Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 26
Found at i:1127978 original size:6 final size:6
Alignment explanation
Indices: 1127917--1127980 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
1127907 ATCATCGTCA
* * * * * *
1127917 TCATCT TCATCG TCAGCT TCATCG TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
1127965 TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCAT
1127981 TGACCGCTTG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:1129787 original size:200 final size:200
Alignment explanation
Indices: 1129444--1131218 Score: 3338
Period size: 200 Copynumber: 8.9 Consensus size: 200
1129434 TTTAAATTAG
*
1129444 TATCGACATAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1129509 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
1129574 TCAACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1129639 AAAAA
196 AAAAA
1129644 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1129709 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
1129774 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1129839 AAAAA
196 AAAAA
* *
1129844 TATCGACACAAACTAAAAAAATGTCGACACATTATTTAGACATATTCTCTCATAAAACCGATATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1129909 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
1129974 TCGATACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1130039 AAAAA
196 AAAAA
1130044 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
1130109 CTTGTACCGGTTAGATTGAAAAATTATATATTGCATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
1130174 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1130239 AAAAA
196 AAAAA
1130244 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1130309 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
1130374 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1130439 AAAAA
196 AAAAA
1130444 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1130509 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
1130574 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1130639 AAAAA
196 AAAAA
1130644 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1130709 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* * **
1130774 TCGACACTTTTTATATATGGTTCGACACTTTATTGTTGCACCCTGTTGGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1130839 AAAAA
196 AAAAA
*
1130844 TATCGACACAAACTGAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
1130909 CTTGTACCGGTTAGATTGAAAAATTACACATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
1130974 TCGACGCTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1131039 AAAAA
196 AAAAA
*
1131044 TATCGACA-ACACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
1131107 CTTGTGCCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTATCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
1131172 TCGACACTTTTTATATATGGTTCGACACTTTATTGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
1131219 GGCCATATTG
Statistics
Matches: 1540, Mismatches: 35, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
198 156 0.10
199 4 0.00
200 1380 0.90
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
AAAAA
Found at i:1131348 original size:18 final size:18
Alignment explanation
Indices: 1131325--1131385 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1131315 TCTCATTCAT
*
1131325 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1131343 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1131362 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1131381 AATTA
1 AATTA
1131386 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1131361 original size:19 final size:19
Alignment explanation
Indices: 1131337--1131385 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1131327 TTATATTCAC
1131337 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1131356 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1131375 ATACAAAATTA
1 ATACAAAATTA
1131386 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1133213 original size:33 final size:33
Alignment explanation
Indices: 1133176--1133241 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1133166 CATCTTAATA
*
1133176 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
* *
1133209 TCACCCCTCAATACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
1133242 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:1133300 original size:21 final size:21
Alignment explanation
Indices: 1133275--1133339 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1133265 CCCCTTATGC
* *
1133275 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1133296 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1133317 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1133338 CT
1 CT
1133340 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1135402 original size:24 final size:24
Alignment explanation
Indices: 1135365--1135417 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1135355 CCGTTCTATT
1135365 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1135389 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1135413 TATTT
1 TATTT
1135418 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1135789 original size:20 final size:19
Alignment explanation
Indices: 1135743--1135789 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1135733 TCCGGTAACG
*
1135743 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
1135762 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
1135783 TTTTACC
1 TTTTACC
1135790 TGGTATATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:1135852 original size:181 final size:182
Alignment explanation
Indices: 1135529--1136001 Score: 662
Period size: 181 Copynumber: 2.6 Consensus size: 182
1135519 CGTACTTACA
* * * *
1135529 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
1135594 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCAACACATTAT
* *
1135659 AGGCGCTAAAACTGTTTATCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTATCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
1135710 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1135775 TATCATATTTTTACCTGGTATATTGTTTTGGATCGATACATTTTTTAAAAGTATCAACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCAACACATTAT
* ** * *
1135840 ATGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTATCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * *
1135892 AAAGTACCGACACTTTAAATGTATCCAGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
1135956 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1136002 AATTTGGATC
Statistics
Matches: 258, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
181 160 0.62
182 97 0.38
183 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCAACACATTAT
AGGAGCTAAAACTGCTTATCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:1137842 original size:30 final size:32
Alignment explanation
Indices: 1137783--1137843 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1137773 TAAGGTAAAC
* *
1137783 TATGTGTTTAGTACCTAAGCTATCAATTTTGG
1 TATGTGTTTAGTACATAAACTATCAATTTTGG
* *
1137815 TATGT-TTTAGTACATAAACTTTCATTTTT
1 TATGTGTTTAGTACATAAACTATCAATTTT
1137844 TTCCAAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (32 bp):
TATGTGTTTAGTACATAAACTATCAATTTTGG
Found at i:1154648 original size:58 final size:58
Alignment explanation
Indices: 1154553--1154668 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
1154543 CTTGAAGAAG
* *
1154553 GGTTAGAATACATATCAAATCAATCAAACACATGAGAAGAGTTTTTCATTCTTATTTT
1 GGTTAGAATACATATCAAAGCAATCAAACACAAGAGAAGAGTTTTTCATTCTTATTTT
*
1154611 GGTTAGAATACATATCCAAGCAATCAAACACAAGAGAAGAGTTTTTCATTCTTATTTT
1 GGTTAGAATACATATCAAAGCAATCAAACACAAGAGAAGAGTTTTTCATTCTTATTTT
1154669 CCTTTCTCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (58 bp):
GGTTAGAATACATATCAAAGCAATCAAACACAAGAGAAGAGTTTTTCATTCTTATTTT
Found at i:1155679 original size:31 final size:31
Alignment explanation
Indices: 1155641--1155710 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1155631 CTTTTAAAAC
** *
1155641 TTGCAATACACTCCCCCAGCATTTAGTCTGT
1 TTGCAATACACTCCCCCAAAATTTAGTCCGT
***
1155672 TTGCAATATGGTCCCCCAAAATTTAGTCCGT
1 TTGCAATACACTCCCCCAAAATTTAGTCCGT
1155703 TTGCAATA
1 TTGCAATA
1155711 TGAACCCTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (31 bp):
TTGCAATACACTCCCCCAAAATTTAGTCCGT
Found at i:1155711 original size:31 final size:31
Alignment explanation
Indices: 1155652--1155712 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1155642 TGCAATACAC
** *
1155652 TCCCCCAGCATTTAGTCTGTTTGCAATATGG
1 TCCCCCAAAATTTAGTCCGTTTGCAATATGG
1155683 TCCCCCAAAATTTAGTCCGTTTGCAATATG
1 TCCCCCAAAATTTAGTCCGTTTGCAATATG
1155713 AACCCTGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.34
Consensus pattern (31 bp):
TCCCCCAAAATTTAGTCCGTTTGCAATATGG
Found at i:1155896 original size:2 final size:2
Alignment explanation
Indices: 1155889--1155914 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1155879 TAACTGAATC
1155889 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1155915 AACTTATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1158431 original size:34 final size:36
Alignment explanation
Indices: 1158370--1158443 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 36
1158360 GTTTTTGACA
1158370 AATAATAAGAGGATTGGATTAATTTGAACCCATCTCTAT
1 AATAATAAGAGGATTGG---AATTTGAACCCATCTCTAT
1158409 AATAATAAGAGGATTGG-A-TTGAACCCATCTCTAT
1 AATAATAAGAGGATTGGAATTTGAACCCATCTCTAT
1158443 A
1 A
1158444 CTAAACAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
34 17 0.49
35 1 0.03
39 17 0.49
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (36 bp):
AATAATAAGAGGATTGGAATTTGAACCCATCTCTAT
Found at i:1163596 original size:7 final size:8
Alignment explanation
Indices: 1163576--1163686 Score: 51
Period size: 7 Copynumber: 14.1 Consensus size: 8
1163566 CCTTCTATAG
1163576 ATATTTTT
1 ATATTTTT
1163584 ATATTTTT
1 ATATTTTT
*
1163592 A-ATTTGT
1 ATATTTTT
1163599 ATTATTTTCT
1 A-TATTTT-T
*
1163609 -TAATTTGT
1 AT-ATTTTT
1163617 ATA-TTTT
1 ATATTTTT
1163624 ATA-TTTT
1 ATATTTTT
*
1163631 ATATTATT
1 ATATTTTT
*
1163639 AT-TTTTG
1 ATATTTTT
1163646 ATGA-TTTT
1 AT-ATTTTT
1163654 AGTA--TTT
1 A-TATTTTT
1163661 ATATTATTT
1 ATATT-TTT
*
1163670 AT-TTTTC
1 ATATTTTT
1163677 ATATCTTTT
1 ATAT-TTTT
1163686 A
1 A
1163687 GATTGTGATG
Statistics
Matches: 79, Mismatches: 10, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
6 2 0.03
7 32 0.41
8 25 0.32
9 19 0.24
10 1 0.01
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (8 bp):
ATATTTTT
Found at i:1163611 original size:18 final size:17
Alignment explanation
Indices: 1163578--1163623 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
1163568 TTCTATAGAT
*
1163578 ATTTTTATA-TTT-TTA
1 ATTTGTATATTTTCTTA
1163593 ATTTGTATTATTTTCTTA
1 ATTTGTA-TATTTTCTTA
1163611 ATTTGTATATTTT
1 ATTTGTATATTTT
1163624 ATATTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 6 0.22
16 2 0.07
17 9 0.33
18 10 0.37
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (17 bp):
ATTTGTATATTTTCTTA
Found at i:1166091 original size:3 final size:3
Alignment explanation
Indices: 1166077--1166136 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
1166067 TTTTTCATTC
* * * * *
1166077 TAT TAT TTT TAT TAT TAT TTT TAT TAT TAT TAT TA- AAT AAA TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1166123 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
1166137 AATAAAAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 3 0.06
3 45 0.94
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1167801 original size:119 final size:117
Alignment explanation
Indices: 1167654--1167890 Score: 271
Period size: 120 Copynumber: 2.0 Consensus size: 117
1167644 ATTTTAATCC
* * * ** *
1167654 TGTTTTAATATTTATTTATTTTTCAATAT-TAAGAAATG-GCAGTCTTAAAACAACTGGATGTTC
1 TGTTTTAATAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAAAAG-TC
* * *
1167717 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
65 ATTTTCTGATATTTCTAAATAAAAAAATATCCTA-TTTATAAA-TATATATAAAT
* * ** *
1167772 TGTTTTAATTAATTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAAAAGTC
1 TGTTTTAA-TAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAAAAGTC
* **
1167837 CTTTTCTGATATTTCTAAATAAAAAAATATTTTATTTATAAATATATATAAAT
65 ATTTTCTGATATTTCTAAATAAAAAAATATCCTATTTATAAATATATATAAAT
1167890 T
1 T
1167891 AATATTTTTT
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
118 19 0.19
119 27 0.27
120 38 0.38
121 15 0.15
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (117 bp):
TGTTTTAATAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAAAAGTCA
TTTTCTGATATTTCTAAATAAAAAAATATCCTATTTATAAATATATATAAAT
Found at i:1167887 original size:29 final size:28
Alignment explanation
Indices: 1167855--1167910 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
1167845 ATATTTCTAA
1167855 ATAAAAAAATATTTTATTTATAAATATAT
1 ATAAAAAAATATTTT-TTTATAAATATAT
** *
1167884 ATAAATTAATATTTTTTTATAATTATA
1 ATAAAAAAATATTTTTTTATAAATATA
1167911 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATAAAAAAATATTTTTTTATAAATATAT
Found at i:1169882 original size:114 final size:114
Alignment explanation
Indices: 1169681--1169904 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 114
1169671 GTGCCATGTT
1169681 CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAACTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAACTGTTCTTTGAGTTATCTGATCTG
* * * *
1169746 ATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 ATTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTG
* *
1169795 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAACTGTTCTTTGAGTTATCTGATCTG
* * *
1169860 GTTCGGTAGGAACCCCAGAACCAATTATTGAAATTGAAAGATGAA
66 ATTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAA
1169905 CAGCATGATC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAACTGTTCTTTGAGTTATCTGATCTG
ATTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTG
Found at i:1170118 original size:31 final size:31
Alignment explanation
Indices: 1170080--1170144 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1170070 CAGCACATAT
1170080 AGAATCTGTCAACTCTGCAATTGATAAATTC
1 AGAATCTGTCAACTCTGCAATTGATAAATTC
*
1170111 AGAATCTGTCAACTCTGCAATTGATGAATTC
1 AGAATCTGTCAACTCTGCAATTGATAAATTC
1170142 AGA
1 AGA
1170145 CCACATCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (31 bp):
AGAATCTGTCAACTCTGCAATTGATAAATTC
Found at i:1172439 original size:22 final size:22
Alignment explanation
Indices: 1172410--1172464 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1172400 ATCTATACTC
1172410 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
1172432 TTTAAAGACGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1172454 TTCAAAGATGA
1 TTCAAAGATGA
1172465 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1173269 original size:76 final size:76
Alignment explanation
Indices: 1173143--1173777 Score: 1155
Period size: 76 Copynumber: 8.4 Consensus size: 76
1173133 CTATTTCCCA
1173143 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1173208 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1173219 CATCTGTAAGTCCTACAGTGTATGATGTTACCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1173284 AGCCTTAGGGT
66 AGCCTTAGGGT
1173295 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1173360 AGCCTTAGGTT
66 AGCCTTAGGGT
* *
1173371 CATCTGTAAGTCCTACAGTGCATGATGCTACCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1173436 AGCCTTAGGGT
66 AGCCTTAGGGT
1173447 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1173512 AGCCTTAGGGT
66 AGCCTTAGGGT
1173523 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1173588 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1173599 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1173664 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1173675 CATCTGCAAGTCCTACAGTACATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1173740 AACCTTCA-GGT
66 AGCCTT-AGGGT
* *
1173751 CATCTGTAAGCCCTTCAGTGCATGATG
1 CATCTGTAAGTCCTACAGTGCATGATG
1173778 ATTTTAAGAC
Statistics
Matches: 539, Mismatches: 19, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
76 538 1.00
77 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1173942 original size:3 final size:3
Alignment explanation
Indices: 1173928--1174003 Score: 84
Period size: 3 Copynumber: 25.7 Consensus size: 3
1173918 TTTTTCATTC
* * * *
1173928 TAT TAT TTT TAT TAT TAT TAT TAT TAT TA- AAT AAA TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1173974 TAT TAT TAT TCT ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
1174004 AATAAAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
2 3 0.05
3 58 0.92
4 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1173971 original size:22 final size:23
Alignment explanation
Indices: 1173940--1174009 Score: 88
Period size: 22 Copynumber: 3.0 Consensus size: 23
1173930 TTATTTTTAT
1173940 TATTATTATTATTATTAAATAAA
1 TATTATTATTATTATTAAATAAA
* **
1173963 TA-TATTATTATTATTATTATTCTA
1 TATTATTATTATTATTA--AATAAA
1173987 TATTATTATTATTATTAAATAAA
1 TATTATTATTATTATTAAATAAA
1174010 AAATACAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 14 0.37
23 5 0.13
24 5 0.13
25 14 0.37
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATTATTATTATTAAATAAA
Found at i:1175466 original size:18 final size:18
Alignment explanation
Indices: 1175442--1175481 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1175432 TTAGCCATAA
*
1175442 ATATATATATATATATATTT
1 ATATA-ATAAATA-ATATTT
1175462 ATATAATAAATAATATTT
1 ATATAATAAATAATATTT
1175480 AT
1 AT
1175482 TTTATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATAATAAATAATATTT
Found at i:1175665 original size:119 final size:119
Alignment explanation
Indices: 1175529--1175763 Score: 298
Period size: 120 Copynumber: 2.0 Consensus size: 119
1175519 ATTTTAATCA
* * * *
1175529 TGTTTTAATATTTATTTA-TTTTTCAATAT-TAAGAAATG-GCAGTCTTAAAACAACTGGATGTC
1 TGTTTTAATATTTATTTAGTTTTT-AATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-
* *
1175591 CATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAAT
64 CATTTTCTGATATTTCTAAATAAAAAAATATCCTA-TTTATAAATATATATATTAAT
* ** *
1175647 TGTTTTAATTATTTATTTAGTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTAGTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
**
1175712 ATTTTCTGATATTTCTAAATAAAAAAATATTTTATTTATAAATATATATATT
65 ATTTTCTGATATTTCTAAATAAAAAAATATCCTATTTATAAATATATATATT
1175764 TTAATATTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
118 8 0.08
119 24 0.24
120 51 0.51
121 17 0.17
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (119 bp):
TGTTTTAATATTTATTTAGTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAAAAAATATCCTATTTATAAATATATATATTAAT
Found at i:1179274 original size:20 final size:20
Alignment explanation
Indices: 1179229--1179274 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1179219 GACCAATAAA
*
1179229 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
1179249 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
1179268 ATCGCAA
1 ATCGCAA
1179275 ATCAGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:1179360 original size:21 final size:21
Alignment explanation
Indices: 1179309--1179361 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1179299 ATTATGACTA
1179309 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1179330 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1179351 TCGCAATGCGA
1 TCGCAATGCGA
1179362 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1179376 original size:20 final size:21
Alignment explanation
Indices: 1179351--1179402 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1179341 TTTTCCCAAT
*
1179351 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1179371 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1179392 TCGCAATGCGA
1 TCGCAATGCGA
1179403 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1179415 original size:41 final size:41
Alignment explanation
Indices: 1179388--1179566 Score: 141
Period size: 41 Copynumber: 4.4 Consensus size: 41
1179378 GCGAATTTGG
*
1179388 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
1179429 AAAATCGCAACGCGATACTGACTTTCGCAACGCG-T-TTAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*** * * * **
1179468 TGACTTTCGCAACGCGATTCTGACTTTCACAACGCGATTCTGAC
1 --AAAATCGCAACGCGATACTGACTATCGCAACGCGATAAT-AC
** * * *
1179512 --TTTCGCAACGAGATTCTGACTATCGCAACGTGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
1179551 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1179567 TTTCAAAGTT
Statistics
Matches: 112, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
39 5 0.04
40 32 0.29
41 71 0.63
42 1 0.01
43 1 0.01
44 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1179416 original size:20 final size:20
Alignment explanation
Indices: 1179391--1179546 Score: 152
Period size: 20 Copynumber: 7.7 Consensus size: 20
1179381 AATTTGGAAA
*
1179391 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1179411 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1179432 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1179452 TTCGCAACGCGTTTACTGACT
1 ATCGCAACGCG-ATACTGACT
* *
1179473 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
1179493 TTCACAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
1179513 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1179533 ATCGCAACGTGATA
1 ATCGCAACGCGATA
1179547 ATACAGAATC
Statistics
Matches: 117, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 79 0.68
21 34 0.29
22 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1180116 original size:34 final size:34
Alignment explanation
Indices: 1180073--1180179 Score: 106
Period size: 40 Copynumber: 3.0 Consensus size: 34
1180063 GACATTCATT
1180073 TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
1 TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
**
1180107 TGACTATCGCAACGCGAAAATGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACG-G-----GGAAATCGCAACGCGAAAA
* * * *
1180147 TGGCTATCGCAACGAGAAAATCGCAATGCGAAA
1 TGACTATCGCAACGGGGAAATCGCAACGCGAAA
1180180 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
34 28 0.47
35 1 0.02
40 30 0.51
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.14
Consensus pattern (34 bp):
TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
Found at i:1180117 original size:20 final size:20
Alignment explanation
Indices: 1180092--1180167 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
1180082 CAACGGGGAA
*
1180092 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
1180112 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1180132 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
1180152 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
1180168 CGCAATGCGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1180223 original size:33 final size:33
Alignment explanation
Indices: 1180186--1180282 Score: 113
Period size: 38 Copynumber: 2.8 Consensus size: 33
1180176 GAAATGAAAA
1180186 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
* *
1180219 TCGCATTGCGATTTTTATTTTGCATTGCGATTTTCATT
1 TCGCATTGCGA---TT-TTCT-CGTTGCGATTTTCATT
* *
1180257 TCGCATTGCGATTCTCTTGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
1180283 AGTCAGTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
33 18 0.34
34 2 0.04
35 2 0.04
36 2 0.04
37 3 0.06
38 26 0.49
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:1180227 original size:19 final size:19
Alignment explanation
Indices: 1180186--1180269 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
1180176 GAAATGAAAA
1180186 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1180202 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1180219 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
1180238 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1180257 TCGCATTGCGATT
1 TCGCATTGCGATT
1180270 CTCTTGTTGC
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
14 11 0.19
16 3 0.05
17 3 0.05
19 42 0.71
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1180299 original size:20 final size:20
Alignment explanation
Indices: 1180274--1180311 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1180264 GCGATTCTCT
1180274 TGTTGCGATAGTCAGTTTCG
1 TGTTGCGATAGTCAGTTTCG
*
1180294 TGTTGCGATAGTCTGTTT
1 TGTTGCGATAGTCAGTTT
1180312 TGCCTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.29, T:0.45
Consensus pattern (20 bp):
TGTTGCGATAGTCAGTTTCG
Found at i:1181909 original size:41 final size:42
Alignment explanation
Indices: 1181855--1181946 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
1181845 CCTCTTCAAC
* * *
1181855 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTAGAGGGGACTCTTGAGG
* *
1181896 GATGATAGGGGCCTCTTGAACGATTAGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTAGAGGGGACTCTTGAGG
1181938 GATGACAGG
1 GATGACAGG
1181947 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTAGAGGGGACTCTTGAGG
Found at i:1181911 original size:21 final size:21
Alignment explanation
Indices: 1181882--1181942 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1181872 GAACGGTGGG
*
1181882 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* ** *
1181903 GGGGCCTCTTGAACGATTAGA
1 GGGGACTCTTGAGGGATGAGA
1181924 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1181943 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1182309 original size:20 final size:20
Alignment explanation
Indices: 1182284--1182336 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1182274 GAAGAATAGT
*
1182284 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
1182304 TTACTTTCGCAACACGAAAA
1 TTACTTTCGCAACACGAAAA
* *
1182324 TGACTATCGCAAC
1 TTACTTTCGCAAC
1182337 GCGGAAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:1182344 original size:20 final size:20
Alignment explanation
Indices: 1182310--1182396 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
1182300 AAACTTACTT
* *
1182310 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1182330 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
1182350 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1182370 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1182389 TCGCAACG
1 TCGCAACG
1182397 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 14 0.24
20 45 0.76
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1182451 original size:19 final size:19
Alignment explanation
Indices: 1182369--1182451 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
1182359 GGAAATGGCT
*
1182369 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
1182388 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
*
1182402 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
*
1182421 ATCGCAACGCGAAA-CACAA
1 ATCGCAATGCGAAATCA-AA
*
1182440 ATCGCATTGCGA
1 ATCGCAATGCGA
1182452 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 35 0.67
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:1182503 original size:19 final size:19
Alignment explanation
Indices: 1182441--1182504 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1182431 GAAACACAAA
1182441 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
1182460 TCACGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1182476 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1182493 TCGCATTGCGAT
1 TCGCATTGCGAT
1182505 AGCCATTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.17
15 3 0.09
16 3 0.09
17 4 0.11
18 3 0.09
19 16 0.46
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1182523 original size:20 final size:19
Alignment explanation
Indices: 1182489--1182543 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1182479 TTGCGATTTT
*
1182489 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1182508 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1182528 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1182544 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1183101 original size:18 final size:18
Alignment explanation
Indices: 1183078--1183138 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
1183068 CGGGTCGATC
1183078 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1183096 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1183114 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1183132 AGGTGAT
1 AGGTGAT
1183139 AACTCCCGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.15, C:0.10, G:0.48, T:0.28
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1184484 original size:20 final size:20
Alignment explanation
Indices: 1184459--1184496 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1184449 AATAGTTTCT
1184459 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
1184479 GAAAATGACAATCGCAAC
1 GAAAATGAAAATCGCAAC
1184497 GAGAGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1184773 original size:22 final size:22
Alignment explanation
Indices: 1184746--1184789 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1184736 GATGGAGATA
1184746 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1184768 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1184790 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1185004 original size:20 final size:20
Alignment explanation
Indices: 1184976--1185087 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
1184966 GATTATGTAT
*
1184976 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1184996 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1185016 TATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
1185036 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1185057 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1185077 TATCGCATTGC
1 TATCGCGTTGC
1185088 AATTTTCCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.77
21 13 0.17
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1185079 original size:41 final size:41
Alignment explanation
Indices: 1184956--1185087 Score: 178
Period size: 41 Copynumber: 3.2 Consensus size: 41
1184946 CGCTTTGAAA
*
1184956 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
1184997 ATCGCGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* *
1185037 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1185078 ATCGCATTGC
1 ATCGCATTGC
1185088 AATTTTCCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 41 0.53
42 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1185109 original size:41 final size:41
Alignment explanation
Indices: 1184976--1185111 Score: 116
Period size: 41 Copynumber: 3.3 Consensus size: 41
1184966 GATTATGTAT
* * * ** *
1184976 TATCTCGTTGCGAAAGTCAGTATCGCGTTGCGAA-AGT-AAG
1 TATCGCGTTGCGATAGTCAGTATCGCATTGC-AATTTTCAAA
* * * ** *
1185016 TATCGCGTTGCGAAAGTTAGTATCGCATTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCAAA
1185057 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTT-CAAA
*
1185099 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
1185112 TTACTTATTC
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 29 0.37
41 46 0.59
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCAAA
Found at i:1185172 original size:21 final size:22
Alignment explanation
Indices: 1185120--1185172 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1185110 ATTTACTTAT
1185120 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1185141 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1185162 TCGCATTGCGA
1 TCGCATTGCGA
1185173 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1192274 original size:20 final size:20
Alignment explanation
Indices: 1192249--1192326 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
1192239 TTCGGTTATG
*
1192249 GCATCCTTTCATGCCTTAAT
1 GCATCCGTTCATGCCTTAAT
*
1192269 GCATCCGTTCATGCATGTTTAGTTAT
1 GCATCCGTTCATGC---CTTA---AT
*
1192295 GGCATCCTTTCATGCCTTAAT
1 -GCATCCGTTCATGCCTTAAT
1192316 GCATCCGTTCA
1 GCATCCGTTCA
1192327 AGCATTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
20 23 0.50
21 2 0.04
23 3 0.07
24 3 0.07
26 2 0.04
27 13 0.28
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.38
Consensus pattern (20 bp):
GCATCCGTTCATGCCTTAAT
Found at i:1192294 original size:47 final size:47
Alignment explanation
Indices: 1192243--1192599 Score: 554
Period size: 47 Copynumber: 7.6 Consensus size: 47
1192233 ATCAATTTCG
*
1192243 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATGTTTA
1 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
*
1192290 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCAAGCATTTTTTTA
1 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCA--TTTTTA
* * *
1192339 GTTATGGCGTCATTTCATGCCTTAATTCATCCGTTCATGCATTTTTA
1 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
* *
1192386 GTTATGACATCCTTTCATGCCTTAATGTATCCGTTCATGCA-TTTTA
1 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
1192432 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
1 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
* * *
1192479 TTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATTCATTTTTA
1 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
* * *
1192526 GTTATGGAATCCTTTCATGCCTTAATGCCTCCGTTCATGCAATTTTA
1 GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
* *
1192573 GTTATGACATCCTTTCATGCCCTAATG
1 GTTATGGCATCCTTTCATGCCTTAATG
1192600 ATAACATAGT
Statistics
Matches: 282, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
46 44 0.16
47 196 0.70
49 42 0.15
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (47 bp):
GTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
Found at i:1192510 original size:20 final size:20
Alignment explanation
Indices: 1192393--1192516 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
1192383 TTAGTTATGA
1192393 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* * *
1192413 TATCCGTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGC--CTTA---AT-G
1192439 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
1192459 CATCCGTTCATGCATTTTTATTTATGG
1 CATCCTTTCATGC---CTTA---AT-G
1192486 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
1192506 CATCCATTCAT
1 CATCCTTTCAT
1192517 TCATTTTTAG
Statistics
Matches: 80, Mismatches: 11, Indels: 26
0.68 0.09 0.22
Matches are distributed among these distances:
20 35 0.44
21 4 0.05
22 3 0.04
23 3 0.04
24 6 0.08
25 2 0.03
26 14 0.17
27 13 0.16
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:1199952 original size:93 final size:94
Alignment explanation
Indices: 1199718--1200015 Score: 456
Period size: 93 Copynumber: 3.2 Consensus size: 94
1199708 CATCAATTTC
*
1199718 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCA
1 AGTTATGGCATCCTTTCATGCCTTAATGTATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCA
* ** * *
1199783 TGCCTTACTATATCAGTTCAAGCATTTTTT
66 TGCCTTAATGCATCCGTTCATGCA-TTTTT
* *
1199813 AGTTATGGCATCCTTTCATGCCTTAAT-TCATCTGTTCATGCGTTTTTAGTTATGGCATCCTTTC
1 AGTTATGGCATCCTTTCATGCCTTAATGT-ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTC
*
1199877 ATACCTTAATGCATCCGTTCATGCA-TTTT
65 ATGCCTTAATGCATCCGTTCATGCATTTTT
*
1199906 AGTTATGGCATCCTTTCATTCCTTAATGTATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCA
1 AGTTATGGCATCCTTTCATGCCTTAATGTATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCA
*
1199971 TGCCTTAATGCATTCGTTCATGCATTTTT
66 TGCCTTAATGCATCCGTTCATGCATTTTT
*
1200000 AGTTATGCCATCCTTT
1 AGTTATGGCATCCTTT
1200016 AATACCCTAA
Statistics
Matches: 185, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
93 86 0.46
94 20 0.11
95 79 0.43
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (94 bp):
AGTTATGGCATCCTTTCATGCCTTAATGTATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCA
TGCCTTAATGCATCCGTTCATGCATTTTT
Found at i:1200027 original size:47 final size:47
Alignment explanation
Indices: 1199718--1200015 Score: 463
Period size: 47 Copynumber: 6.3 Consensus size: 47
1199708 CATCAATTTC
1199718 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTT
1 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTT
* ** * *
1199765 AGTTATGGCATCCTTTCATGCCTTACTATATCAGTTCAAGCATTTTTT
1 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCA-TTTTT
* * *
1199813 AGTTATGGCATCCTTTCATGCCTTAATTCATCTGTTCATGCGTTTTT
1 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTT
*
1199860 AGTTATGGCATCCTTTCATACCTTAATGCATCCGTTCATGCA-TTTT
1 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTT
* *
1199906 AGTTATGGCATCCTTTCATTCCTTAATGTATCCGTTCATGCATTTTT
1 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTT
*
1199953 AGTTATGGCATCCTTTCATGCCTTAATGCATTCGTTCATGCATTTTT
1 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTT
*
1200000 AGTTATGCCATCCTTT
1 AGTTATGGCATCCTTT
1200016 AATACCCTAA
Statistics
Matches: 228, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
46 44 0.19
47 143 0.63
48 41 0.18
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (47 bp):
AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTT
Found at i:1205328 original size:55 final size:55
Alignment explanation
Indices: 1205279--1205865 Score: 768
Period size: 55 Copynumber: 10.7 Consensus size: 55
1205269 GATATGGTCA
* * *
1205279 TTCATAAACATATTATGAATTACGTGGTTTTGCACACTTAGTGTCGATATGGTTG
1 TTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
* *
1205334 TTCATAAACATATTATGAA-TTCTGTGGTTTTGCATACTTAGTGTCGATACGGTTG
1 TTCATAAACATATTATGAATTTC-GTGGTTTTGCACACTTAGTGCCGATACGGTTG
*
1205389 TTCATAAACATATTATGAATTAT-GTGGTTTTACACACTTAGTGCCGATACGGTTG
1 TTCATAAACATATTATGAATT-TCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
* * * *
1205444 TTCATAAACATATTATGAATTTCGTGGTTTTACACAATTAGTGCCAATATGGTTG
1 TTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
* ** *
1205499 TTCATAAACATATTTTGAATTAT-GTGGTTTTGCACACTTAGTGTTGATACAGTTG
1 TTCATAAACATATTATGAATT-TCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
* *
1205554 TTTATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGCCTATACGGTTG
1 TTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
* * * * * *
1205609 CTCATAAACATATTATGAATTTCGTGGTTTTGTAGACTTAGTACCGATATGATTG
1 TTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
* * * * * *
1205664 TTCATAAACATATTATGAATTTTGTGGTTTTACACACTTAGTACTGATACGATTA
1 TTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
* * * *
1205719 ATCACAAACATATTATGAA-TTCTGTGATTTAGCACACTTAGTGCCGATACGGTTG
1 TTCATAAACATATTATGAATTTC-GTGGTTTTGCACACTTAGTGCCGATACGGTTG
* *
1205774 TTCATAAACATATTATGAATTCCGTGGTTTTGCACACTTAGTGTCGATACGGTTG
1 TTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
* ** *
1205829 TTCATAAATATATTATGAATTTTTTGGTTTTGTACAC
1 TTCATAAACATATTATGAATTTCGTGGTTTTGCACAC
1205866 AATGCTGATA
Statistics
Matches: 464, Mismatches: 60, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
54 6 0.01
55 453 0.98
56 4 0.01
57 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (55 bp):
TTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGCCGATACGGTTG
Found at i:1210347 original size:83 final size:83
Alignment explanation
Indices: 1210241--1210560 Score: 487
Period size: 83 Copynumber: 3.9 Consensus size: 83
1210231 CTCTTTGGTG
* * * *
1210241 AAGGCTTACAAATTACCCAAAGGATTTAATCATCAAGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
*
1210306 ACTTATCATCTTACTCTA
66 ACTTATCATCTTGCTCTA
* * ** *
1210324 AAGGCTTATAGATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAACCGAAGA
1 AAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1210389 ACTTATCATCTTGCTCTA
66 ACTTATCATCTTGCTCTA
*
1210407 AAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGG
1 AAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
*
1210472 ACTTATTATCTTGCTCTA
66 ACTTATCATCTTGCTCTA
* * * * *
1210490 AAGACTTACAGATGACCCGAAGGATTTAATCACCATGATCGAAAGATTTACTGATGGCCAGAAGG
1 AAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1210555 ACTTAT
66 ACTTAT
1210561 AGATTGTGAA
Statistics
Matches: 215, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 215 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (83 bp):
AAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTATCATCTTGCTCTA
Found at i:1210555 original size:42 final size:42
Alignment explanation
Indices: 1210255--1210555 Score: 313
Period size: 42 Copynumber: 7.2 Consensus size: 42
1210245 CTTACAAATT
* *
1210255 ACCCAAAGGATTTAATCATCAAGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * * * * * *
1210297 GCCCGAAGGACTT-ATCATCTTACTCTAAAGGCTTA-TAGATA
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACT-GATG
1210338 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * * * * * *
1210380 AACCGAAGAACTT-ATCATCTTGCTCTAAAGGCTTACAGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
*
1210421 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAATGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * * * * *
1210463 GCCCGAAGGACTT-ATTATCTTGCTCTAAAGACTTACAGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * *
1210504 ACCCGAAGGATTTAATCACCATGATCGAAAGATTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* *
1210546 GCCAGAAGGA
1 ACCCGAAGGA
1210556 CTTATAGATT
Statistics
Matches: 205, Mismatches: 49, Indels: 10
0.78 0.19 0.04
Matches are distributed among these distances:
40 1 0.00
41 99 0.48
42 104 0.51
43 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (42 bp):
ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
Found at i:1210927 original size:217 final size:215
Alignment explanation
Indices: 1210459--1211196 Score: 1113
Period size: 217 Copynumber: 3.4 Consensus size: 215
1210449 AAGACTTAAT
* * * * * *
1210459 GATGGCCCGAAGGACTTATTATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAATCACC
1 GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTACAGATGACCCAAAGGATTTAAGCATC
* * * * *
1210524 ATGATCGAAAGATTTACTGATGGCCAGAAGGACTTATAGATTGTGAAATTTTGAAAATCGCATTA
66 ATGCTCGAAAGACTTACTGATGGCCCGAA-GACTTATAAATTGTGAAATTTTGAAAATCGCATTC
* *
1210589 TTCGTTTTCAAAAATTCCATTTTCTTAAAACATCATATTTTTTTCATTTTCAAATTCATGTGAAA
130 TTCGTTTTCAAAAATTCCATCTTCTTAAAACA-C-TATTTTTTTTATTTTCAAATTCATGTGAAA
1210654 ACATCCTACCCGAAGGTTTTATG
193 ACATCCTACCCGAAGGTTTTATG
** *
1210677 GATGGCATGAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACCCAAAGGATTTTAAGCAT
1 GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTACAGATGACCCAAAGGA-TTTAAGCAT
*
1210742 CATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATAAATTGTGAAAATTTGAAAATCGCATT
65 CATGCTCGAAAGACTTACTGATGGCCCGAA-GACTTATAAATTGTGAAATTTTGAAAATCGCATT
*
1210807 CTTCGTTTTAAAAAATTCCATCTTCTTAAAACACTATTTTTTTTATTTTCAAATTCATGTGAAAA
129 CTTCGTTTTCAAAAATTCCATCTTCTTAAAACACTATTTTTTTTATTTTCAAATTCATGTGAAAA
*
1210872 CATCATACCCGAAGGTTTTATG
194 CATCCTACCCGAAGGTTTTATG
* *
1210894 GATGGCCCGAAGGACTTATCATCTTTCTCAAAAGGATTACAGATGACCCAAAGGATTTTAAGCAT
1 GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTACAGATGACCCAAAGGA-TTTAAGCAT
* *
1210959 TATGC-CTGAAAGACTTACTGATGGACCGAAGTACTTATAAATTGTGAAATTTTGAAAATCGCAT
65 CATGCTC-GAAAGACTTACTGATGGCCCGAAG-ACTTATAAATTGTGAAATTTTGAAAATCGCAT
1211023 TCTTCGTTTTCAAAAATTCCATCTTCTTAAAACACTA--TTTTTTATTTTCAAATTCATGTGAAA
128 TCTTCGTTTTCAAAAATTCCATCTTCTTAAAACACTATTTTTTTTATTTTCAAATTCATGTGAAA
* *
1211086 ACATCCTACCCGATGGTCTTATG
193 ACATCCTACCCGAAGGTTTTATG
* *
1211109 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTACAGATGACCCAAAGGATTTAAGCATC
** *
1211174 ATGCTAAAAAAACTTACTGATGG
66 ATGCTCGAAAGACTTACTGATGG
1211197 ATTTGCTTCA
Statistics
Matches: 476, Mismatches: 40, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
214 28 0.06
215 97 0.20
216 2 0.00
217 204 0.43
218 49 0.10
219 96 0.20
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (215 bp):
GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTACAGATGACCCAAAGGATTTAAGCATC
ATGCTCGAAAGACTTACTGATGGCCCGAAGACTTATAAATTGTGAAATTTTGAAAATCGCATTCT
TCGTTTTCAAAAATTCCATCTTCTTAAAACACTATTTTTTTTATTTTCAAATTCATGTGAAAACA
TCCTACCCGAAGGTTTTATG
Found at i:1211238 original size:34 final size:34
Alignment explanation
Indices: 1211200--1211334 Score: 198
Period size: 34 Copynumber: 3.9 Consensus size: 34
1211190 CTGATGGATT
1211200 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* *
1211234 TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
** *
1211268 TGCTTCACTACTCTTTTGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-G
* *
1211303 TGCTTCACTCCTCTTTGGTGAAGGCTTAAGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1211335 TGACTTGCCC
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
34 63 0.68
35 30 0.32
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (34 bp):
TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
Found at i:1213410 original size:2 final size:2
Alignment explanation
Indices: 1213399--1213447 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1213389 TTGTATACAA
1213399 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1213440 AT AT AT AT
1 AT AT AT AT
1213448 TGTTGGGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1215862 original size:22 final size:22
Alignment explanation
Indices: 1215834--1215878 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1215824 CATGTCTTTA
1215834 TGAATGGTCTTCTCGTCCTTGG
1 TGAATGGTCTTCTCGTCCTTGG
*
1215856 TGAATGGTCTTTTCGTCCTTGG
1 TGAATGGTCTTCTCGTCCTTGG
1215878 T
1 T
1215879 ATGACTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.44
Consensus pattern (22 bp):
TGAATGGTCTTCTCGTCCTTGG
Found at i:1217815 original size:21 final size:23
Alignment explanation
Indices: 1217789--1217831 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1217779 AAATTAAGTT
1217789 AAATGAATTT-TAAG-ATTTTCC
1 AAATGAATTTCTAAGTATTTTCC
*
1217810 AAATGATTTTCTAAGTATTTTC
1 AAATGAATTTCTAAGTATTTTC
1217832 GATAGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (23 bp):
AAATGAATTTCTAAGTATTTTCC
Found at i:1250252 original size:55 final size:55
Alignment explanation
Indices: 1250181--1250633 Score: 558
Period size: 55 Copynumber: 8.3 Consensus size: 55
1250171 ATTTAAGGTA
* * * ** * * *
1250181 CACACGTAGTGCCGATACGGTCGTTCATAATTATATTATGAATTACATGGTATTG
1 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGTTTTG
* *
1250236 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTTGTGGTTCTG
1 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGTTTTG
* * *
1250291 CACACTTAGTGTCGATACAGTTGTTCATAAGC--A-TATGAATTTTGTGGTTTTG
1 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGTTTTG
* *
1250343 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAAATAT-GTGGTTTTA
1 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATG-AATTTCGTGGTTTTG
* * * *
1250398 TACACTTAGTGCCGATACGGTTGTTCATAAATATATTATGAATTTTGTGGTTTTG
1 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGTTTTG
* * *
1250453 CACACTTAGTGCCGATACAGTTGTTCATAAACATATTATGAA-TTCTGAGGTTTT-
1 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTC-GTGGTTTTG
* * *
1250507 AACACTTAGTGTCGATACTGTTGTTCATAAATATATTATGAATTTCGTGGTTTTG
1 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGTTTTG
* * ** *
1250562 CACACTTAGTGTTGAAACTATTGTTCATAAACATATTATGAATTTCGTGATTTTG
1 CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGTTTTG
* *
1250617 CACTCTTAGTGTTGATA
1 CACACTTAGTGTCGATA
1250634 ATACACATAG
Statistics
Matches: 350, Mismatches: 40, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
52 48 0.14
53 1 0.00
54 52 0.15
55 245 0.70
56 4 0.01
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (55 bp):
CACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGTTTTG
Found at i:1250590 original size:164 final size:162
Alignment explanation
Indices: 1250182--1250627 Score: 599
Period size: 162 Copynumber: 2.7 Consensus size: 162
1250172 TTTAAGGTAC
* * * * * * *
1250182 ACACGTAGTGCCGATACGGTCGTTCATAATTATATTATGAATTACATGGTATTGCACACTTAGTG
1 ACACTTAGTGTCGATACGGTTGTTCATAAATATATTATGAATTTCGTGGTTTTGCACACTTAGTG
* *
1250247 TCGATACGGTTGTTCATAAACATATTATGAATTTTGTGGTTCTGCACACTTAGTGTCGATACAGT
66 TCGATACGGTTGTTCATAAACATATTATGAATTTTGTGGTTTTGCACACTTAGTGCCGATACAGT
* * * *
1250312 TGTTCATAAGCATATGAATTTTGTGGTTTTGC
131 TGTTCATAAACATATGAATTCTGAGGTTTTGA
* * **
1250344 ACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAAATAT-GTGGTTTTATACACTTAGT
1 ACACTTAGTGTCGATACGGTTGTTCATAAATATATTATG-AATTTCGTGGTTTTGCACACTTAGT
* *
1250408 GCCGATACGGTTGTTCATAAATATATTATGAATTTTGTGGTTTTGCACACTTAGTGCCGATACAG
65 GTCGATACGGTTGTTCATAAACATATTATGAATTTTGTGGTTTTGCACACTTAGTGCCGATACAG
1250473 TTGTTCATAAACATATTATGAATTCTGAGGTTTT-A
130 TTGTTCATAAAC--A-TATGAATTCTGAGGTTTTGA
*
1250508 ACACTTAGTGTCGATACTGTTGTTCATAAATATATTATGAATTTCGTGGTTTTGCACACTTAGTG
1 ACACTTAGTGTCGATACGGTTGTTCATAAATATATTATGAATTTCGTGGTTTTGCACACTTAGTG
* * ** * * *
1250573 TTGAAACTATTGTTCATAAACATATTATGAATTTCGTGATTTTGCACTCTTAGTG
66 TCGATACGGTTGTTCATAAACATATTATGAATTTTGTGGTTTTGCACACTTAGTG
1250628 TTGATAATAC
Statistics
Matches: 246, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
162 121 0.49
163 7 0.03
164 102 0.41
165 16 0.07
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (162 bp):
ACACTTAGTGTCGATACGGTTGTTCATAAATATATTATGAATTTCGTGGTTTTGCACACTTAGTG
TCGATACGGTTGTTCATAAACATATTATGAATTTTGTGGTTTTGCACACTTAGTGCCGATACAGT
TGTTCATAAACATATGAATTCTGAGGTTTTGA
Found at i:1253831 original size:14 final size:13
Alignment explanation
Indices: 1253812--1253841 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
1253802 TGACTGATAC
1253812 TTTTACTTCTTTTT
1 TTTTACTT-TTTTT
1253826 TTTTACTTTTTTT
1 TTTTACTTTTTTT
1253839 TTT
1 TTT
1253842 CTTTTGAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTACTTTTTTT
Found at i:1255624 original size:18 final size:18
Alignment explanation
Indices: 1255601--1255641 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1255591 TCGTTCTCAA
1255601 GCTTCATATAAATTCTTG
1 GCTTCATATAAATTCTTG
1255619 GCTTCATATAAATTCTTG
1 GCTTCATATAAATTCTTG
*
1255637 TCTTC
1 GCTTC
1255642 TAATTGCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (18 bp):
GCTTCATATAAATTCTTG
Found at i:1258352 original size:16 final size:19
Alignment explanation
Indices: 1258305--1258387 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
1258295 GCAATCTTAG
1258305 CCAAACATGCTTTCTAACC
1 CCAAACATGCTTTCTAACC
*
1258324 CCAAACATACTTTCT-A-C
1 CCAAACATGCTTTCTAACC
*
1258341 CC-TACATGCTTTCTAACC
1 CCAAACATGCTTTCTAACC
*
1258359 CCAAACATACTTTCT-ACC
1 CCAAACATGCTTTCTAACC
1258377 CC--ACATGCTTT
1 CCAAACATGCTTT
1258388 AGATAACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
16 18 0.33
17 4 0.07
18 9 0.16
19 24 0.44
ACGTcount: A:0.29, C:0.37, G:0.04, T:0.30
Consensus pattern (19 bp):
CCAAACATGCTTTCTAACC
Found at i:1258355 original size:35 final size:35
Alignment explanation
Indices: 1258309--1258387 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
1258299 TCTTAGCCAA
*
1258309 ACATGCTTTCTAACCCCAAACATACTTTCTACCCT
1 ACATGCTTTCTAACCCCAAACATACTTTCTACCCC
1258344 ACATGCTTTCTAACCCCAAACATACTTTCTACCCC
1 ACATGCTTTCTAACCCCAAACATACTTTCTACCCC
1258379 ACATGCTTT
1 ACATGCTTT
1258388 AGATAACATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.28, C:0.37, G:0.04, T:0.32
Consensus pattern (35 bp):
ACATGCTTTCTAACCCCAAACATACTTTCTACCCC
Found at i:1261481 original size:24 final size:24
Alignment explanation
Indices: 1261454--1261500 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1261444 TTTCTAATCC
1261454 TTCCTCATTCAAAATCCCTAACTA
1 TTCCTCATTCAAAATCCCTAACTA
* *
1261478 TTCCTCGTTTAAAATCCCTAACT
1 TTCCTCATTCAAAATCCCTAACT
1261501 GGGGTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.36
Consensus pattern (24 bp):
TTCCTCATTCAAAATCCCTAACTA
Found at i:1266635 original size:24 final size:24
Alignment explanation
Indices: 1266608--1266654 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1266598 TTTTCTAATC
1266608 CTTCCTCATTCAAAATCCCTAACT
1 CTTCCTCATTCAAAATCCCTAACT
* *
1266632 CTTCCTCGTTTAAAATCCCTAAC
1 CTTCCTCATTCAAAATCCCTAAC
1266655 CGGGGTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.36, G:0.02, T:0.34
Consensus pattern (24 bp):
CTTCCTCATTCAAAATCCCTAACT
Found at i:1268358 original size:16 final size:16
Alignment explanation
Indices: 1268337--1268368 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1268327 CAATTATATA
1268337 TATAAGAAGTGTTGAC
1 TATAAGAAGTGTTGAC
1268353 TATAAGAAGTGTTGAC
1 TATAAGAAGTGTTGAC
1268369 CTAAAGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (16 bp):
TATAAGAAGTGTTGAC
Found at i:1268721 original size:5 final size:5
Alignment explanation
Indices: 1268713--1268738 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1268703 TTTTATTATT
1268713 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
1268739 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1276580 original size:17 final size:17
Alignment explanation
Indices: 1276546--1276583 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1276536 AAATATTAAA
*
1276546 TTATATTGTATATTATT
1 TTATATTGTATATAATT
*
1276563 TTATATTTTATATAATT
1 TTATATTGTATATAATT
1276580 TTAT
1 TTAT
1276584 TACTTACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATATTGTATATAATT
Found at i:1277696 original size:8 final size:8
Alignment explanation
Indices: 1277680--1277713 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1277670 TACGGATAAG
1277680 TAATTAAA
1 TAATTAAA
*
1277688 TAGTTAAA
1 TAATTAAA
*
1277696 TAATTGAA
1 TAATTAAA
1277704 TAATTAAA
1 TAATTAAA
1277712 TA
1 TA
1277714 TATAAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:1292269 original size:55 final size:55
Alignment explanation
Indices: 1292185--1292940 Score: 995
Period size: 55 Copynumber: 13.7 Consensus size: 55
1292175 AACGATAATC
* * *
1292185 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* *
1292240 GAAGATTGTTCGAGTCTTATACTCTCTGAAAAAAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGACACGATTGAT
* * * *
1292296 GAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATATGGAGCAGACACGATGGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * *
1292351 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* *
1292406 GAAGATTGTTCGAGTCTTATACTCTCTGAAAAAAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGACACGATTGAT
* * * *
1292462 GAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATATGGAGCAGACACGATGGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * *
1292517 GAAGATTGTTCGAGTCTTGTACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
*
1292572 GAAGATTGTTCGAGTCTTATACTCTCTGCA-AAATAGGGAGCAGACACGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
**
1292626 GAAGATTGTTCGAGTCTTATACTCTCTGCGGAAATAGGGAGCAGACACGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* *
1292681 GAAGATTGTTCAAGTCTTATACTCTCTGAA-AGAATGGGGAGCAGACACGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACGATTGAT
* * * *
1292736 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGATTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGAT
* * *
1292792 GAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAGCAGACACGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * ** * * * * *
1292847 GAAGATTCTTCAAGT-TCCTACTCCCT-AAGAAAGAGGGAAC-GAACCCG-TTGACA
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGA-T
* * *
1292900 GAAGATTGTTCGAGT-TCTATACTCCCCGAAGAAAGAGGGAG
1 GAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAG
1292941 TGAACTCGTT
Statistics
Matches: 623, Mismatches: 68, Indels: 20
0.88 0.10 0.03
Matches are distributed among these distances:
52 5 0.01
53 29 0.05
54 67 0.11
55 365 0.59
56 157 0.25
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
Found at i:1292370 original size:111 final size:110
Alignment explanation
Indices: 1292185--1292853 Score: 998
Period size: 111 Copynumber: 6.1 Consensus size: 110
1292175 AACGATAATC
* *
1292185 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
*
1292250 CGAGTCTTATACTCTCTGAAAAAAATAGGGAGCAGACACGATTGTT
66 CGAGTCTTATACTCTCTG-AAAAAATAGGGAGCAGACACGATTGAT
* * * * * *
1292296 GAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATATGGAGCAGACACGATGGATGAAGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
* * *
1292361 CGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTT
66 CGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGAT
* *
1292406 GAAGATTGTTCGAGTCTTATACTCTCTGAAAAAAATAGGGAGCAGACACGATTGTTGAAAATTGT
1 GAAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGACACGATTGTTGAAGATTGT
* * * *
1292471 TCGAGTCTTATACTCTCTGCAGAAATATGGAGCAGACACGATGGAT
65 TCGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGAT
* *
1292517 GAAGATTGTTCGAGTCTTGTACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
*
1292582 CGAGTCTTATACTCTCTG-CAAAATAGGGAGCAGACACGATTGAT
66 CGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGAT
** *
1292626 GAAGATTGTTCGAGTCTTATACTCTCTGCGGAAATAGGGAGCAGACACGATTGATGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
* * *
1292691 CAAGTCTTATACTCTCTGAAAGAATGGGGAGCAGACACGATTGAT
66 CGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGAT
* * *
1292736 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGATTTGTTGAAGATTGT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGTTGAAGATTGT
* * **
1292801 TTGGGTCTTATACTCTCTGAGGAAATAGGGAGCAGACACGATTGAT
65 TCGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGAT
1292847 GAAGATT
1 GAAGATT
1292854 CTTCAAGTTC
Statistics
Matches: 502, Mismatches: 53, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
109 99 0.20
110 172 0.34
111 231 0.46
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
CGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGAT
Found at i:1292459 original size:166 final size:165
Alignment explanation
Indices: 1292185--1292853 Score: 1074
Period size: 166 Copynumber: 4.0 Consensus size: 165
1292175 AACGATAATC
1292185 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
1 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
1292250 CGAGTCTTATACTCTCTGAAAAAAATAGGGAGCAGACACGATTGTTGAAAATTGTTCGAGTCTTA
66 CGAGTCTTATACTCTCTG-AAAAAATAGGGAGCAGACACGATTGTTGAAAATTGTTCGAGTCTTA
*
1292315 TACTCTCTGCAGAAATATGGAGCAGACACGATGGAT
130 TACTCTCTGCAGAAATAGGGAGCAGACACGATGGAT
1292351 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
1 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
1292416 CGAGTCTTATACTCTCTGAAAAAAATAGGGAGCAGACACGATTGTTGAAAATTGTTCGAGTCTTA
66 CGAGTCTTATACTCTCTG-AAAAAATAGGGAGCAGACACGATTGTTGAAAATTGTTCGAGTCTTA
*
1292481 TACTCTCTGCAGAAATATGGAGCAGACACGATGGAT
130 TACTCTCTGCAGAAATAGGGAGCAGACACGATGGAT
* *
1292517 GAAGATTGTTCGAGTCTTGTACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
1 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
* * *
1292582 CGAGTCTTATACTCTCTG-CAAAATAGGGAGCAGACACGATTGATGAAGATTGTTCGAGTCTTAT
66 CGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGTTGAAAATTGTTCGAGTCTTAT
* *
1292646 ACTCTCTGCGGAAATAGGGAGCAGACACGATTGAT
131 ACTCTCTGCAGAAATAGGGAGCAGACACGATGGAT
* * * * *
1292681 GAAGATTGTTCAAGTCTTATACTCTCTGAA-AGAATGGGGAGCAGACACGATTGATGAAGATTGT
1 GAAGATTGATCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACGCGATTGTTGAAGATTGT
* * * * * * *
1292745 TTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGATTTGTTGAAGATTGTTTGGGTCTT
65 TCGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGA-TTGTTGAAAATTGTTCGAGTCTT
*
1292810 ATACTCTCTG-AGGAAATAGGGAGCAGACACGATTGAT
129 ATACTCTCTGCA-GAAATAGGGAGCAGACACGATGGAT
1292847 GAAGATT
1 GAAGATT
1292854 CTTCAAGTTC
Statistics
Matches: 477, Mismatches: 22, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
163 1 0.00
164 149 0.31
165 18 0.04
166 309 0.65
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (165 bp):
GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTGTT
CGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGTTGAAAATTGTTCGAGTCTTAT
ACTCTCTGCAGAAATAGGGAGCAGACACGATGGAT
Found at i:1292904 original size:53 final size:54
Alignment explanation
Indices: 1292847--1292992 Score: 172
Period size: 55 Copynumber: 2.7 Consensus size: 54
1292837 CACGATTGAT
* * *
1292847 GAAGATTCTTCAAGTTC-CTACTCCCTAAGAAAGAGGGAACGAACCCGTT-GACA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAACGAACCCGTTCG-CA
* ** *
1292900 GAAGATTGTTCGAGTTCTATACTCCCCGAAGAAAGAGGGAGTGAACTCGTTCGCA
1 GAAGATTGTTCGAGTTCTATACT-CCCTAAGAAAGAGGGAACGAACCCGTTCGCA
* *
1292955 GAAAATTGTTCGAGTTCTATACTCCCTAA-AATGAGGGA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGA
1292993 GCGAGCTCGT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
53 23 0.29
54 9 0.11
55 47 0.59
56 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAACGAACCCGTTCGCA
Found at i:1293287 original size:8 final size:8
Alignment explanation
Indices: 1293271--1293304 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1293261 TACGGATAAG
1293271 TAATTAAA
1 TAATTAAA
*
1293279 TAGTTAAA
1 TAATTAAA
*
1293287 TAATTGAA
1 TAATTAAA
1293295 TAATTAAA
1 TAATTAAA
1293303 TA
1 TA
1293305 TAAAAATATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:1295074 original size:2 final size:2
Alignment explanation
Indices: 1295067--1295097 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1295057 GTATAGAGTG
1295067 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
1295098 TTTAAATGTG
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:1296200 original size:20 final size:22
Alignment explanation
Indices: 1296164--1296207 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
1296154 TTTATTTACA
1296164 TTTTACAATTCTTTAAATAACT
1 TTTTACAATTCTTTAAATAACT
*
1296186 TTTTACAA-T-TTTAAATTACT
1 TTTTACAATTCTTTAAATAACT
1296206 TT
1 TT
1296208 ATCAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTACAATTCTTTAAATAACT
Found at i:1296773 original size:48 final size:48
Alignment explanation
Indices: 1296719--1297138 Score: 222
Period size: 48 Copynumber: 9.2 Consensus size: 48
1296709 ATATAAGTCG
*
1296719 CCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAATCTCCA
1 CCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCA
* *
1296767 CCACCACCACC-T------CC--G-GT--TTACAAGTATAAGTCTCCA
1 CCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCA
* * * * * * *
1296803 CCACCTCCA--GTGCACTATCCTCCACCA-CCTTATAAGTACAAGTCCCCA
1 CCACCACCACCAT-CACCA-CC-CAAGCATCCTTACAAGTACAAGTCTCCA
* *
1296851 CCACCACCACCGCCATCACCACCAAAACATCCTTACAAGTACAAGTCT---
1 CCACCACCA---CCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCA
* * *
1296899 CCACCACCACTATCACCACCCAAACATGCTTACAAGTACAAGTCTCCA
1 CCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCA
* *
1296947 -C-CC-CC-GC--CACC-TCC-AG--T--TTACAAGTACAAGTCTCCA
1 CCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCA
* ** * * ** *
1296983 CCACC-TC-CGGTGCACTATCCTCCA-CCCCCTTACAAGTACAAGTCCCCA
1 CCACCACCACCAT-CACCA-CC-CAAGCATCCTTACAAGTACAAGTCTCCA
* * *
1297031 CCACCTCCACCACCATCACCACCCAAACATCCTTACAAATACAAGTCACCA
1 CCA---CCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCA
* * *
1297082 CCACCTCCTCCATCCCCACCCAAGCATCCTTACAAGTACAAGTCTCCA
1 CCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCA
1297130 CCACCACCA
1 CCACCACCA
1297139 GTGCACTCTC
Statistics
Matches: 281, Mismatches: 48, Indels: 86
0.68 0.12 0.21
Matches are distributed among these distances:
35 1 0.00
36 44 0.16
37 1 0.00
38 5 0.02
39 1 0.00
40 1 0.00
41 7 0.02
42 4 0.01
43 2 0.01
44 2 0.01
45 36 0.13
46 2 0.01
47 2 0.01
48 111 0.40
50 5 0.02
51 45 0.16
52 9 0.03
53 3 0.01
ACGTcount: A:0.31, C:0.45, G:0.07, T:0.17
Consensus pattern (48 bp):
CCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCA
Found at i:1296796 original size:81 final size:84
Alignment explanation
Indices: 1296681--1296861 Score: 208
Period size: 81 Copynumber: 2.2 Consensus size: 84
1296671 TACAAGTCTC
* * *
1296681 CTCCACCACCTCCAACTTCAGTTTACAAATATAAGTCGCCACCACCACCA-T-CACCA-CC-CAA
1 CTCCACCACCACCACCTCCAGTTTACAAATATAAGTCGCCACCACCACCAGTGCACCATCCTCAA
*
1296742 GCATCCTTACAAGTACAAAT
66 CCA-CCTTACAAGTACAAAT
* * * * * *
1296762 CTCCACCACCACCACCTCCGGTTTACAAGTATAAGTCTCCACCACCTCCAGTGCACTATCCTCCA
1 CTCCACCACCACCACCTCCAGTTTACAAATATAAGTCGCCACCACCACCAGTGCACCATCCTCAA
* *
1296827 CCACCTTATAAGTACAAGT
66 CCACCTTACAAGTACAAAT
*
1296846 CCCCACCACCACCACC
1 CTCCACCACCACCACC
1296862 GCCATCACCA
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 43 0.52
82 1 0.01
83 4 0.05
84 31 0.37
85 4 0.05
ACGTcount: A:0.30, C:0.43, G:0.07, T:0.19
Consensus pattern (84 bp):
CTCCACCACCACCACCTCCAGTTTACAAATATAAGTCGCCACCACCACCAGTGCACCATCCTCAA
CCACCTTACAAGTACAAAT
Found at i:1296891 original size:51 final size:49
Alignment explanation
Indices: 1296830--1296957 Score: 138
Period size: 45 Copynumber: 2.6 Consensus size: 49
1296820 TCCTCCACCA
*
1296830 CCTTATAAGTACAAGTCCCCACCACCACCACCGCCATCACCACCAAAACAT
1 CCTTACAAGTACAAGT-CCCACCACCACCACC-CCATCACCACCAAAACAT
* * *
1296881 CCTTACAAGTACAAGT--CTCCACCACCA--CTATCACCACCCAAACAT
1 CCTTACAAGTACAAGTCCCACCACCACCACCCCATCACCACCAAAACAT
* * *
1296926 GCTTACAAGTACAAGTCTCCACCCCCGCCACC
1 CCTTACAAGTACAAGTC-CCACCACCACCACC
1296958 TCCAGTTTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
45 31 0.48
48 18 0.28
51 15 0.23
ACGTcount: A:0.33, C:0.45, G:0.07, T:0.16
Consensus pattern (49 bp):
CCTTACAAGTACAAGTCCCACCACCACCACCCCATCACCACCAAAACAT
Found at i:1296906 original size:180 final size:180
Alignment explanation
Indices: 1296703--1297138 Score: 665
Period size: 180 Copynumber: 2.4 Consensus size: 180
1296693 CAACTTCAGT
* * *
1296703 TTACAAATATAAGTCGCCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAATCTCCAC
1 TTACAAATACAAGTCACCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCAC
* *
1296768 CACCACCACCTCCGGTTTACAAGTATAAGTCTCCACCACCTCCAGTGCACTATCCTCCACCACCT
66 CACCACCACCTCCAGTTTACAAGTACAAGTCTCCACCACCTCCAGTGCACTATCCTCCACCACCT
* *
1296833 TATAAGTACAAGTCCCCACCACCACCACCGCCATCACCACCAAAACATCC
131 TACAAGTACAAGTCCCCACCACCACCACCACCATCACCACCAAAACATCC
* * * * *
1296883 TTACAAGTACAAGTCTCCACCACCACTATCACCACCCAAACATGCTTACAAGTACAAGTCTCCAC
1 TTACAAATACAAGTCACCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCAC
* * * *
1296948 CCCCGCCACCTCCAGTTTACAAGTACAAGTCTCCACCACCTCCGGTGCACTATCCTCCACCCCCT
66 CACCACCACCTCCAGTTTACAAGTACAAGTCTCCACCACCTCCAGTGCACTATCCTCCACCACCT
* *
1297013 TACAAGTACAAGTCCCCACCACCTCCACCACCATCACCACCCAAACATCC
131 TACAAGTACAAGTCCCCACCACCACCACCACCATCACCACCAAAACATCC
* *
1297063 TTACAAATACAAGTCACCACCACCTCCTCCATCCCCACCCAAGCATCCTTACAAGTACAAGTCTC
1 TTACAAATACAAGTCACCACCA---CCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTC
1297128 CACCACCACCA
63 CACCACCACCA
1297139 GTGCACTCTC
Statistics
Matches: 227, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
180 183 0.81
183 44 0.19
ACGTcount: A:0.31, C:0.44, G:0.07, T:0.18
Consensus pattern (180 bp):
TTACAAATACAAGTCACCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCAC
CACCACCACCTCCAGTTTACAAGTACAAGTCTCCACCACCTCCAGTGCACTATCCTCCACCACCT
TACAAGTACAAGTCCCCACCACCACCACCACCATCACCACCAAAACATCC
Found at i:1297161 original size:48 final size:50
Alignment explanation
Indices: 1296964--1297176 Score: 183
Period size: 48 Copynumber: 4.4 Consensus size: 50
1296954 CACCTCCAGT
* * * * *
1296964 TTACAAGTACAAGTCTCCACCACCTCCGGTGCACTATCC-TCC-ACC-CCC
1 TTACAAGTACAAGTCTCCACCACCTCC-ATCCACTCTCCACCCAACCATCC
* * *
1297012 TTACAAGTACAAGTCCCCACCACCTCCA-CCACCATCACCACCCAAACATCC
1 TTACAAGTACAAGTCTCCACCACCTCCATCCA-C-TCTCCACCCAACCATCC
* * * *
1297063 TTACAAATACAAGTCACCACCACCTCC-TCCA-TCCCCACCCAAGCATCC
1 TTACAAGTACAAGTCTCCACCACCTCCATCCACTCTCCACCCAACCATCC
* * *
1297111 TTACAAGTACAAGTCTCCACCACCACCAGTGCACTCTCC-TCC-ACCA-CC
1 TTACAAGTACAAGTCTCCACCACCTCCA-TCCACTCTCCACCCAACCATCC
*
1297159 TTATAAGTACAAGTCTCC
1 TTACAAGTACAAGTCTCC
1297177 TCATCCTCCT
Statistics
Matches: 136, Mismatches: 20, Indels: 18
0.78 0.11 0.10
Matches are distributed among these distances:
46 2 0.01
47 1 0.01
48 87 0.64
49 5 0.04
50 7 0.05
51 34 0.25
ACGTcount: A:0.29, C:0.45, G:0.07, T:0.19
Consensus pattern (50 bp):
TTACAAGTACAAGTCTCCACCACCTCCATCCACTCTCCACCCAACCATCC
Found at i:1297806 original size:14 final size:14
Alignment explanation
Indices: 1297787--1297816 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1297777 GTCCTTCAAC
1297787 TAGTAAAAGTATAA
1 TAGTAAAAGTATAA
1297801 TAGTAAAAGTATAA
1 TAGTAAAAGTATAA
1297815 TA
1 TA
1297817 TGGTCACTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (14 bp):
TAGTAAAAGTATAA
Found at i:1300155 original size:31 final size:30
Alignment explanation
Indices: 1300115--1300257 Score: 166
Period size: 31 Copynumber: 4.7 Consensus size: 30
1300105 TTATAATATG
*
1300115 TTCTAAACTTTTAAAAATATATTTTATTTTT
1 TTCTTAACTTTT-AAAATATATTTTATTTTT
1300146 TTCTTAACTTATT-AAATATATTTTATCTTTT
1 TTCTTAACTT-TTAAAATATATTTTAT-TTTT
*
1300177 TTCTTAACTTTTGAAAATATATTTTACTTTT
1 TTCTTAACTTTT-AAAATATATTTTATTTTT
* *
1300208 TTCTT--CTCTTAAAATATATTTTATTCTT
1 TTCTTAACTTTTAAAATATATTTTATTTTT
* *
1300236 ATCTTAATTTTTAAATATATAT
1 TTCTTAACTTTTAAA-ATATAT
1300258 ATTTTAAATA
Statistics
Matches: 97, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
28 20 0.21
29 4 0.04
30 21 0.22
31 38 0.39
32 14 0.14
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59
Consensus pattern (30 bp):
TTCTTAACTTTTAAAATATATTTTATTTTT
Found at i:1300264 original size:15 final size:15
Alignment explanation
Indices: 1300244--1300285 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1300234 TTATCTTAAT
1300244 TTTTAAATATATATA
1 TTTTAAATATATATA
*
1300259 TTTTAAATATCT-TA
1 TTTTAAATATATATA
*
1300273 ATTTAAA-ATATAT
1 TTTTAAATATATAT
1300286 TAATCTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 3 0.13
14 9 0.39
15 11 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTAAATATATATA
Found at i:1300350 original size:29 final size:29
Alignment explanation
Indices: 1300291--1300402 Score: 104
Period size: 29 Copynumber: 3.8 Consensus size: 29
1300281 TATATTAATC
*
1300291 TTATTTTAA--TATAAAA-ATATTTGATTA
1 TTATTTTAACTTA-AAAATATATTTCATTA
* *
1300318 TTATTTTTACTTAAAAATATATTTCATTC
1 TTATTTTAACTTAAAAATATATTTCATTA
* * *
1300347 TTATTTTAAATTAGAAATATATTTTATTA
1 TTATTTTAACTTAAAAATATATTTCATTA
*
1300376 TTATCTTAACTTTTAAAAAATATATTT
1 TTATTTTAAC--TT-AAAAATATATTT
1300403 TTAAATATAT
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 8 0.12
28 4 0.06
29 43 0.63
31 2 0.03
32 11 0.16
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (29 bp):
TTATTTTAACTTAAAAATATATTTCATTA
Found at i:1300377 original size:58 final size:57
Alignment explanation
Indices: 1300266--1300402 Score: 144
Period size: 58 Copynumber: 2.4 Consensus size: 57
1300256 ATATTTTAAA
1300266 TATCTTAA-TTT--AAAATATA-TTAATCTTATTTTAATATAAAAATATTTGATTAT
1 TATCTTAACTTTAAAAAATATATTTAATCTTATTTTAATATAAAAATATTTGATTAT
* * * *
1300319 TATTTTTAC-TT-AAAAATATATTTCATTCTTATTTTAA-ATTAGAAATATATTTTATTAT
1 TATCTTAACTTTAAAAAATATATTT-AATCTTATTTTAATA-TA-AAA-ATATTTGATTAT
1300377 TATCTTAACTTTTAAAAAATATATTT
1 TATCTTAAC-TTTAAAAAATATATTT
1300403 TTAAATATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
53 8 0.12
54 8 0.12
55 3 0.04
56 14 0.21
57 3 0.04
58 18 0.26
60 2 0.03
61 12 0.18
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (57 bp):
TATCTTAACTTTAAAAAATATATTTAATCTTATTTTAATATAAAAATATTTGATTAT
Found at i:1300545 original size:31 final size:32
Alignment explanation
Indices: 1300471--1300545 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 32
1300461 CAATATTTTG
*
1300471 AAAACAT-T-TTTTTAAGATTAAGATAAGAAT
1 AAAACATATATTTTTAAGATGAAGATAAGAAT
* * *
1300501 -AAA-ATATACTTTTAAG-TGAAGATAGGATT
1 AAAACATATATTTTTAAGATGAAGATAAGAAT
1300530 AAAACATATATTTTTA
1 AAAACATATATTTTTA
1300546 TATTAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.06
29 14 0.39
30 10 0.28
31 10 0.28
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (32 bp):
AAAACATATATTTTTAAGATGAAGATAAGAAT
Found at i:1300565 original size:60 final size:59
Alignment explanation
Indices: 1300471--1300584 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 59
1300461 CAATATTTTG
* *
1300471 AAAACATTTTTTTAAGATTAAGATAAGAATAAAATATACTTT-TAAGTGAAGATAGGATT
1 AAAACATTTTTTTAAGATTAAAATAAGAATAAAATAGA-TTTATAAGTGAAGATAGGATT
* * *
1300530 AAAACATATATTTTT-ATATTAAAATTAGAATAAAATAGATTTATAAGTTAAGATA
1 AAAACAT-T-TTTTTAAGATTAAAATAAGAATAAAATAGATTTATAAGTGAAGATA
1300585 AAATAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 10 0.21
60 32 0.68
61 5 0.11
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (59 bp):
AAAACATTTTTTTAAGATTAAAATAAGAATAAAATAGATTTATAAGTGAAGATAGGATT
Found at i:1303191 original size:60 final size:60
Alignment explanation
Indices: 1303045--1303221 Score: 171
Period size: 60 Copynumber: 3.0 Consensus size: 60
1303035 GTATCATATG
** * * ** *
1303045 TCCTCAAACTAT-AAACTCATTTTAAATTATTCCTTAAACTTTTGAATATTTTAATTTTA
1 TCCTCAAACTATGACTCTCATTTTAAATTAGTCCATAAACTTTTGAATATTCCAATTTAA
** *
1303104 TCCTCAAACTATGACTCTCATCCTAAATTAGTCCATAAACTTTTGAACATTCCAATTTAA
1 TCCTCAAACTATGACTCTCATTTTAAATTAGTCCATAAACTTTTGAATATTCCAATTTAA
* ** ** *
1303164 TTCTCAAACTATGAC-CTTTTTTTTAAA-TAGGTCCCCATACTTTTGAATATTCCAATTT
1 TCCTCAAACTATGACTC-TCATTTTAAATTA-GTCCATAAACTTTTGAATATTCCAATTT
1303222 CATCTACATA
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
59 15 0.16
60 81 0.84
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (60 bp):
TCCTCAAACTATGACTCTCATTTTAAATTAGTCCATAAACTTTTGAATATTCCAATTTAA
Found at i:1303454 original size:29 final size:28
Alignment explanation
Indices: 1303415--1303514 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 28
1303405 TAAATGTCAT
1303415 AGTTTGGGGATGTAATTGAAATATTTAAA
1 AGTTTGGGGAT-TAATTGAAATATTTAAA
* * * *
1303444 AGTTTGAGGATTAATTTAGAATGATAGTAAT
1 AGTTTGGGGATTAATTGA-AAT-AT-TTAAA
*
1303475 AGTTTGGGGATAAAAGTTG-AATATTTAAA
1 AGTTTGGGGAT-TAA-TTGAAATATTTAAA
*
1303504 AGTTTAGGGAT
1 AGTTTGGGGAT
1303515 CAAATTAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
28 6 0.11
29 26 0.46
30 4 0.07
31 16 0.29
32 2 0.04
33 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.37
Consensus pattern (28 bp):
AGTTTGGGGATTAATTGAAATATTTAAA
Found at i:1303463 original size:60 final size:59
Alignment explanation
Indices: 1303386--1303513 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 59
1303376 TGTTCAAAGT
* **
1303386 GTTTGGGACTAATTTAGAATAA-ATGTCATAGTTTGGGGATGTAA-TTGAAATATTTAAAA
1 GTTTGGGACTAATTTAGAATAATA-GTAATAGTTTGGGGATAAAAGTTG-AATATTTAAAA
* *
1303445 GTTTGAGGATTAATTTAGAATGATAGTAATAGTTTGGGGATAAAAGTTGAATATTTAAAA
1 GTTTG-GGACTAATTTAGAATAATAGTAATAGTTTGGGGATAAAAGTTGAATATTTAAAA
1303505 GTTTAGGGA
1 GTTT-GGGA
1303514 TCAAATTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
59 5 0.08
60 50 0.83
61 5 0.08
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (59 bp):
GTTTGGGACTAATTTAGAATAATAGTAATAGTTTGGGGATAAAAGTTGAATATTTAAAA
Found at i:1303479 original size:31 final size:30
Alignment explanation
Indices: 1303386--1303485 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 30
1303376 TGTTCAAAGT
* * *
1303386 GTTT-GGGACTAATTTAGAATAAATGTCATA
1 GTTTGGGGATTAATTTAGAATATA-GTAATA
* * *
1303416 GTTTGGGGATGTAATTGA-AATAT-TTAAAA
1 GTTTGGGGAT-TAATTTAGAATATAGTAATA
*
1303445 GTTTGAGGATTAATTTAGAATGATAGTAATA
1 GTTTGGGGATTAATTTAGAAT-ATAGTAATA
1303476 GTTTGGGGAT
1 GTTTGGGGAT
1303486 AAAAGTTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
28 6 0.11
29 15 0.28
30 6 0.11
31 21 0.39
32 6 0.11
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (30 bp):
GTTTGGGGATTAATTTAGAATATAGTAATA
Found at i:1303526 original size:29 final size:28
Alignment explanation
Indices: 1303428--1303526 Score: 65
Period size: 29 Copynumber: 3.4 Consensus size: 28
1303418 TTGGGGATGT
* *
1303428 AATTGAAATATTTAAAAGTTTGAGGATTA
1 AATTAAAATATTTAAAAGTTTG-GGATAA
* * * *
1303457 ATTTAGAATGATAGTAATAGTTTGGGGATAA
1 AATTAAAAT-AT-TTAAAAGTTT-GGGATAA
* *
1303488 AAGTT-GAATATTTAAAAGTTTAGGGATCA
1 AA-TTAAAATATTTAAAAGTTT-GGGATAA
1303517 AATTAAAATA
1 AATTAAAATA
1303527 AGGATAATAC
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
28 2 0.04
29 26 0.49
30 4 0.08
31 18 0.34
32 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.35
Consensus pattern (28 bp):
AATTAAAATATTTAAAAGTTTGGGATAA
Found at i:1303535 original size:60 final size:60
Alignment explanation
Indices: 1303413--1303525 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
1303403 AATAAATGTC
** * * *
1303413 ATAGTTTGGGGATGTAATTGAAATATTTAAAAGTTTGAGGATTAATTTAGAATGATAGTA
1 ATAGTTTGGGGATAAAATTGAAATATTTAAAAGTTTGAGGATCAAATTAAAATGATAGTA
1303473 ATAGTTTGGGGATAAAAGTTG-AATATTTAAAAGTTT-AGGGATCAAATTAAAAT
1 ATAGTTTGGGGATAAAA-TTGAAATATTTAAAAGTTTGA-GGATCAAATTAAAAT
1303526 AAGGATAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 42 0.91
61 3 0.07
ACGTcount: A:0.41, C:0.01, G:0.22, T:0.36
Consensus pattern (60 bp):
ATAGTTTGGGGATAAAATTGAAATATTTAAAAGTTTGAGGATCAAATTAAAATGATAGTA
Found at i:1319292 original size:336 final size:336
Alignment explanation
Indices: 1318679--1319354 Score: 1352
Period size: 336 Copynumber: 2.0 Consensus size: 336
1318669 TTTTCTTATG
1318679 CTTGCAAAGCATTTCTTTCCAACATGAAACTATGCCCTCTGGTTAAAATCGGTAAGGCGAGGTTG
1 CTTGCAAAGCATTTCTTTCCAACATGAAACTATGCCCTCTGGTTAAAATCGGTAAGGCGAGGTTG
1318744 AGGCTGACCGTTCAAAGTTTGGTTGTTGGTGGATGACTGAGGCACCTGCTGCTGTTGCTGTTGTT
66 AGGCTGACCGTTCAAAGTTTGGTTGTTGGTGGATGACTGAGGCACCTGCTGCTGTTGCTGTTGTT
1318809 GCAGTCTCTGCAGTACACCAAAGGTATGTGGAGCAGGTTGATGGGGTAAAAATTGAGGCGGCACT
131 GCAGTCTCTGCAGTACACCAAAGGTATGTGGAGCAGGTTGATGGGGTAAAAATTGAGGCGGCACT
1318874 CCTCTATTGAAAGGATTTCCATTCATCGTGGACACTTGGCCAGGTTGTATCCTAAGCCGTTGAAC
196 CCTCTATTGAAAGGATTTCCATTCATCGTGGACACTTGGCCAGGTTGTATCCTAAGCCGTTGAAC
1318939 TTCTTCCCTCAATTTTTCATGCAAAGCTACAGAGCAGAAAAGTAAAGACCAAATATATAAGTACC
261 TTCTTCCCTCAATTTTTCATGCAAAGCTACAGAGCAGAAAAGTAAAGACCAAATATATAAGTACC
1319004 TTCACGCCTAA
326 TTCACGCCTAA
1319015 CTTGCAAAGCATTTCTTTCCAACATGAAACTATGCCCTCTGGTTAAAATCGGTAAGGCGAGGTTG
1 CTTGCAAAGCATTTCTTTCCAACATGAAACTATGCCCTCTGGTTAAAATCGGTAAGGCGAGGTTG
1319080 AGGCTGACCGTTCAAAGTTTGGTTGTTGGTGGATGACTGAGGCACCTGCTGCTGTTGCTGTTGTT
66 AGGCTGACCGTTCAAAGTTTGGTTGTTGGTGGATGACTGAGGCACCTGCTGCTGTTGCTGTTGTT
1319145 GCAGTCTCTGCAGTACACCAAAGGTATGTGGAGCAGGTTGATGGGGTAAAAATTGAGGCGGCACT
131 GCAGTCTCTGCAGTACACCAAAGGTATGTGGAGCAGGTTGATGGGGTAAAAATTGAGGCGGCACT
1319210 CCTCTATTGAAAGGATTTCCATTCATCGTGGACACTTGGCCAGGTTGTATCCTAAGCCGTTGAAC
196 CCTCTATTGAAAGGATTTCCATTCATCGTGGACACTTGGCCAGGTTGTATCCTAAGCCGTTGAAC
1319275 TTCTTCCCTCAATTTTTCATGCAAAGCTACAGAGCAGAAAAGTAAAGACCAAATATATAAGTACC
261 TTCTTCCCTCAATTTTTCATGCAAAGCTACAGAGCAGAAAAGTAAAGACCAAATATATAAGTACC
1319340 TTCACGCCTAA
326 TTCACGCCTAA
1319351 CTTG
1 CTTG
1319355 TTTGCTATCT
Statistics
Matches: 340, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
336 340 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (336 bp):
CTTGCAAAGCATTTCTTTCCAACATGAAACTATGCCCTCTGGTTAAAATCGGTAAGGCGAGGTTG
AGGCTGACCGTTCAAAGTTTGGTTGTTGGTGGATGACTGAGGCACCTGCTGCTGTTGCTGTTGTT
GCAGTCTCTGCAGTACACCAAAGGTATGTGGAGCAGGTTGATGGGGTAAAAATTGAGGCGGCACT
CCTCTATTGAAAGGATTTCCATTCATCGTGGACACTTGGCCAGGTTGTATCCTAAGCCGTTGAAC
TTCTTCCCTCAATTTTTCATGCAAAGCTACAGAGCAGAAAAGTAAAGACCAAATATATAAGTACC
TTCACGCCTAA
Found at i:1329237 original size:17 final size:18
Alignment explanation
Indices: 1329212--1329245 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1329202 GGATAAGAAT
1329212 AAATATTAAA-ATGATTG
1 AAATATTAAATATGATTG
*
1329229 AAATTTTAAATATGATT
1 AAATATTAAATATGATT
1329246 TTTTTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
AAATATTAAATATGATTG
Found at i:1329737 original size:2 final size:2
Alignment explanation
Indices: 1329732--1329794 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1329722 AAAATAAGGT
1329732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1329774 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1329795 TAATCTGATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1332581 original size:42 final size:41
Alignment explanation
Indices: 1332511--1332599 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 41
1332501 TAACATATGA
*
1332511 ATATGAGTGCATGTATCATATGTTATTTATGTTAAATGAGTG
1 ATATGAGTGCATGTATCATATGTAATTTATGTTAAATGA-TG
* * *
1332553 ATATGATTGCATGTAT-ATGTGATAATTTATGTTAAATGATT
1 ATATGAGTGCATGTATCATATG-TAATTTATGTTAAATGATG
1332594 ATATGA
1 ATATGA
1332600 ACATGAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 11 0.26
42 31 0.74
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (41 bp):
ATATGAGTGCATGTATCATATGTAATTTATGTTAAATGATG
Found at i:1332997 original size:21 final size:21
Alignment explanation
Indices: 1332911--1333005 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
1332901 TCGAGGGTTC
* *
1332911 TATGTGGTCCTTCGGGATATA
1 TATGTGGTCCTTCGGAACATA
** *
1332932 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTCGGAACATA
* * *
1332953 TATGCGGTTCTTCGGAACACA
1 TATGTGGTCCTTCGGAACATA
* * *
1332974 TATTTGGTCCTTTGGAATATA
1 TATGTGGTCCTTCGGAACATA
*
1332995 TATGTGATCCT
1 TATGTGGTCCT
1333006 AATGGAGTGG
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (21 bp):
TATGTGGTCCTTCGGAACATA
Found at i:1334533 original size:21 final size:21
Alignment explanation
Indices: 1334507--1334556 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1334497 GTCGAGGGTT
* *
1334507 TTATGTGGTCCTCCGGGATAA
1 TTATGTGGTCATCCGGGACAA
*
1334528 TTATGTGGTCATTCGGGACAA
1 TTATGTGGTCATCCGGGACAA
*
1334549 ATATGTGG
1 TTATGTGG
1334557 CACTTTGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (21 bp):
TTATGTGGTCATCCGGGACAA
Found at i:1334577 original size:23 final size:23
Alignment explanation
Indices: 1334554--1334630 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
1334544 GACAAATATG
* *
1334554 TGGCACTTTGGTACAACCCTATG
1 TGGCACTTTGATACAACCCTATA
1334577 TGGCACTTTGATACAACCCTATA
1 TGGCACTTTGATACAACCCTATA
** *
1334600 TGGCACTTCAATGCAACCCTATA
1 TGGCACTTTGATACAACCCTATA
1334623 TGGCACTT
1 TGGCACTT
1334631 CGGTGTAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (23 bp):
TGGCACTTTGATACAACCCTATA
Found at i:1334643 original size:23 final size:23
Alignment explanation
Indices: 1334571--1334648 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 23
1334561 TTGGTACAAC
* ** * *
1334571 CCTATGTGGCACTTTGATACAAC
1 CCTATATGGCACTTCAATGCAAA
*
1334594 CCTATATGGCACTTCAATGCAAC
1 CCTATATGGCACTTCAATGCAAA
** *
1334617 CCTATATGGCACTTCGGTGTAAA
1 CCTATATGGCACTTCAATGCAAA
1334640 CCTATATGG
1 CCTATATGG
1334649 ATCTTCACGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (23 bp):
CCTATATGGCACTTCAATGCAAA
Found at i:1339563 original size:16 final size:16
Alignment explanation
Indices: 1339516--1339568 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1339506 AAGTTAATAC
*
1339516 TTTATAAATATTTTATA
1 TTTAT-AATATTTTATT
* *
1339533 CTTATAAT-TGATTATT
1 TTTATAATAT-TTTATT
1339549 TTTATAATATTTTATT
1 TTTATAATATTTTATT
1339565 TTTA
1 TTTA
1339569 AAAAAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.03
16 23 0.79
17 5 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTATAATATTTTATT
Found at i:1341299 original size:21 final size:21
Alignment explanation
Indices: 1341275--1341320 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1341265 TATTATACAA
* *
1341275 TTTGATTTTTTAAATTTTATG
1 TTTGAGTTTATAAATTTTATG
* *
1341296 TTTGGGTTTATAAGTTTTATG
1 TTTGAGTTTATAAATTTTATG
1341317 TTTG
1 TTTG
1341321 TACATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (21 bp):
TTTGAGTTTATAAATTTTATG
Found at i:1344489 original size:18 final size:17
Alignment explanation
Indices: 1344451--1344483 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1344441 CATGTGACGG
1344451 TTTATTTATACTTATTTA
1 TTTATTTATA-TTATTTA
1344469 TTTATTTAT-TTATTT
1 TTTATTTATATTATTT
1344484 TAATTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTATATTATTTA
Found at i:1346083 original size:22 final size:23
Alignment explanation
Indices: 1346049--1346098 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1346039 AGATTTTTTA
* *
1346049 TGAATAGTGATGAACAGTA-CCG
1 TGAACAGTAATGAACAGTACCCG
*
1346071 TGAACAGTAATGAACATTACCCG
1 TGAACAGTAATGAACAGTACCCG
1346094 TGAAC
1 TGAAC
1346099 TGTGCATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (23 bp):
TGAACAGTAATGAACAGTACCCG
Found at i:1346200 original size:30 final size:30
Alignment explanation
Indices: 1346164--1346223 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1346154 AATTGATATT
* * *
1346164 ATGCATCGATACGCTATAGTAGCTGCTACA
1 ATGCATCGATACACTACAGTAACTGCTACA
1346194 ATGCATCGATACACTACAGTAACTGCTACA
1 ATGCATCGATACACTACAGTAACTGCTACA
1346224 GTAACTTCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (30 bp):
ATGCATCGATACACTACAGTAACTGCTACA
Found at i:1346663 original size:24 final size:24
Alignment explanation
Indices: 1346591--1346663 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1346581 CCATTTATTA
1346591 ACCATAAGCTCGTAAGCTTATTTT
1 ACCATAAGCTCGTAAGCTTATTTT
* * *
1346615 ACCA-AA-ATAC-TTA-C-CATTTGT
1 ACCATAAGCT-CGTAAGCTTATTT-T
1346636 ACCATAAGCTCGTAAGCTTATTTT
1 ACCATAAGCTCGTAAGCTTATTTT
1346660 ACCA
1 ACCA
1346664 ATACACTTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
22 6 0.17
23 6 0.17
24 10 0.28
25 4 0.11
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (24 bp):
ACCATAAGCTCGTAAGCTTATTTT
Found at i:1346677 original size:45 final size:45
Alignment explanation
Indices: 1346591--1346677 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
1346581 CCATTTATTA
*
1346591 ACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATTTGT
* *
1346636 ACCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCATT
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATT
1346678 ATTCCATAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.34
Consensus pattern (45 bp):
ACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATTTGT
Found at i:1346859 original size:59 final size:59
Alignment explanation
Indices: 1346767--1346895 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
1346757 CGTAGTGCTA
* * * **
1346767 TCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTAAAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTAAAG
* ** *
1346826 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTAAAG
1346885 TCCCGAATATG
1 TCCCGAATATG
1346896 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTAAAG
Found at i:1351105 original size:54 final size:54
Alignment explanation
Indices: 1351047--1351380 Score: 425
Period size: 54 Copynumber: 6.2 Consensus size: 54
1351037 CTCTGGGGTA
* * **
1351047 CACACGTAGTGCCGATACGATCGTTCATAAACACATTATGAATTTTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTG
** *
1351101 CACACTTAGTATCGATACGGTCGTTCATAAACACATTATGAATTCCATGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTG
* * *
1351155 CACACTTAGTGTCGATACGGTCGTTTATAAACACATTACGAATTCCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTG
* * * * * ** *
1351209 CACTCATAGTGCTGATACGATCGTTCATGAACACATTATGAATTATGTGGATTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTG
** * * *
1351263 CACACTTAGTGTTGATACTGTCGTTCATAAACATATTATGAATTCGGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTG
* * *
1351317 CACTCTTAGTGCCGATACGGTCATTCATAAACACATTATGAATTCCGTGGTTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTG
*
1351371 CACAATTAGT
1 CACACTTAGT
1351381 ACTGATGTAA
Statistics
Matches: 238, Mismatches: 42, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 238 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
CACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTTG
Found at i:1351327 original size:162 final size:162
Alignment explanation
Indices: 1351053--1351373 Score: 498
Period size: 162 Copynumber: 2.0 Consensus size: 162
1351043 GGTACACACG
* *
1351053 TAGTGCCGATACGATCGTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTAGTATCGATA
1 TAGTGCCGATACGATCGTTCATAAACACATTATGAATTATGTGGATTGCACACTTAGTATCGATA
* * *
1351118 CGGTCGTTCATAAACACATTATGAATTCCATGGGTTGCACACTTAGTGTCGATACGGTCGTTTAT
66 CGGTCGTTCATAAACACATTATGAATTCCATGGGTTGCACACTTAGTGCCGATACGGTCATTCAT
1351183 AAACACATTACGAATTCCGTGGGTTGCACTCA
131 AAACACATTACGAATTCCGTGGGTTGCACTCA
* * * *
1351215 TAGTGCTGATACGATCGTTCATGAACACATTATGAATTATGTGGATTGCACACTTAGTGTTGATA
1 TAGTGCCGATACGATCGTTCATAAACACATTATGAATTATGTGGATTGCACACTTAGTATCGATA
* * ** *
1351280 CTGTCGTTCATAAACATATTATGAATTCGGTGGGTTGCACTCTTAGTGCCGATACGGTCATTCAT
66 CGGTCGTTCATAAACACATTATGAATTCCATGGGTTGCACACTTAGTGCCGATACGGTCATTCAT
* *
1351345 AAACACATTATGAATTCCGTGGTTTGCAC
131 AAACACATTACGAATTCCGTGGGTTGCAC
1351374 AATTAGTACT
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
162 143 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (162 bp):
TAGTGCCGATACGATCGTTCATAAACACATTATGAATTATGTGGATTGCACACTTAGTATCGATA
CGGTCGTTCATAAACACATTATGAATTCCATGGGTTGCACACTTAGTGCCGATACGGTCATTCAT
AAACACATTACGAATTCCGTGGGTTGCACTCA
Done.