynumber: 3.2 Consensus size: 198
1168800 TGACCATTTA
* *
1168810 CATTCTAGACA-AAATGTATCGACACAAATTCAA-AGAGTGTCGATACTTTATATACACCTGTTT
1 CATTCTAGACACAAA-GTATAGACACAAATTCAACA-AGTGTCGATACTTTATGTACACCTGTTT
*
1168873 TCTCATAAACCGGTGTATTTAGACCGATTATATTCATAATTTACCTATTACATTATAATTATGGG
64 TCTCATAAACCGGTGTATTTAGACCGATTATATTCATAATTTACCTATTACTTTATAATTATGGG
*
1168938 TCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAG
129 TCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGATGACCTTGGTAAG
1169003 GAAAT
194 GAAAT
* * * * *
1169008 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTATGTTC
1 CATTCTAGACACAAAGTATAGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
* * * * *
1169073 TCATAAACTGGTATATTTAGATC-AGTTAGATTGATAATTTACCTATTACTTTATAATTATGGGT
66 TCATAAACCGGTGTATTTAGACCGA-TTATATTCATAATTTACCTATTACTTTATAATTATGGGT
*
1169137 CTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGATGACCTTGTTAAGG
130 CTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGATGACCTTGGTAAGG
1169202 AAAT
195 AAAT
* *
1169206 CATTCTGGACACAAAGTATAGACACAAATTCAACAAGTGTTGATACTTTATGTACACCTG-TTT-
1 CATTCTAGACACAAAGTATAGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
* * * *
1169269 TCACAAACCGGTGTATTTAGACCGGTTATATTCATAATTTACCTATTACTTTAAAATTATGAGTC
66 TCATAAACCGGTGTATTTAGACCGATTATATTCATAATTTACCTATTACTTTATAATTATGGGTC
* * * * * * *
1169334 TTGATGTTTTTGGGATTGATACTTGTTATAAATGTATCAACACATT-TCCATG-CAATTGGTAAA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTAT-GATGAC-CTTGGTAAG
1169397 GAAAT
194 GAAAT
1169402 CATTCTAGACACAAAGTATAGACACAAATTCAACAAGTGTCGATACT
1 CATTCTAGACACAAAGTATAGACACAAATTCAACAAGTGTCGATACT
1169449 GTAACATCCC
Statistics
Matches: 398, Mismatches: 37, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
195 2 0.01
196 156 0.39
197 3 0.01
198 233 0.59
199 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (198 bp):
CATTCTAGACACAAAGTATAGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
TCATAAACCGGTGTATTTAGACCGATTATATTCATAATTTACCTATTACTTTATAATTATGGGTC
TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGATGACCTTGGTAAGGA
AAT
Found at i:1173467 original size:36 final size:36
Alignment explanation
Indices: 1173420--1173490 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
1173410 TCTTGCAAAT
1173420 GTGATAACTTTAAGAGCTATAGAGAAAGGGCTAGAG
1 GTGATAACTTTAAGAGCTATAGAGAAAGGGCTAGAG
*
1173456 GTGATAGCTTTAAGAGCTATAGAGAAAGGGCTAGA
1 GTGATAACTTTAAGAGCTATAGAGAAAGGGCTAGA
1173491 TGTCAAGCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (36 bp):
GTGATAACTTTAAGAGCTATAGAGAAAGGGCTAGAG
Found at i:1173541 original size:22 final size:23
Alignment explanation
Indices: 1173513--1173566 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1173503 ACTACAGTGT
1173513 AATTCTACGCGGCA-TCCGGTGC
1 AATTCTACGCGGCACTCCGGTGC
* *
1173535 AATTCTACGTGGCACTTCGGTGC
1 AATTCTACGCGGCACTCCGGTGC
*
1173558 AATTATACG
1 AATTCTACG
1173567 AGTTGTGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (23 bp):
AATTCTACGCGGCACTCCGGTGC
Found at i:1174830 original size:19 final size:19
Alignment explanation
Indices: 1174806--1174855 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1174796 TTACATTCAC
*
1174806 ATACAAAATTATAAATCAT
1 ATACAAAATTAAAAATCAT
*
1174825 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCAT
1174844 ATACAAAATTAA
1 ATACAAAATTAA
1174856 CCCTACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCAT
Found at i:1176859 original size:182 final size:180
Alignment explanation
Indices: 1176544--1177118 Score: 740
Period size: 182 Copynumber: 3.2 Consensus size: 180
1176534 ATTAAAGTAC
* * * * * *
1176544 CGACACTTTCAACATAACTGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * ** *
1176609 TTTTTACATATTATATTGTTATGGATCGATACATTTTCATAAAGTATATACACTTTT-TAGGTGC
66 -TTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACA-TTTTATAGGCGC
*
1176673 TATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
129 TATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATTAATTTAT
* * *
1176726 CGACACTTTCAATATATCCGATAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
*
1176791 TTCTTACATGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACATTTTATAGGCGCT
66 TT-TTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTTTATAGGCGCT
**
1176856 ATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAACGTAT
130 ATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATTAATTTAT
* * * *
1176908 CGACACTTTTAATATATCTGGTAACTCTTTACCGGTTTTATCATTTCGTGACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * * *
1176973 CTTATACCTGTTATATTGTTATGGATCGATACGTTTTTATAAAGTATCGACACTTTATAGGCGTT
66 -TTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTTTATAGGCGCT
* * * * *
1177038 ATTACTTCTTTTCTTTTAAATTCCAAAAGTGTTGATACTTATTTTAAATCTAAT
130 ATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATT-AAT-TTAT
* * *
1177092 CGATACTTTCGATATATCCAGTA-CTCT
1 CGACACTTTCAATATATCCGGTAGCTCT
1177119 GTTTTGAAAA
Statistics
Matches: 343, Mismatches: 43, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
181 7 0.02
182 307 0.90
183 9 0.03
184 20 0.06
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (180 bp):
CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
TTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTTTATAGGCGCTA
TAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTATATTAATTTAT
Found at i:1178092 original size:18 final size:18
Alignment explanation
Indices: 1178069--1178108 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1178059 CCGGTTCACT
1178069 AACCGGTCCGGTTCTGAA
1 AACCGGTCCGGTTCTGAA
1178087 AACCGGTCCGGTTCTGAA
1 AACCGGTCCGGTTCTGAA
1178105 AACC
1 AACC
1178109 ATGATCCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (18 bp):
AACCGGTCCGGTTCTGAA
Found at i:1179980 original size:31 final size:31
Alignment explanation
Indices: 1179936--1180008 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
1179926 AAAAATAAGT
*
1179936 TTTGATAAATTT-AATGAGTATTTTATAATAG
1 TTTGATAAATTTAAAT-AGTATTTTATAATAA
* * * *
1179967 TTTGATCAGTTTAAATATTATTTTGTAATAA
1 TTTGATAAATTTAAATAGTATTTTATAATAA
1179998 TTTGA-AAATTT
1 TTTGATAAATTT
1180009 TTAATGACAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 4 0.12
31 27 0.79
32 3 0.09
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (31 bp):
TTTGATAAATTTAAATAGTATTTTATAATAA
Found at i:1182062 original size:17 final size:17
Alignment explanation
Indices: 1182008--1182062 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1181998 TTGTTAAGAG
*
1182008 TTAAAGATTAAAATTAAT
1 TTAAAGATT-TAATTAAT
**
1182026 TTAAAGATTTAATTGGT
1 TTAAAGATTTAATTAAT
**
1182043 TTAATTATTTAATTAAT
1 TTAAAGATTTAATTAAT
1182060 TTA
1 TTA
1182063 TTTTTCAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
TTAAAGATTTAATTAAT
Found at i:1187162 original size:21 final size:22
Alignment explanation
Indices: 1187138--1187188 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
1187128 AGTAGTTTCA
1187138 TTTAAA-A-TATATGTTTAATGT
1 TTTAAATATTATATGTTTAA-GT
*
1187159 TTTAAATATTATATTTTTAAGT
1 TTTAAATATTATATGTTTAAGT
1187181 TTCTAAAT
1 TT-TAAAT
1187189 CATAACGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 6 0.23
22 5 0.19
23 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTAAATATTATATGTTTAAGT
Found at i:1187912 original size:14 final size:15
Alignment explanation
Indices: 1187887--1187915 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1187877 ATTATTCTTG
1187887 TTTTTTATAAAATAT
1 TTTTTTATAAAATAT
1187902 TTTTTTA-AAAATAT
1 TTTTTTATAAAATAT
1187916 AAACATGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTTATAAAATAT
Found at i:1188416 original size:14 final size:14
Alignment explanation
Indices: 1188389--1188419 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1188379 ATTTAAATAC
1188389 TTAAATTTTAAAAT
1 TTAAATTTTAAAAT
1188403 TTAAATTTTAAAAT
1 TTAAATTTTAAAAT
1188417 TTA
1 TTA
1188420 TTATGTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAATTTTAAAAT
Found at i:1197599 original size:26 final size:26
Alignment explanation
Indices: 1197563--1197633 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
1197553 GGTCCACCCG
*
1197563 ACCCGACCCGACCAAAATAAAGTTTT
1 ACCCGACCCGACCAAAATAAAGTTTC
1197589 ACCCGACCCGACCAAAATAAAGTTTC
1 ACCCGACCCGACCAAAATAAAGTTTC
* *
1197615 ACCCGCCCCGACCAGAATA
1 ACCCGACCCGACCAAAATA
1197634 TATGAATTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.14
Consensus pattern (26 bp):
ACCCGACCCGACCAAAATAAAGTTTC
Found at i:1197876 original size:32 final size:31
Alignment explanation
Indices: 1197807--1197933 Score: 128
Period size: 32 Copynumber: 3.8 Consensus size: 31
1197797 ACCTGAACCT
* * *
1197807 GACCCGAATATCACACTTTAAAAAATCCGATC
1 GACCCGAATATCACACTTAAAAAAAT-AGACC
*
1197839 GACCCGAATATCACACTTAAAAAAATTGACC
1 GACCCGAATATCACACTTAAAAAAATAGACC
1197870 GAACCCGACACAAATATCACACTTAAAAAAACTAGACCC
1 G-ACCCG-----AATATCACACTTAAAAAAA-TAGA-CC
*
1197909 GACCCGAATATCAAACTTAAAAAAA
1 GACCCGAATATCACACTTAAAAAAA
1197934 CCCGACCTGA
Statistics
Matches: 82, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
31 4 0.05
32 30 0.37
33 18 0.22
37 19 0.23
38 8 0.10
39 3 0.04
ACGTcount: A:0.47, C:0.27, G:0.09, T:0.17
Consensus pattern (31 bp):
GACCCGAATATCACACTTAAAAAAATAGACC
Found at i:1197919 original size:33 final size:34
Alignment explanation
Indices: 1197807--1197934 Score: 136
Period size: 33 Copynumber: 3.8 Consensus size: 34
1197797 ACCTGAACCT
* * *
1197807 GACCCGAATATCACACTTTAAAAAA-TCCGA-TC
1 GACCCGAATATCACACTTAAAAAAACTCAGACCC
* *
1197839 GACCCGAATATCACACTTAAAAAAATTGACCGAACCC
1 GACCCGAATATCACACTTAAAAAAACT--CAG-ACCC
* *
1197876 GACACAAATATCACACTTAAAAAAACT-AGACCC
1 GACCCGAATATCACACTTAAAAAAACTCAGACCC
*
1197909 GACCCGAATATCAAACTTAAAAAAAC
1 GACCCGAATATCACACTTAAAAAAAC
1197935 CCGACCTGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
32 24 0.29
33 28 0.34
34 1 0.01
35 3 0.04
36 1 0.01
37 25 0.30
ACGTcount: A:0.47, C:0.27, G:0.09, T:0.17
Consensus pattern (34 bp):
GACCCGAATATCACACTTAAAAAAACTCAGACCC
Found at i:1198021 original size:32 final size:32
Alignment explanation
Indices: 1197979--1198053 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
1197969 CGACCCGAAC
*
1197979 CCGACCCGAATATCACAC-TTATAAAAACCCGA
1 CCGACCCGAATATCAAACTTTA-AAAAACCCGA
*
1198011 CCGACTCGAATATCAAACTTTAAAAAACCCGA
1 CCGACCCGAATATCAAACTTTAAAAAACCCGA
1198043 CCTGAACCCGA
1 CC-G-ACCCGA
1198054 TTTTTAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 28 0.76
33 4 0.11
34 5 0.14
ACGTcount: A:0.40, C:0.33, G:0.11, T:0.16
Consensus pattern (32 bp):
CCGACCCGAATATCAAACTTTAAAAAACCCGA
Found at i:1198046 original size:104 final size:105
Alignment explanation
Indices: 1197868--1198058 Score: 303
Period size: 104 Copynumber: 1.8 Consensus size: 105
1197858 AAAAAATTGA
*
1197868 CCGAACCCGACACAAATATCACACTTAAAAAAACTAGACCCGACCCGAATATCAAACTTAAAAAA
1 CCGAACCCGACACAAATATCACACTTAAAAAAACCAGACCCGACCCGAATATCAAACTTAAAAAA
1197933 ACCCGACCTGAACCCAATTTTTTTTATAAAAAAAACCGAC
66 ACCCGACCTGAACCCAATTTTTTTTATAAAAAAAACCGAC
* * * * * *
1197973 CCGAACCCGACCCGAATATCACACTTATAAAAACCCGA-CCGACTCGAATATCAAACTTTAAAAA
1 CCGAACCCGACACAAATATCACACTTAAAAAAACCAGACCCGACCCGAATATCAAACTTAAAAAA
*
1198037 ACCCGACCTGAACCCGATTTTT
66 ACCCGACCTGAACCCAATTTTT
1198059 AAAAAAAAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
104 45 0.58
105 33 0.42
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (105 bp):
CCGAACCCGACACAAATATCACACTTAAAAAAACCAGACCCGACCCGAATATCAAACTTAAAAAA
ACCCGACCTGAACCCAATTTTTTTTATAAAAAAAACCGAC
Found at i:1208782 original size:104 final size:105
Alignment explanation
Indices: 1208589--1208795 Score: 256
Period size: 104 Copynumber: 2.0 Consensus size: 105
1208579 GACCATATAT
* *
1208589 AAATTCCTTAAGAACCATATATATATACCAAGGATCAAGAAAGTGTCTCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAGAAAGTGTCTCAAAAGACCTCATACAT
*
1208654 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAAA
66 GCTCCAAAGAATACATATACGTCCCGAAAGACCACGTAAA
* * * * * *
1208694 AAATTCCTTAAGAATCATATACATATGCTAA-GACCAA-ATACGTGTCTCAAAAGACCTTATAGA
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAGA-AAGTGTCTCAAAAGACCTCATACA
* * * * * *
1208757 TGTTCCATAGGATACCTATATGTCCCGAAAGACCGCGTA
65 TGCTCCAAAGAATACATATACGTCCCGAAAGACCACGTA
1208796 GACCCTCGAC
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
103 1 0.01
104 58 0.67
105 27 0.31
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (105 bp):
AAATTCCTTAAGAACCATATACATATACCAAGGACCAAGAAAGTGTCTCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCGAAAGACCACGTAAA
Found at i:1208993 original size:53 final size:53
Alignment explanation
Indices: 1208936--1209099 Score: 147
Period size: 53 Copynumber: 3.1 Consensus size: 53
1208926 ACACATACAT
*
1208936 GTAATCACGTAGTTCATATCAATTCTCATAGGATTTCATATTCATATAATCAC
1 GTAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCAC
* ** * * * * * ** *
1208989 GTAATTCACTTA-CACATAGCATATTTTCAT-GTAATTCATA--GATATCCCTTAGC
1 GTAA-TCACGTAGTTCATACCA-ATTCTCATAGGATTTCATATTCATAT-AATCA-C
*
1209042 TTAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCAC
1 GTAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCAC
1209095 GTAAT
1 GTAAT
1209100 TCACTTACAC
Statistics
Matches: 79, Mismatches: 24, Indels: 16
0.66 0.20 0.13
Matches are distributed among these distances:
51 4 0.05
52 15 0.19
53 41 0.52
54 15 0.19
55 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (53 bp):
GTAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCAC
Found at i:1209079 original size:106 final size:104
Alignment explanation
Indices: 1208937--1209148 Score: 379
Period size: 106 Copynumber: 2.0 Consensus size: 104
1208927 CACATACATG
*
1208937 TAATCACGTAGTTCATATCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
*
1209002 ACATAGCATATTTTCATGTAATTCATAGATATCCCTTAGCT
66 ACATAGCACATTTTCATGTAATTC--AGATATCCCTTAGCT
1209043 TAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
*
1209108 ACATAGCACATTTTCATGTAATTCAGATGTCCCTTAGCT
66 ACATAGCACATTTTCATGTAATTCAGATATCCCTTAGCT
1209147 TA
1 TA
1209149 TGTCTCTTGA
Statistics
Matches: 103, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 16 0.16
106 87 0.84
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.38
Consensus pattern (104 bp):
TAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
ACATAGCACATTTTCATGTAATTCAGATATCCCTTAGCT
Found at i:1214128 original size:105 final size:104
Alignment explanation
Indices: 1213921--1214134 Score: 259
Period size: 105 Copynumber: 2.0 Consensus size: 104
1213911 GATTGTCCAT
* * * *
1213921 AAGGACCACATATAAATTCCTTAAGAACCATATACATATACCAATGATCAAGTAAGTGTCTCAAA
1 AAGGACCACATAAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAA
1213986 AGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
66 AGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * *** **
1214025 AAGGACCACGTAGAAAATTCCTTAAGAATCATATACATATGTTAAGGACCAAATGCGTGTCTCAA
1 AAGGACCACATA-AAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
* * * **
1214090 AAGACCTCATAGATGTTCCATAAG-ATACCTATGTGTCCCG
65 AAGACCTCATACATGCTCCA-AAGAATACATATACGTCCCG
1214130 AAGGA
1 AAGGA
1214135 ACGTGTAGAC
Statistics
Matches: 92, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
104 11 0.12
105 78 0.85
106 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (104 bp):
AAGGACCACATAAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAA
AGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:1214421 original size:106 final size:105
Alignment explanation
Indices: 1214284--1214496 Score: 372
Period size: 106 Copynumber: 2.0 Consensus size: 105
1214274 CACATACATG
*
1214284 TAATCACATATTCATATCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTACA
1 TAATCACATATTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTACA
1214349 CATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
66 CATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
* * *
1214389 TAATCACGTAGTTCATGCCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTTC
1 TAATCACATA-TTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
*
1214454 ACATAGCACATTTTCATGTAATTCACAGATGTCCCTTAGCT
65 ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
1214495 TA
1 TA
1214497 TGTCTCTTGA
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
105 9 0.09
106 93 0.91
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.37
Consensus pattern (105 bp):
TAATCACATATTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTACA
CATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
Found at i:1215781 original size:21 final size:22
Alignment explanation
Indices: 1215725--1215796 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
1215715 GGGGGTATCA
*
1215725 ATTCCCCTTTGAATGGGTACTG
1 ATTCCCCATTGAATGGGTACTG
* **
1215747 ATTCCCCCTTGAATGGGTTTTG
1 ATTCCCCATTGAATGGGTACTG
* * *
1215769 ATT-CCCATTGAATCGATACCG
1 ATTCCCCATTGAATGGGTACTG
1215790 ATTCCCC
1 ATTCCCC
1215797 TAGCCCAGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 15 0.38
22 25 0.62
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (22 bp):
ATTCCCCATTGAATGGGTACTG
Found at i:1217080 original size:24 final size:24
Alignment explanation
Indices: 1216990--1217082 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 24
1216980 TCTTATTTGA
* * * *
1216990 ATTCTGTTATGATACCTAACCTGG
1 ATTCTGATATGATACTTGACTTGG
* **
1217014 ATTCTGATCTGATA-TTGACACGG
1 ATTCTGATATGATACTTGACTTGG
* *
1217037 ATT-TGATCTGATACATGACTTGG
1 ATTCTGATATGATACTTGACTTGG
1217060 ATTCTGATATGATACTTGACTTG
1 ATTCTGATATGATACTTGACTTG
1217083 AATTATGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 10 0.18
23 17 0.30
24 29 0.52
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACTTGG
Found at i:1217096 original size:24 final size:24
Alignment explanation
Indices: 1217040--1217089 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1217030 GACACGGATT
* * *
1217040 TGATCTGATACATGACTTGGATTC
1 TGATATGATACATGACTTGAATTA
*
1217064 TGATATGATACTTGACTTGAATTA
1 TGATATGATACATGACTTGAATTA
1217088 TG
1 TG
1217090 TTTTGATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATATGATACATGACTTGAATTA
Found at i:1219904 original size:29 final size:29
Alignment explanation
Indices: 1219871--1219939 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
1219861 AAAAACATTA
*
1219871 ATTAAATAAAATATTAAAAAAT-TTAAAT
1 ATTAAATAAAATATAAAAAAATATTAAAT
1219899 ACTTAAAT-AAAT-TAAAAAAATATTAAAT
1 A-TTAAATAAAATATAAAAAAATATTAAAT
1219927 A-T-AATAAAATATA
1 ATTAAATAAAATATA
1219940 CCTTAAACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 10 0.28
28 12 0.33
29 6 0.17
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (29 bp):
ATTAAATAAAATATAAAAAAATATTAAAT
Found at i:1219934 original size:20 final size:21
Alignment explanation
Indices: 1219895--1219935 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1219885 TAAAAAATTT
1219895 AAATACTTAAATAAATTAAAA
1 AAATACTTAAATAAATTAAAA
1219916 AAATA-TTAAATATAA-TAAAA
1 AAATACTTAAATA-AATTAAAA
1219936 TATACCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATACTTAAATAAATTAAAA
Found at i:1219937 original size:17 final size:16
Alignment explanation
Indices: 1219862--1219938 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 16
1219852 ATATCTGTAA
* *
1219862 AAAACATTAATTAAAT
1 AAAATATTAAATAAAT
1219878 AAAATATTAAA-AAATT
1 AAAATATTAAATAAA-T
*
1219894 TAAATACTTAAATAAATT
1 AAAATA-TTAAATAAA-T
1219912 AAAAAAATATTAAATATAAT
1 ---AAAATATTAAATA-AAT
1219932 AAAATAT
1 AAAATAT
1219939 ACCTTAAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.06
16 15 0.30
17 12 0.24
18 5 0.10
20 8 0.16
21 7 0.14
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:1229435 original size:24 final size:24
Alignment explanation
Indices: 1229408--1229510 Score: 129
Period size: 24 Copynumber: 4.3 Consensus size: 24
1229398 TTCCAGTTGA
*
1229408 ACCAAAGGCGGGGGTGCTTGTAGC
1 ACCAAAGGCAGGGGTGCTTGTAGC
1229432 ACCAAAGGCAGGGGTGCTTGT-GAC
1 ACCAAAGGCAGGGGTGCTTGTAG-C
*
1229456 ACCAAAGGCAGGGGTGCTTG-AGGA
1 ACCAAAGGCAGGGGTGCTTGTA-GC
** *
1229480 ACCAAAGGCAGAAGTGCTTGTGGC
1 ACCAAAGGCAGGGGTGCTTGTAGC
1229504 ACCAAAG
1 ACCAAAG
1229511 CTACCAACTG
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.01
24 67 0.97
25 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.37, T:0.15
Consensus pattern (24 bp):
ACCAAAGGCAGGGGTGCTTGTAGC
Found at i:1229464 original size:48 final size:48
Alignment explanation
Indices: 1229408--1229510 Score: 145
Period size: 48 Copynumber: 2.1 Consensus size: 48
1229398 TTCCAGTTGA
* * **
1229408 ACCAAAGGCGGGGGTGCTTGTA-GCACCAAAGGCAGGGGTGCTTGTGAC
1 ACCAAAGGCAGGGGTGCTTG-AGGAACCAAAGGCAGAAGTGCTTGTGAC
*
1229456 ACCAAAGGCAGGGGTGCTTGAGGAACCAAAGGCAGAAGTGCTTGTGGC
1 ACCAAAGGCAGGGGTGCTTGAGGAACCAAAGGCAGAAGTGCTTGTGAC
1229504 ACCAAAG
1 ACCAAAG
1229511 CTACCAACTG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 48 0.98
ACGTcount: A:0.28, C:0.20, G:0.37, T:0.15
Consensus pattern (48 bp):
ACCAAAGGCAGGGGTGCTTGAGGAACCAAAGGCAGAAGTGCTTGTGAC
Found at i:1229676 original size:279 final size:278
Alignment explanation
Indices: 1229265--1229789 Score: 739
Period size: 279 Copynumber: 1.9 Consensus size: 278
1229255 AGATGGGCTA
1229265 GACCCAAAGCTGAATGAAGGAGTAGAAGATGCCCCAAAAGCAGGTGTGCTTGGTGCTCCAAAAGT
1 GACCCAAAGCTGAATGAAGGAGTAGAAGATGCCCCAAAAGCAGGTGTGCTTGGTGCTCCAAAAGT
* * * **
1229330 GCCTCCAGTTCCAAAGATCGTGGTGTTAGGCGTACCAAATGCAATTCCACTGCTCCCAAATGCTG
66 ACCTCCAGTTCCAAAGACCGGGGCATTAGGCG-ACCAAATGCAATTCCACTGCTCCCAAATGCTG
* * * * * * *
1229395 GACTTCCAGTTGAACCAAAGGCGGGGGTGCTTGTAGCACCAAAGGCAGGGGTGCTTG-TGACACC
130 GACTTCCAGTGGAACCAAAAGCAGGGGTACTTGTAGAACCAAAGGCAGGGGTGCTCGCGGA-ACC
* * *
1229459 AAAGGCAGGGGTGCTTGAGGAACCAAAGGCAGAAGTGCTTGTGGCACCAAAGCTACCAACTGCAG
194 AAAGGCAGGGGTGCTCGAGGAACCAAAGGAAGAAGTGCTCGTGGCACCAAAGCTACCAACTGCAG
1229524 GAGTTGACTGGCCAAATGCT
259 GAGTTGACTGGCCAAATGCT
* * * *
1229544 GACCCAAAGCTGAATGATGGAGTTGAAGATGCTCCAAAAGCAGGTGTGCTTGGTGCTCCAAATGT
1 GACCCAAAGCTGAATGAAGGAGTAGAAGATGCCCCAAAAGCAGGTGTGCTTGGTGCTCCAAAAGT
* * ** *
1229609 ACTTCCTGTTCCAAAGACCGGGGCATTAGAGAC-ACCAAATGCGGTTCCAGTGCTCCCAAATGCT
66 ACCTCCAGTTCCAAAGACCGGGGCATTAG-G-CGACCAAATGCAATTCCACTGCTCCCAAATGCT
*
1229673 GGACTTCCAGTGGAACCAAAAGCAGGGGTACTTGTGGAACCAAAGGCAGGGGTGCTCGCGGAACC
129 GGACTTCCAGTGGAACCAAAAGCAGGGGTACTTGTAGAACCAAAGGCAGGGGTGCTCGCGGAACC
* * **
1229738 AAAGGCAGGGGTGCTCGTGGCACCAAAGGAAGGGGTGCTCGTGGCACCAAAG
194 AAAGGCAGGGGTGCTCGAGGAACCAAAGGAAGAAGTGCTCGTGGCACCAAAG
1229790 GAAGGGTGCT
Statistics
Matches: 214, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
279 210 0.98
280 3 0.01
281 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.18
Consensus pattern (278 bp):
GACCCAAAGCTGAATGAAGGAGTAGAAGATGCCCCAAAAGCAGGTGTGCTTGGTGCTCCAAAAGT
ACCTCCAGTTCCAAAGACCGGGGCATTAGGCGACCAAATGCAATTCCACTGCTCCCAAATGCTGG
ACTTCCAGTGGAACCAAAAGCAGGGGTACTTGTAGAACCAAAGGCAGGGGTGCTCGCGGAACCAA
AGGCAGGGGTGCTCGAGGAACCAAAGGAAGAAGTGCTCGTGGCACCAAAGCTACCAACTGCAGGA
GTTGACTGGCCAAATGCT
Found at i:1229952 original size:23 final size:24
Alignment explanation
Indices: 1229682--1229949 Score: 350
Period size: 24 Copynumber: 11.3 Consensus size: 24
1229672 TGGACTTCCA
* * * *
1229682 GTGGAACCAAAAGCAGGGGTACTT
1 GTGGCACCAAAGGCAGGGGTGCTC
*
1229706 GTGGAACCAAAGGCAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
* *
1229730 GCGGAACCAAAGGCAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
1229754 GTGGCACCAAAGGAAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
1229778 GTGGCACCAAAGG-AAGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
1229801 GTGGCACCAAAGG-AAGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
1229824 GTGGCACC-AAGGCAGGCGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
1229847 ATGGCACCAAAGGCAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
1229871 GTGGCACCGAAA-GCAGGGGTGCTC
1 GTGGCACC-AAAGGCAGGGGTGCTC
1229895 GTGGCACCGAAA-GCAGGGGTGCTC
1 GTGGCACC-AAAGGCAGGGGTGCTC
* *
1229919 GTGGCACCGAA-GCAGGGGTGCTG
1 GTGGCACCAAAGGCAGGGGTGCTC
1229942 GTGGCACC
1 GTGGCACC
1229950 GAATGCAGAC
Statistics
Matches: 226, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
22 4 0.02
23 76 0.34
24 143 0.63
25 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.40, T:0.13
Consensus pattern (24 bp):
GTGGCACCAAAGGCAGGGGTGCTC
Found at i:1229977 original size:141 final size:142
Alignment explanation
Indices: 1229680--1229978 Score: 349
Period size: 141 Copynumber: 2.1 Consensus size: 142
1229670 GCTGGACTTC
* **
1229680 CAGTGGAACCAAAA-GCAGGGGTACTTGTGGAACCAAAGGCAGGGGTGCTCGCGGAACCAAAGGC
1 CAGTGGAACCAAAAGGCAGGCGTACTCATGGAACCAAAGGCAGGGGTGCTCGCGGAACCAAAGGC
*
1229744 AGGGGTGCTCGTGGCACCAAAGGAAGGGGTGCTCGTGGCACCAAAGGAAGGGTGCTCGTGGCACC
66 AGGGGTGCTCGTGGCACCAAAGGAAGGGGTGCTCGTGGCACCAAAGCAAGGGTGCTCGTGGCACC
**
1229809 AAAGGAAGGGTG
131 AAAGGAAGACTG
* * * * * *
1229821 CTCGTGGCACC--AAGGCAGGCGTGCTCATGGCACCAAAGGCAGGGGTGCTCGTGGCACCGAAA-
1 C-AGTGGAACCAAAAGGCAGGCGTACTCATGGAACCAAAGGCAGGGGTGCTCGCGGAACC-AAAG
* * * *
1229883 GCAGGGGTGCTCGTGGCACCGAAA-GCAGGGGTGCTCGTGGCACCGAAGCAGGGGTGCTGGTGGC
64 GCAGGGGTGCTCGTGGCACC-AAAGGAAGGGGTGCTCGTGGCACCAAAGCAAGGGTGCTCGTGGC
* * *
1229947 ACCGAATGCAGACTG
128 ACCAAAGGAAGACTG
*
1229962 -AGTTGAACCAAAAGGCA
1 CAGTGGAACCAAAAGGCA
1229979 CAGAGGAACC
Statistics
Matches: 130, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
139 6 0.05
140 2 0.02
141 109 0.84
142 13 0.10
ACGTcount: A:0.25, C:0.23, G:0.39, T:0.13
Consensus pattern (142 bp):
CAGTGGAACCAAAAGGCAGGCGTACTCATGGAACCAAAGGCAGGGGTGCTCGCGGAACCAAAGGC
AGGGGTGCTCGTGGCACCAAAGGAAGGGGTGCTCGTGGCACCAAAGCAAGGGTGCTCGTGGCACC
AAAGGAAGACTG
Found at i:1234187 original size:12 final size:12
Alignment explanation
Indices: 1234162--1234222 Score: 86
Period size: 12 Copynumber: 5.1 Consensus size: 12
1234152 CAACTTATAT
* *
1234162 ATACACGCACAC
1 ATACATGCATAC
1234174 ATACATGCATAC
1 ATACATGCATAC
* *
1234186 ATACACGCACAC
1 ATACATGCATAC
1234198 ATACATGCATAC
1 ATACATGCATAC
1234210 ATACATGCATAC
1 ATACATGCATAC
1234222 A
1 A
1234223 AAAAAAGGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.43, C:0.31, G:0.08, T:0.18
Consensus pattern (12 bp):
ATACATGCATAC
Found at i:1234189 original size:24 final size:24
Alignment explanation
Indices: 1234162--1234214 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
1234152 CAACTTATAT
1234162 ATACACGCACACATACATGCATAC
1 ATACACGCACACATACATGCATAC
1234186 ATACACGCACACATACATGCATAC
1 ATACACGCACACATACATGCATAC
1234210 ATACA
1 ATACA
1234215 TGCATACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.32, G:0.08, T:0.17
Consensus pattern (24 bp):
ATACACGCACACATACATGCATAC
Found at i:1238193 original size:37 final size:37
Alignment explanation
Indices: 1238102--1238491 Score: 350
Period size: 37 Copynumber: 10.6 Consensus size: 37
1238092 ATATTTTGTA
* *
1238102 AAACTA-ATATTATATATA-TTTCAAAAAATATTTTCA
1 AAACTATATATTATATATATTTTC-AAAAATGTTTTCT
*
1238138 AAACCTATATATTATATATATATTCAAAAATGTTTTCT
1 AAA-CTATATATTATATATATTTTCAAAAATGTTTTCT
* **
1238176 AAAGTATATATTATATATATTTTTCAAAAAAAACTTTT-T
1 AAACTATATATTATATATA-TTTTC--AAAAATGTTTTCT
1238215 AAAACTATATATTATATATATTTTC-AAAA------CT
1 -AAACTATATATTATATATATTTTCAAAAATGTTTTCT
* * * *
1238246 ATA-TAT-TATCTATATATTTTTT--AAAATGTTTACA
1 AAACTATATAT-TATATATATTTTCAAAAATGTTTTCT
*
1238280 AAACTATATATTATATATATTTTTTCAAAAATGTTTTCA
1 AAACTATATATTATATATA--TTTTCAAAAATGTTTTCT
1238319 AAACTATATATTATATATATGTTTTCAAAAATGTTTT-T
1 AAACTATATATTATATATA--TTTTCAAAAATGTTTTCT
*
1238357 AAAACTATATA-T-TATATATTTTCAAAAAAACG-TTT-T
1 -AAACTATATATTATATATATTTTC--AAAAATGTTTTCT
* *
1238393 AAGACTATATATTATATATATTTTCGAAAATGTTTTCA
1 AA-ACTATATATTATATATATTTTCAAAAATGTTTTCT
*
1238431 AAACTATATATTATATATATTTTCAAAAATGTTTTCA
1 AAACTATATATTATATATATTTTCAAAAATGTTTTCT
* * *
1238468 AAATTATATATTATGTATACTTTC
1 AAACTATATATTATATATATTTTC
1238492 GAAGAGAAAA
Statistics
Matches: 301, Mismatches: 24, Indels: 57
0.79 0.06 0.15
Matches are distributed among these distances:
28 7 0.02
29 14 0.05
30 2 0.01
31 1 0.00
34 3 0.01
35 17 0.06
36 27 0.09
37 93 0.31
38 44 0.15
39 66 0.22
40 27 0.09
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (37 bp):
AAACTATATATTATATATATTTTCAAAAATGTTTTCT
Found at i:1238244 original size:25 final size:26
Alignment explanation
Indices: 1238210--1238265 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
1238200 CAAAAAAAAC
*
1238210 TTTTTAAAACTATATATTA-TATATA
1 TTTTCAAAACTATATATTACTATATA
1238235 TTTTCAAAACTATATATTATCTATATA
1 TTTTCAAAACTATATATTA-CTATATA
1238262 TTTT
1 TTTT
1238266 TTAAAATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 18 0.64
27 10 0.36
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTCAAAACTATATATTACTATATA
Found at i:1238251 original size:104 final size:102
Alignment explanation
Indices: 1238129--1238458 Score: 289
Period size: 103 Copynumber: 3.1 Consensus size: 102
1238119 ATTTCAAAAA
* * * *
1238129 ATATTTTCAAAACCTATATATTA--TATATATATTCAAAAATGTTTTCTAAAGTATATATTATAT
1 ATATTTTCAAAA-C-ATATATTATCTATATATTTTCAAAAATGTTTACAAAACTATATATTATAT
*
1238192 ATA-TTTTTCAAAAAAAACTTTTTAAAACTATATATTATAT
64 ATATTTTTTC--AAAAAACTTTTCAAAACTATATATTATAT
**
1238232 ATATTTTCAAAACTATATATTATCTATATATTTTTTAAAATGTTTACAAAACTATATATTATATA
1 ATATTTTCAAAAC-ATATATTATCTATATATTTTCAAAAATGTTTACAAAACTATATATTATATA
**
1238297 TATTTTTTCAAAAATGTTTTCAAAACTATATATTATAT
65 TATTTTTTCAAAAAACTTTTCAAAACTATATATTATAT
* * *
1238335 ATATGTTTTCAAAA-ATGTTTTTAAAACTATATAT-TATATATTTTCAAAAAAACGTTT-TAAGA
1 ATA--TTTTCAAAACA------T---A-TAT-TATCTATATATTTTC--AAAAATGTTTACAAAA
* **
1238397 CTATATATTATATATA--TTTTCGAAAATGTTTTCAAAACTATATATTATAT
51 CTATATATTATATATATTTTTTCAAAAAACTTTTCAAAACTATATATTATAT
1238447 ATATTTTCAAAA
1 ATATTTTCAAAA
1238459 ATGTTTTCAA
Statistics
Matches: 194, Mismatches: 15, Indels: 29
0.82 0.06 0.12
Matches are distributed among these distances:
102 10 0.05
103 42 0.22
104 37 0.19
105 15 0.08
109 1 0.01
110 9 0.05
112 37 0.19
113 13 0.07
114 22 0.11
115 8 0.04
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (102 bp):
ATATTTTCAAAACATATATTATCTATATATTTTCAAAAATGTTTACAAAACTATATATTATATAT
ATTTTTTCAAAAAACTTTTCAAAACTATATATTATAT
Found at i:1239915 original size:40 final size:41
Alignment explanation
Indices: 1239832--1239919 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
1239822 TTAACAAATG
1239832 TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
1 TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
1239873 TTATATTTATTCATTTTAAAATATTTT-AAAACACTTAATA
1 TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
1239913 TTATATT
1 TTATATT
1239920 AATTTTTAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 20 0.43
41 27 0.57
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (41 bp):
TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
Found at i:1249117 original size:62 final size:62
Alignment explanation
Indices: 1249045--1249164 Score: 190
Period size: 62 Copynumber: 1.9 Consensus size: 62
1249035 CATCATTATT
1249045 ACTAACATAAAAATAAATATAATGATGATAACACATT-TATAA-TTAACTTTATCATAATCAAC
1 ACTAACATAAAAATAAATATAATGATGATAACACATTAT-TAACTT-ACTTTATCATAATCAAC
* *
1249107 ACTAATATAAAAATAAATATAATGATGATAATACATTATTAACTTACTTTATCATAAT
1 ACTAACATAAAAATAAATATAATGATGATAACACATTATTAACTTACTTTATCATAAT
1249165 TGAAACACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
62 51 0.94
63 3 0.06
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (62 bp):
ACTAACATAAAAATAAATATAATGATGATAACACATTATTAACTTACTTTATCATAATCAAC
Found at i:1249187 original size:62 final size:62
Alignment explanation
Indices: 1249045--1249178 Score: 184
Period size: 62 Copynumber: 2.1 Consensus size: 62
1249035 CATCATTATT
*
1249045 ACTAACATAAAAATAAATATAATGATGATAACACATTTATAATTAACTTTATCATAATCAAC
1 ACTAACATAAAAATAAATATAATGATGATAACACATTTATAATTAACTTTATCATAATAAAC
* *
1249107 ACTAATATAAAAATAAATATAATGATGATAATACA-TTATTAACTT-ACTTTATCATAATTGAAA
1 ACTAACATAAAAATAAATATAATGATGATAACACATTTA-TAA-TTAACTTTATCATAA-T-AAA
1249170 C
62 C
1249171 AC-AACATA
1 ACTAACATA
1249179 TACAAAATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
61 3 0.05
62 48 0.75
63 8 0.12
64 5 0.08
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (62 bp):
ACTAACATAAAAATAAATATAATGATGATAACACATTTATAATTAACTTTATCATAATAAAC
Found at i:1251567 original size:58 final size:58
Alignment explanation
Indices: 1251484--1251593 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
1251474 CTTAAATTTA
* * * * * *
1251484 TAAATATTTTTATTTTATCCTTAAACTATG-CTTATCATTTTAAATTATTCCCAAACTT
1 TAAACATTTTAATTTCATCCTTAAACTATGACAT-TCATTCTAAATTAGTCCCAAACTT
*
1251542 TAAACATTTTAATTTCATCGTTAAACTATGACATTCATTCTAAATTAGTCCC
1 TAAACATTTTAATTTCATCCTTAAACTATGACATTCATTCTAAATTAGTCCC
1251594 CAAAAATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 42 0.95
59 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (58 bp):
TAAACATTTTAATTTCATCCTTAAACTATGACATTCATTCTAAATTAGTCCCAAACTT
Found at i:1251817 original size:60 final size:60
Alignment explanation
Indices: 1251753--1251865 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
1251743 TGGGAATCAC
* *
1251753 TTTAGAAAGAG-GATCATAAG-TTAAGGATGAAATTAGAA-TTTTCAAAAGTTTAAAAACTAA
1 TTTAGAAAGAGAG-TCA-AAGTTTAAGGATAAAATTAGAACATTT-AAAAGTTTAAAAACTAA
*
1251813 TTTAGAATGAGAGTCAAAGTTTAAGGATAAAATTAGAACATTTAAAAGTTTAA
1 TTTAGAAAGAGAGTCAAAGTTTAAGGATAAAATTAGAACATTTAAAAGTTTAA
1251866 GGACCGACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
59 3 0.06
60 40 0.85
61 4 0.09
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (60 bp):
TTTAGAAAGAGAGTCAAAGTTTAAGGATAAAATTAGAACATTTAAAAGTTTAAAAACTAA
Found at i:1251882 original size:60 final size:60
Alignment explanation
Indices: 1251773--1251886 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
1251763 GGATCATAAG
* * * * *
1251773 TTAAGGATGAAATTAGAATTTTCAAAAGTTTAAAAACTAATTTAGAATGAGAGTCAAAGT
1 TTAAGGATAAAATTAGAAATTTCAAAAGTTTAAAAACCAACTTAAAATGAGAGTCAAAGT
** *
1251833 TTAAGGATAAAATTAGAACATTT-AAAAGTTTAAGGACCGACTTAAAATGAGAGT
1 TTAAGGATAAAATTAGAA-ATTTCAAAAGTTTAAAAACCAACTTAAAATGAGAGT
1251887 TATAATTTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
60 42 0.93
61 3 0.07
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (60 bp):
TTAAGGATAAAATTAGAAATTTCAAAAGTTTAAAAACCAACTTAAAATGAGAGTCAAAGT
Found at i:1253938 original size:20 final size:20
Alignment explanation
Indices: 1253909--1253947 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1253899 AGTATGTTCA
*
1253909 GGGGGTATCGATTCCCCCTG
1 GGGGGAATCGATTCCCCCTG
1253929 GGGGGAATCGATTCCCCCT
1 GGGGGAATCGATTCCCCCT
1253948 AAAGGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.31, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCCTG
Found at i:1257293 original size:2 final size:2
Alignment explanation
Indices: 1257286--1257316 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1257276 ATTTGGATCC
1257286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1257317 GGTTAAGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1261070 original size:38 final size:38
Alignment explanation
Indices: 1261027--1261109 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
1261017 ATAGGTCGTA
* * *
1261027 CGGGACACAGATTACATCCTTCGGGATGACAGGTCTTT
1 CGGGACACAGATGACATCATTCGGGATGACAGGTCCTT
*
1261065 CGGGACACAGATGACATCATTCGGGATGATAGGTCCTT
1 CGGGACACAGATGACATCATTCGGGATGACAGGTCCTT
1261103 CGGGACA
1 CGGGACA
1261110 TAATTTATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (38 bp):
CGGGACACAGATGACATCATTCGGGATGACAGGTCCTT
Found at i:1265066 original size:13 final size:13
Alignment explanation
Indices: 1265048--1265072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1265038 TAAATAAATA
1265048 AAAATTAATAATT
1 AAAATTAATAATT
1265061 AAAATTAATAAT
1 AAAATTAATAAT
1265073 ATATTTAAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAATAATT
Found at i:1265775 original size:60 final size:59
Alignment explanation
Indices: 1265604--1265776 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 59
1265594 TATGTCCCCC
* *
1265604 AACTATGACCCTCATTTCA-AATTGGTCCATAAACTTTTGAATATTCCAATTCCATCCTCA
1 AACTATGACCCTC-TTT-ATAATTAGTCCATAAACTTTTGAATATTCCAATTTCATCCTCA
*** * * *
1265664 AACTATGACTCAAGTTCTA-AATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCC-CTA
1 AACTATGAC-CCTCTT-TATAATTAGTCCATAAACTTTTGAATATTCCAATTTCATCCTC-A
**
1265724 AACTATGACCCTCTTTATAGATTAGTCCCCAAACTTTTGAATATTCCAATTTC
1 AACTATGACCCTCTTTATA-ATTAGTCCATAAACTTTTGAATATTCCAATTTC
1265777 TTCTCCAAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
58 2 0.02
59 5 0.05
60 84 0.90
61 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (59 bp):
AACTATGACCCTCTTTATAATTAGTCCATAAACTTTTGAATATTCCAATTTCATCCTCA
Found at i:1269937 original size:29 final size:30
Alignment explanation
Indices: 1269878--1269937 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1269868 TGGGATTTTC
*
1269878 TCTTTCAACTTATCACCAGAAACAAGTAAG
1 TCTTTAAACTTATCACCAGAAACAAGTAAG
* *
1269908 TCTTTAAACTTATCA-TAGAAACATGTAAG
1 TCTTTAAACTTATCACCAGAAACAAGTAAG
1269937 T
1 T
1269938 TATAATTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (30 bp):
TCTTTAAACTTATCACCAGAAACAAGTAAG
Found at i:1272122 original size:34 final size:34
Alignment explanation
Indices: 1272079--1272148 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
1272069 AAATGGAGGT
*
1272079 TTGTCTACATGGTTAGTCCATTCCATGAGAATGC
1 TTGTCTACATGGTTAGCCCATTCCATGAGAATGC
1272113 TTGTCTACATGGTTAGCCCATTCCATGAGAATGC
1 TTGTCTACATGGTTAGCCCATTCCATGAGAATGC
1272147 TT
1 TT
1272149 AAATTCAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (34 bp):
TTGTCTACATGGTTAGCCCATTCCATGAGAATGC
Found at i:1275973 original size:31 final size:31
Alignment explanation
Indices: 1275938--1276008 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
1275928 TTAGGTTCAT
1275938 AAGAAATTATCAGTCGGTGATGAACCTATAC
1 AAGAAATTATCAGTCGGTGATGAACCTATAC
1275969 AAGAAATTATCAGTCGGTGATGAACCTATAC
1 AAGAAATTATCAGTCGGTGATGAACCTATAC
1276000 AAGAAATTA
1 AAGAAATTA
1276009 CCAGCAACGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (31 bp):
AAGAAATTATCAGTCGGTGATGAACCTATAC
Found at i:1280361 original size:31 final size:30
Alignment explanation
Indices: 1280323--1280431 Score: 110
Period size: 31 Copynumber: 3.4 Consensus size: 30
1280313 CCTTAGGTCC
1280323 ATAAGGAATTACCAGTAGGTGTTGAACCTAT
1 ATAAGGAATTACCAGTA-GTGTTGAACCTAT
* * *
1280354 ATAAGGAATTACCAATAGTGACTGAACCTACCAGAG
1 ATAAGGAATTACCAGTAGTG-TTGAACCT-----AT
1280390 ATAAGGAATTACCAGTCAGTGTTGAACCTAT
1 ATAAGGAATTACCAGT-AGTGTTGAACCTAT
*
1280421 ACAAGGAATTA
1 ATAAGGAATTA
1280432 TCAGCAGCGA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
30 3 0.05
31 34 0.53
36 23 0.36
37 4 0.06
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (30 bp):
ATAAGGAATTACCAGTAGTGTTGAACCTAT
Found at i:1280431 original size:67 final size:67
Alignment explanation
Indices: 1280323--1280456 Score: 198
Period size: 67 Copynumber: 2.0 Consensus size: 67
1280313 CCTTAGGTCC
* * * *
1280323 ATAAGGAATTACCAGTAGGTGTTGAACCTATATAAGGAATTACCAATAGTGACTGAACCTACCAG
1 ATAAGGAATTACCAGTAGGTGTTGAACCTATACAAGGAATTACCAACAGCGACTAAACCTACCAG
1280388 AG
66 AG
* *
1280390 ATAAGGAATTACCAGTCA-GTGTTGAACCTATACAAGGAATTATCAGCAGCGACTAAACCTACCA
1 ATAAGGAATTACCAGT-AGGTGTTGAACCTATACAAGGAATTACCAACAGCGACTAAACCTACCA
1280454 GAG
65 GAG
1280457 TCTTCAGTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 59 0.98
68 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (67 bp):
ATAAGGAATTACCAGTAGGTGTTGAACCTATACAAGGAATTACCAACAGCGACTAAACCTACCAG
AG
Found at i:1282177 original size:25 final size:25
Alignment explanation
Indices: 1282130--1282178 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1282120 AACTTAAAAC
*
1282130 AAAAGAAAAGAAAAATGAAAACTTG
1 AAAAGAAAAGAAAAATAAAAACTTG
1282155 AAAAGAAAAG-AAAATAAATAACTT
1 AAAAGAAAAGAAAAATAAA-AACTT
1282179 TATAAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.14
Consensus pattern (25 bp):
AAAAGAAAAGAAAAATAAAAACTTG
Found at i:1307706 original size:24 final size:24
Alignment explanation
Indices: 1307674--1307726 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
1307664 ATTCGTGGCT
1307674 GTAAATTGTAAATCAGAGATTTTA
1 GTAAATTGTAAATCAGAGATTTTA
1307698 GTAAATTGTAAATCAGAGATTTTA
1 GTAAATTGTAAATCAGAGATTTTA
1307722 GTAAA
1 GTAAA
1307727 ATATAGTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (24 bp):
GTAAATTGTAAATCAGAGATTTTA
Found at i:1316849 original size:14 final size:14
Alignment explanation
Indices: 1316832--1316865 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1316822 ATAAACAAAT
1316832 GTAAACGAACAAGC
1 GTAAACGAACAAGC
*
1316846 GTAAACGAACGAGC
1 GTAAACGAACAAGC
*
1316860 ATAAAC
1 GTAAAC
1316866 AAATATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.09
Consensus pattern (14 bp):
GTAAACGAACAAGC
Found at i:1316875 original size:10 final size:10
Alignment explanation
Indices: 1316859--1316889 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1316849 AACGAACGAG
1316859 CATAAACAAA
1 CATAAACAAA
*
1316869 TATAAACAAA
1 CATAAACAAA
1316879 CATAAACAAA
1 CATAAACAAA
1316889 C
1 C
1316890 GTACATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (10 bp):
CATAAACAAA
Found at i:1320963 original size:3 final size:3
Alignment explanation
Indices: 1320951--1320982 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1320941 GGGCTTTGTA
1320951 TAT T-T TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1320983 TAATGATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:1321419 original size:76 final size:76
Alignment explanation
Indices: 1321173--1322428 Score: 2446
Period size: 76 Copynumber: 16.6 Consensus size: 76
1321163 GAAATATTGA
*
1321173 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCATTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321238 AGGCTTTTTGG
66 AGGCTTTTTGG
1321249 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321313 AGGCTTTTTGG
66 AGGCTTTTTGG
1321324 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
1321389 AGGCGTTTTGG
66 AGGCTTTTTGG
1321400 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321465 AGGCTTTTTGG
66 AGGCTTTTTGG
1321476 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321541 AGGCTTTTTGG
66 AGGCTTTTTGG
1321552 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA-ATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321616 AGGCTTTTTGG
66 AGGCTTTTTGG
1321627 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321692 AGGCTTTTTGG
66 AGGCTTTTTGG
1321703 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321768 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1321779 AAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321844 AGGCTTTTTGG
66 AGGCTTTTTGG
1321855 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA-ATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321919 AGGCTTTTTGG
66 AGGCTTTTTGG
1321930 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321995 AGGCTTTTTGG
66 AGGCTTTTTGG
1322006 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
1322071 AGGCTTTTTGA
66 AGGCTTTTTGG
1322082 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1322147 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1322158 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAATCATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1322223 AGGCTTTTTGG
66 AGGCTTTTTGG
1322234 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1322299 AGGCTTTTTGG
66 AGGCTTTTTGG
1322310 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1322375 AGGCTTTTTGG
66 AGGCTTTTTGG
1322386 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
1322429 TTTGGAAACA
Statistics
Matches: 1168, Mismatches: 9, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
75 225 0.19
76 943 0.81
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1321720 original size:303 final size:303
Alignment explanation
Indices: 1321173--1322428 Score: 2449
Period size: 303 Copynumber: 4.1 Consensus size: 303
1321163 GAAATATTGA
*
1321173 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCATTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
1321238 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAACATCAAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAATCAAA
1321303 AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
131 AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
*
1321368 AAAACATCAAAAAGCTCCCGAAGGCGTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
196 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1321433 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
261 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
1321476 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321541 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAATCAAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAATCAAA
1321606 AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
131 AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
1321671 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
196 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1321736 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
261 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
1321779 AAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1321844 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAATCAAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAATCAAA
1321909 AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
131 AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
1321974 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
196 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
*
1322039 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGA
261 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
1322082 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
1322147 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAATCATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAA-AATCAA
1322212 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
130 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
1322277 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
195 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
1322342 CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
260 CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
1322386 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
1322429 TTTGGAAACA
Statistics
Matches: 944, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
303 723 0.77
304 221 0.23
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (303 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAATCAAA
AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:1322424 original size:47 final size:48
Alignment explanation
Indices: 1322370--1322463 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
1322360 TCAAAAAGCT
1322370 CCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
*
1322417 CCCGAAGGCTTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 CCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1322464 TGAGAAATAG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 9 0.20
48 36 0.80
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (48 bp):
CCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:1323162 original size:22 final size:22
Alignment explanation
Indices: 1323137--1323213 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
1323127 CATAAAGCTT
1323137 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * * *
1323159 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTGAAAAGAGAATCTA
**
1323181 TCATCTTTGAAGTGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1323203 TTATCTTTGAA
1 TCATCTTTGAA
1323214 GAGTGTAGAT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1323659 original size:54 final size:54
Alignment explanation
Indices: 1323577--1323688 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
1323567 AGAATAGCAG
*** *
1323577 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGATAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAC
**
1323631 GTTCGTAAAACATTTGATAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAC
1 GTTCGTAAAACATTTGATAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAC
1323685 GTTC
1 GTTC
1323689 TCAATCATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGATAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAC
Found at i:1326039 original size:114 final size:114
Alignment explanation
Indices: 1325839--1326061 Score: 428
Period size: 114 Copynumber: 2.0 Consensus size: 114
1325829 TATGCAGTTC
*
1325839 ATCTTTTAATTCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1325904 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTT
66 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTT
1325953 ATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
*
1326018 CTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTACTATGAGCA
66 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
1326062 CATGGCACTT
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (114 bp):
ATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTT
Found at i:1328346 original size:13 final size:13
Alignment explanation
Indices: 1328328--1328352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1328318 TCAATTTTCC
1328328 TTTTTCTTCTTTT
1 TTTTTCTTCTTTT
1328341 TTTTTCTTCTTT
1 TTTTTCTTCTTT
1328353 CTTTGTTGGA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTCTTTT
Found at i:1332990 original size:15 final size:16
Alignment explanation
Indices: 1332967--1333007 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1332957 TTAATACCTG
1332967 AATAA-AAAAACAAT-
1 AATAATAAAAACAATA
* *
1332981 ATTAATAAAAATAATA
1 AATAATAAAAACAATA
1332997 AATAATAAAAA
1 AATAATAAAAA
1333008 TTTGAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 4 0.18
15 8 0.36
16 10 0.45
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAATAAAAACAATA
Found at i:1345756 original size:14 final size:15
Alignment explanation
Indices: 1345728--1345757 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1345718 ATGTTCTAAT
1345728 TGAATCTTCAAAATA
1 TGAATCTTCAAAATA
1345743 TGAATCTT-AAAATA
1 TGAATCTTCAAAATA
1345757 T
1 T
1345758 TAATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (15 bp):
TGAATCTTCAAAATA
Found at i:1349221 original size:24 final size:24
Alignment explanation
Indices: 1349194--1349239 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1349184 AAGTCACTTA
*
1349194 CCGTTAAATCAACATCGATCACAG
1 CCGTCAAATCAACATCGATCACAG
*
1349218 CCGTCAAATCAACTTCGATCAC
1 CCGTCAAATCAACATCGATCAC
1349240 TATTAATTGG
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:0.35, C:0.33, G:0.11, T:0.22
Consensus pattern (24 bp):
CCGTCAAATCAACATCGATCACAG
Found at i:1353543 original size:22 final size:22
Alignment explanation
Indices: 1353489--1353545 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
1353479 GCAACGCGAT
*
1353489 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
1353511 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
1353530 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
1353546 TTGCGATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 16 0.53
20 2 0.07
21 2 0.07
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:1353560 original size:22 final size:19
Alignment explanation
Indices: 1353494--1353579 Score: 73
Period size: 19 Copynumber: 4.2 Consensus size: 19
1353484 GCGATTTTGA
*
1353494 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
1353513 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
1353534 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
** *
1353557 AAAAAATATTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
1353576 AAAA
1 AAAA
1353580 ATTCAAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
19 32 0.58
21 1 0.02
22 8 0.15
23 2 0.04
24 2 0.04
25 10 0.18
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:1353569 original size:44 final size:41
Alignment explanation
Indices: 1353489--1353570 Score: 101
Period size: 44 Copynumber: 1.9 Consensus size: 41
1353479 GCAACGCGAT
* ** *
1353489 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAATATTGCGAGAG
1353530 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAATATTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAATATTGCGA
1353571 TAGTGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
43 2 0.06
44 23 0.68
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAATATTGCGAGAG
Found at i:1353916 original size:21 final size:21
Alignment explanation
Indices: 1353890--1353947 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1353880 TCGACACGTG
1353890 ATTATCGCGTTGCGATTTTGT
1 ATTATCGCGTTGCGATTTTGT
*
1353911 ATTATCGAGTTGCGATTTTGT
1 ATTATCGCGTTGCGATTTTGT
1353932 ATTATCGCGTTGCGAT
1 ATTATCGCGTTGCGAT
1353948 AGTCAGAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.45
Consensus pattern (21 bp):
ATTATCGCGTTGCGATTTTGT
Found at i:1355358 original size:11 final size:11
Alignment explanation
Indices: 1355338--1355399 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
1355328 GTCATTAAAT
*
1355338 TTATTGAATTA
1 TTATTAAATTA
1355349 TTATTAAATTTA
1 TTATTAAA-TTA
*
1355361 TCGA-TAAA-T-
1 T-TATTAAATTA
1355370 TTATTAAATTA
1 TTATTAAATTA
1355381 TTA-TAAATTGA
1 TTATTAAATT-A
1355392 TTATTAAA
1 TTATTAAA
1355400 CTACATTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
8 1 0.02
9 5 0.12
10 8 0.20
11 14 0.34
12 12 0.29
13 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (11 bp):
TTATTAAATTA
Found at i:1357034 original size:25 final size:25
Alignment explanation
Indices: 1356988--1357035 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1356978 ATTACTAGAA
**
1356988 AATAATTAATGAATAATTTTAAATC
1 AATAATTAATGAATAAGGTTAAATC
* *
1357013 AATAATTAATGATTGAGGTTAAA
1 AATAATTAATGAATAAGGTTAAA
1357036 ATTATATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (25 bp):
AATAATTAATGAATAAGGTTAAATC
Found at i:1357280 original size:3 final size:3
Alignment explanation
Indices: 1357272--1357334 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
1357262 ATATGTAAAA
*
1357272 AAT AAT AAT -AT AAT -AT AAA AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* *
1357316 AAT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
1357335 TACAAAAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 44 0.86
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1357293 original size:19 final size:18
Alignment explanation
Indices: 1357269--1357319 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
1357259 AAAATATGTA
1357269 AAAAATAATAATATAATAT
1 AAAAATAATAATATAA-AT
1357288 AAAAATAATAATAATAAAT
1 AAAAATAATAAT-ATAAAT
*
1357307 AATAATAATAATA
1 AAAAATAATAATA
1357320 ACGATAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 25 0.83
20 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATAATAATATAAAT
Found at i:1357294 original size:13 final size:14
Alignment explanation
Indices: 1357281--1357341 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 14
1357271 AAATAATAAT
1357281 ATAATATAAAAATA
1 ATAATATAAAAATA
1357295 ATAATAATAAATAATA
1 ATAAT-ATAAA-AATA
1357311 ATAATAATAACGATAATA
1 ATAAT-ATAA--A-AATA
1357329 ATAATATACAAAA
1 ATAATATA-AAAA
1357342 AAGACCCGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 15 0.36
17 3 0.07
18 12 0.29
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (14 bp):
ATAATATAAAAATA
Found at i:1357296 original size:16 final size:16
Alignment explanation
Indices: 1357267--1357334 Score: 75
Period size: 16 Copynumber: 4.1 Consensus size: 16
1357257 CAAAAATATG
1357267 TAAAAAATAATAATATAA
1 TAAAAAATAAT-A-ATAA
1357285 TATAAAAATAATAATAA
1 TA-AAAAATAATAATAA
*
1357302 TAAATAATAATAATAA
1 TAAAAAATAATAATAA
**
1357318 T-AACGATAATAATAA
1 TAAAAAATAATAATAA
1357333 TA
1 TA
1357335 TACAAAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
15 13 0.29
16 14 0.31
17 6 0.13
18 3 0.07
19 9 0.20
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (16 bp):
TAAAAAATAATAATAA
Found at i:1357871 original size:130 final size:128
Alignment explanation
Indices: 1357544--1357910 Score: 556
Period size: 130 Copynumber: 2.8 Consensus size: 128
1357534 ACATGGTTCC
* * * * * *
1357544 TACGTGATGAGGAAATCTAGTCGAGGG-ATGACACTGCTCATACATGATGAAGAGTTCTGGTCAT
1 TACGTGATGAAGAGATCTGGTCG-GGGAATGACACAGCTCATACGTGATGAAGAGTTCTGGCCAT
*
1357608 CTTTAGGAGGAGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTAGGATGACACGG
65 C--TA--AAG-GTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTAGGATGACACGG
*
1357673 CTCC
125 CTCA
*
1357677 TACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC
1 TACGTGATGAAGAGATCTGGTCGGGGAATGACACAGCTCATACGTGATGAAGAGTTCTGGCCATC
* *
1357742 TAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCA
66 TAAAGGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTA-GGATGACACGGCTCA
1357806 TACGTGATGAAGAGATCTGGTCTGGGGAATGACACAGCTCATACGTGATGAAGAGTTCTGGCCAT
1 TACGTGATGAAGAGATCTGGTC-GGGGAATGACACAGCTCATACGTGATGAAGAGTTCTGGCCAT
1357871 CTAAAGGTGATAACACGATTCCTACGTGATGAGGACGGCT
65 CTAAAGGTGATAACACGATTCCTACGTGATGAGGACGGCT
1357911 TGCCATCTTT
Statistics
Matches: 219, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
128 42 0.19
129 37 0.17
130 80 0.37
131 2 0.01
132 3 0.01
133 55 0.25
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (128 bp):
TACGTGATGAAGAGATCTGGTCGGGGAATGACACAGCTCATACGTGATGAAGAGTTCTGGCCATC
TAAAGGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTAGGATGACACGGCTCA
Found at i:1357982 original size:28 final size:28
Alignment explanation
Indices: 1357951--1358027 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
1357941 AAACCAAATT
1357951 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
1357979 AAAGATTCGTTTCAAGAA-AAACAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
1358007 AAAGATGATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
1358028 CAACTGTCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 29 0.71
29 2 0.05
30 3 0.07
31 7 0.17
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:1358438 original size:15 final size:15
Alignment explanation
Indices: 1358414--1358457 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1358404 AAGATGATCT
*
1358414 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
1358429 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
1358444 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
1358458 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:1358599 original size:27 final size:27
Alignment explanation
Indices: 1358559--1358723 Score: 111
Period size: 27 Copynumber: 5.9 Consensus size: 27
1358549 TCTCGAGAGA
* *
1358559 CAAA-ATTTTGTTTCAAAGGAAACCACT
1 CAAAGATTTT-TTTCAAAAGAAACGACT
* *
1358586 CAAAGATTTTTTTCAAAAGAAATTGTCT
1 CAAAGATTTTTTTCAAAAGAAA-CGACT
* * *
1358614 TAGGAGATAAATTTTTTCAAAAGAAATAGACT
1 CA-AAGAT---TTTTTTCAAAAGAAA-CGACT
* *
1358646 CAAAGA-TATTTTCAAAAGAAACAACT
1 CAAAGATTTTTTTCAAAAGAAACGACT
1358672 CAAAGATTTTTATTCAAAAGGAATA-GACT
1 CAAAGATTTTT-TTCAAAA-GAA-ACGACT
* * *
1358701 CAAAGATTTATCTCAAGAGAAAC
1 CAAAGATTTTTTTCAAAAGAAAC
1358724 TGTCTCCAGA
Statistics
Matches: 109, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
26 10 0.09
27 35 0.32
28 20 0.18
29 20 0.18
30 1 0.01
31 3 0.03
32 20 0.18
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (27 bp):
CAAAGATTTTTTTCAAAAGAAACGACT
Found at i:1359187 original size:105 final size:105
Alignment explanation
Indices: 1359043--1359239 Score: 288
Period size: 105 Copynumber: 1.9 Consensus size: 105
1359033 ACGATCTCAA
* *
1359043 GTGAGATCAACTTTGTTTAATGTAAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGGTCTCA
1 GTGAGATCAACTTTGTTTAATGTAAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTCA
1359108 AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
66 AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
* * * * * *
1359148 GTGAGATTAATTTTGTTTTAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTC
1 GTGAGATCAACTTTG-TTTAATGTAAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTC
* *
1359212 AAGCGAGACGAAGTTTGTTTTAAGAGAA
65 AAGCGAGACGAAATTTGTTTTAAAAGAA
1359240 TTTGTCTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 76 0.94
106 5 0.06
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (105 bp):
GTGAGATCAACTTTGTTTAATGTAAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTCA
AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
Found at i:1359246 original size:36 final size:36
Alignment explanation
Indices: 1359206--1359342 Score: 152
Period size: 36 Copynumber: 3.8 Consensus size: 36
1359196 AAAGGAAAAA
* * *
1359206 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* * * **
1359242 TGTCTCAAACGCGACAAAATTTGTTTTTAG-GAAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
**
1359277 TGTCTCAAGCGAGACAAAATTTGCTTCGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAAT
1359313 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC-AAAATTTGTTTTAA
1359343 AATTCTCAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
35 24 0.29
36 50 0.61
37 8 0.10
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:1359316 original size:71 final size:72
Alignment explanation
Indices: 1359206--1359340 Score: 184
Period size: 71 Copynumber: 1.9 Consensus size: 72
1359196 AAAGGAAAAA
* * ** * *
1359206 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTCAAACGCGAC-AAAATTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTCGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
1359270 AGGAAGC
66 AGGAAGC
*
1359277 TGTCTCAAGCGAGACAAAATTTGCTTCGAA-AGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTG-TTCGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTT
1359341 AAAATTCTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
71 39 0.71
72 16 0.29
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (72 bp):
TGTCTCAAGCGAGACAAAATTTGTTCGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
AGGAAGC
Found at i:1359727 original size:16 final size:16
Alignment explanation
Indices: 1359691--1359742 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
1359681 ATGCAAATTT
1359691 TATGTATT-ATGTATG
1 TATGTATTGATGTATG
*
1359706 TATGTATTGATATATG
1 TATGTATTGATGTATG
*
1359722 TTTGTATTGATGTATG
1 TATGTATTGATGTATG
1359738 TATGT
1 TATGT
1359743 TGATTTGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (16 bp):
TATGTATTGATGTATG
Found at i:1363351 original size:31 final size:32
Alignment explanation
Indices: 1363295--1363356 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1363285 TGACAAAATG
1363295 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1363327 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
1363357 AATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:1364859 original size:17 final size:18
Alignment explanation
Indices: 1364829--1364862 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1364819 AAAAACACAC
*
1364829 ATTACATTATTAAAATAA
1 ATTACATTAGTAAAATAA
1364847 ATTA-ATTAGTAAAATA
1 ATTACATTAGTAAAATA
1364863 TAATCGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTACATTAGTAAAATAA
Found at i:1366857 original size:3 final size:3
Alignment explanation
Indices: 1366849--1366909 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
1366839 ATGTAAAAAT
*
1366849 ATA ATA AT- ATA A-A TATA AAA ATA ATA ATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
**
1366894 ATA ACG ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
1366910 ATATACAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 3 0.06
3 41 0.85
4 4 0.08
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1367706 original size:11 final size:11
Alignment explanation
Indices: 1367690--1367721 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1367680 GTCATTAAAT
1367690 TTATTGAATTA
1 TTATTGAATTA
1367701 TTATTGAATTA
1 TTATTGAATTA
*
1367712 TTATTAAATT
1 TTATTGAATT
1367722 TATCGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (11 bp):
TTATTGAATTA
Found at i:1367759 original size:22 final size:21
Alignment explanation
Indices: 1367690--1367763 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
1367680 GTCATTAAAT
* *
1367690 TTATTGAATTATTATTGAATTA
1 TTATTAAATTATTA-TAAATTA
*
1367712 TTATTAAATTTATCGATAAATT-
1 TTATTAAA-TTAT-TATAAATTA
1367734 TTATTAAATTATTATAAATTGA
1 TTATTAAATTATTATAAATT-A
1367756 TTATTAAA
1 TTATTAAA
1367764 CTTACATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.16
21 4 0.09
22 23 0.52
23 9 0.20
24 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATTAAATTATTATAAATTA
Found at i:1375463 original size:3 final size:3
Alignment explanation
Indices: 1375434--1375485 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
1375424 TTGGGTTTTG
* *
1375434 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1375481 TAA TA
1 TAA TA
1375486 TAAATAACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1381980 original size:3 final size:3
Alignment explanation
Indices: 1381967--1382001 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1381957 TAAAATATTA
1381967 AAT AA- AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1382002 TCTAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1381990 original size:14 final size:14
Alignment explanation
Indices: 1381967--1382002 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1381957 TAAAATATTA
*
1381967 AATAAAATAATAAT
1 AATAATATAATAAT
1381981 AATAATATAATAAT
1 AATAATATAATAAT
1381995 AATAATAT
1 AATAATAT
1382003 CTAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATATAATAAT
Found at i:1381992 original size:17 final size:17
Alignment explanation
Indices: 1381967--1382001 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1381957 TAAAATATTA
1381967 AATAAAATAATAATAAT
1 AATAAAATAATAATAAT
*
1381984 AATATAATAATAATAAT
1 AATAAAATAATAATAAT
1382001 A
1 A
1382002 TCTAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAAATAATAATAAT
Found at i:1389836 original size:26 final size:26
Alignment explanation
Indices: 1389800--1389853 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1389790 CAACCTCAAC
1389800 CCCTCCCCCCAAACACCCGTGTGCTT
1 CCCTCCCCCCAAACACCCGTGTGCTT
1389826 CCCTCCCCCCAAACACCCGTGTGCTT
1 CCCTCCCCCCAAACACCCGTGTGCTT
1389852 CC
1 CC
1389854 GCATGTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.15, C:0.56, G:0.11, T:0.19
Consensus pattern (26 bp):
CCCTCCCCCCAAACACCCGTGTGCTT
Found at i:1390598 original size:59 final size:59
Alignment explanation
Indices: 1390506--1390655 Score: 266
Period size: 59 Copynumber: 2.5 Consensus size: 59
1390496 ATAAAATCAT
1390506 AATTTTTCAAATTTGTTAATCATACCACTTAACTA-TGGACATATTCTATTTTTACCATC
1 AATTTTTCAAATTTGTTAATCATACCACTTAACTACT-GACATATTCTATTTTTACCATC
1390565 AATTTTTCAAATTTGTTAATCATACCACTTAACTACTGACATATTCTATTTTTACCATC
1 AATTTTTCAAATTTGTTAATCATACCACTTAACTACTGACATATTCTATTTTTACCATC
* *
1390624 AATCTTTCAAATTTTTTAATCATACCACTTAA
1 AATTTTTCAAATTTGTTAATCATACCACTTAA
1390656 TTGTTTAAGT
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
59 87 0.99
60 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (59 bp):
AATTTTTCAAATTTGTTAATCATACCACTTAACTACTGACATATTCTATTTTTACCATC
Done.