Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007799.1 Hibiscus syriacus cultivar Beakdansim tig00110109_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: 1433344
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:1074589 original size:23 final size:23
Alignment explanation
Indices: 1074570--1074639 Score: 95
Period size: 24 Copynumber: 3.0 Consensus size: 23
1074560 TGTGTTTGTG
*
1074570 CTGTTCGTTTGTGTTCGTTTATT
1 CTGTTCGTTTATGTTCGTTTATT
* * *
1074593 ATGTTCGTTTATGTTCATTCATT
1 CTGTTCGTTTATGTTCGTTTATT
1074616 CGTGTTCGTTTATGTTCGTTTATT
1 C-TGTTCGTTTATGTTCGTTTATT
1074640 TATTAAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.59
Consensus pattern (23 bp):
CTGTTCGTTTATGTTCGTTTATT
Found at i:1080550 original size:22 final size:21
Alignment explanation
Indices: 1080525--1080569 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1080515 CTGAAAAAAC
* *
1080525 ATATACACACACATATATATAT
1 ATATACAAACAAATAT-TATAT
*
1080547 ATATATAAACAAATATTATAT
1 ATATACAAACAAATATTATAT
1080568 AT
1 AT
1080570 TATAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATACAAACAAATATTATAT
Found at i:1080562 original size:20 final size:20
Alignment explanation
Indices: 1080537--1080580 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1080527 ATACACACAC
1080537 ATATATATATATATATAAACAA
1 ATAT-TATATAT-TATAAACAA
*
1080559 ATATTATATATTATAAATAA
1 ATATTATATATTATAAACAA
1080579 AT
1 AT
1080581 TTTGAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 7 0.33
22 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATTATATATTATAAACAA
Found at i:1081642 original size:65 final size:65
Alignment explanation
Indices: 1081567--1081696 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
1081557 GGTACGATCG
1081567 AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
1 AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
1081632 AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
1 AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
1081697 GTGAAAAAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (65 bp):
AATACTTTCTACTACAATATTTATCGTTAATCAAGATCAAAAGTGAACTCAAGAGTCGATTACAC
Found at i:1082029 original size:3 final size:3
Alignment explanation
Indices: 1082023--1082051 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1082013 AATTGTAACA
1082023 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1082052 CGACAAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1084906 original size:22 final size:22
Alignment explanation
Indices: 1084881--1084924 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1084871 ATAATAAATT
*
1084881 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
1084903 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1084925 CTAAAATATA
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:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1084935 original size:22 final size:22
Alignment explanation
Indices: 1084885--1084939 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1084875 TAAATTTTTT
* * *
1084885 AAAATAAATCAATTCATATTTT
1 AAAATAAATCAATCCATATCTA
1084907 AAAATAAATCAATCCATA-CTA
1 AAAATAAATCAATCCATATCTA
1084928 AAATATAAATCA
1 AAA-ATAAATCA
1084940 GTTTGCACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAAATCAATCCATATCTA
Found at i:1086550 original size:2 final size:2
Alignment explanation
Indices: 1086543--1086575 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1086533 TCATTTAACC
1086543 TA 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 TA T
1086576 GTATGCGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1090044 original size:21 final size:23
Alignment explanation
Indices: 1090002--1090050 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
1089992 AAATCGTCCC
1090002 TTTGTAATTCTTCTTTTATTTAT
1 TTTGTAATTCTTCTTTTATTTAT
*
1090025 TTTGTATTTTCTTTCTTTTATATTAT
1 TTTGTA-ATTC-TTCTTTTAT-TTAT
1090051 ATAATCTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 3 0.14
25 9 0.41
26 4 0.18
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTGTAATTCTTCTTTTATTTAT
Found at i:1096435 original size:20 final size:20
Alignment explanation
Indices: 1096410--1096458 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1096400 AAATTTTAAT
**
1096410 TTAAAAAACTTAAAACTATA
1 TTAAAAAAAATAAAACTATA
1096430 TTAAAAAAAATAAAACTATA
1 TTAAAAAAAATAAAACTATA
1096450 TTAAAAAAA
1 TTAAAAAAA
1096459 TTCTAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (20 bp):
TTAAAAAAAATAAAACTATA
Found at i:1096564 original size:18 final size:19
Alignment explanation
Indices: 1096526--1096570 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1096516 GTAGCATCTC
*
1096526 CCCTTGTTGATCGTTGTCG
1 CCCTTGTTGATCGTCGTCG
*
1096545 CCCTTGTTG-TTGTCGTCG
1 CCCTTGTTGATCGTCGTCG
1096563 CCCTTGTT
1 CCCTTGTT
1096571 ATTGACCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.02, C:0.29, G:0.24, T:0.44
Consensus pattern (19 bp):
CCCTTGTTGATCGTCGTCG
Found at i:1096995 original size:2 final size:2
Alignment explanation
Indices: 1096990--1097021 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1096980 ATAAAATTTA
1096990 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
1097022 GACACGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1097810 original size:115 final size:112
Alignment explanation
Indices: 1097597--1097832 Score: 316
Period size: 115 Copynumber: 2.1 Consensus size: 112
1097587 TCTCTGCATA
* *
1097597 TATTTATGATCCTTTGTCTCTTGAGATATGATGATGTTAGATTTTGTTTAAATTATATAGTATAT
1 TATTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGATTTTG-TT--ATTATAGAGTATAT
* *
1097662 TTTTAAAATAAATATTATAAATATATAT-GTTTTTAAAAAAAAGTAAATAT
63 TTTTAAAATAAATATTAAAAATATATATATTTTTTAAAAAAAA-TAAATAT
*
1097712 TATTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTG-T-TTATAGAGTATATTTT
1 TATTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGATTTTGTTATTATAGAGTATATTTT
*
1097775 TAAAATAAATATCTAAAATATATTATAAATATTTTTTTAAAAAAATAAATAT
66 TAAAATAAATAT-TAAAA-ATA-TAT--ATATTTTTTAAAAAAAATAAATAT
1097827 TATTTA
1 TATTTA
1097833 AAAAAGTAAA
Statistics
Matches: 109, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
110 27 0.25
111 4 0.04
112 3 0.03
113 4 0.04
115 59 0.54
116 12 0.11
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (112 bp):
TATTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGATTTTGTTATTATAGAGTATATTTT
TAAAATAAATATTAAAAATATATATATTTTTTAAAAAAAATAAATAT
Found at i:1097822 original size:20 final size:20
Alignment explanation
Indices: 1097799--1097848 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1097789 AAAATATATT
*
1097799 ATAAATATTTTTTTAAAAAA
1 ATAAATATTTATTTAAAAAA
1097819 ATAAATA-TTATTTAAAAAA
1 ATAAATATTTATTTAAAAAA
*
1097838 GTAAATATTTA
1 ATAAATATTTA
1097849 ATTTTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAAATATTTATTTAAAAAA
Found at i:1098107 original size:19 final size:18
Alignment explanation
Indices: 1098083--1098118 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1098073 GAGTAAAATT
1098083 ATCTATCCATTGTATTAAA
1 ATCTATCCATTGT-TTAAA
*
1098102 ATCTATTCATTGTTTAA
1 ATCTATCCATTGTTTAA
1098119 CAGATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (18 bp):
ATCTATCCATTGTTTAAA
Found at i:1100032 original size:21 final size:20
Alignment explanation
Indices: 1099946--1100103 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1099936 AAATGACCAA
**
1099946 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1099965 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1099985 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1100005 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1100026 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1100047 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1100067 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
1100088 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1100104 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1100096 original size:20 final size:20
Alignment explanation
Indices: 1100071--1100265 Score: 122
Period size: 20 Copynumber: 9.7 Consensus size: 20
1100061 GATTTTCAAT
*
1100071 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
*
1100091 AATCGCAACGCGAACAC-ATA
1 AATCGCAACGCGAATACGA-A
* * *
1100111 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
1100131 AATCGCAACGTGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* ** *
1100152 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAATACGAA
* * * *
1100172 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * * *
1100192 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
** *
1100212 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAATAC-GAA
* * *
1100233 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
1100253 AATCGCAACGCGA
1 AATCGCAACGCGA
1100266 TATTTAAAGC
Statistics
Matches: 140, Mismatches: 31, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
19 1 0.01
20 109 0.78
21 30 0.21
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:1100154 original size:61 final size:61
Alignment explanation
Indices: 1100071--1100264 Score: 248
Period size: 61 Copynumber: 3.2 Consensus size: 61
1100061 GATTTTCAAT
* ** *
1100071 AATCGCAACGCGAATATG-AAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
1100131 AATCGCAACGTGTATCCGTAAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
1100192 TATCGCAACGCGTATCCGT-AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
1100253 AATCGCAACGCG
1 AATCGCAACGCG
1100265 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
60 28 0.25
61 84 0.75
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (61 bp):
AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:1100161 original size:81 final size:80
Alignment explanation
Indices: 1100071--1100265 Score: 239
Period size: 81 Copynumber: 2.4 Consensus size: 80
1100061 GATTTTCAAT
* * *
1100071 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCG
1 AATCGCAACGCGTATACGTAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGTAAATCG
* * *
1100136 CAACG-TGTATCCGTAA
65 CAACGAT-AATACATAA
** * * * *
1100152 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCG
1 AATCGCAACGCGTATACGTAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGTAAATCG
1100217 CAACGATAATACATAA
65 CAACGATAATACATAA
*
1100233 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATACGTAAATCGCAACGCGA
1100266 TATTTAAAGC
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 94 0.96
82 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGTATACGTAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGTAAATCGC
AACGATAATACATAA
Found at i:1100162 original size:41 final size:41
Alignment explanation
Indices: 1100110--1100262 Score: 211
Period size: 41 Copynumber: 3.8 Consensus size: 41
1100100 GCGAACACAT
1100110 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
** * *
1100151 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT-
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
* * * *
1100191 ATATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACATA
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGTA
1100232 AAATCGCAACGCGTATCCGTAAATCGCAACG
1 AAATCGCAACGCGTATCCGTAAATCGCAACG
1100263 CGATATTTAA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 31 0.32
41 66 0.68
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (41 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
Found at i:1100684 original size:33 final size:33
Alignment explanation
Indices: 1100642--1100712 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1100632 TTCACTTAGA
1100642 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
***
1100675 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
1100708 TTTCA
1 TTTCA
1100713 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
Found at i:1100852 original size:14 final size:14
Alignment explanation
Indices: 1100833--1100887 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1100823 AGAATGACTG
1100833 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1100847 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
1100866 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1100880 TCGCAACG
1 TCGCAACG
1100888 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1100870 original size:33 final size:33
Alignment explanation
Indices: 1100833--1100903 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1100823 AGAATGACTG
**
1100833 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1100866 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1100899 TCGCA
1 TCGCA
1100904 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1100921 original size:19 final size:19
Alignment explanation
Indices: 1100899--1100996 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1100889 GAAACCAAAA
*
1100899 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1100918 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1100932 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1100951 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1100965 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1100984 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1100997 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1100940 original size:14 final size:14
Alignment explanation
Indices: 1100921--1101010 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1100911 TTTCATTTCG
1100921 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1100935 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1100954 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1100968 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1100985 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1101001 CGTTGCGATT
1 CGTTGCGATT
1101011 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1100946 original size:33 final size:33
Alignment explanation
Indices: 1100904--1101018 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1100894 CAAAATCGCA
1100904 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1100937 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1100970 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1101003 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1101019 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1102920 original size:92 final size:93
Alignment explanation
Indices: 1102714--1103091 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
1102704 TAGATTGCTT
*
1102714 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1102779 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1102807 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1102871 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1102899 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1102963 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1102990 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1103055 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1103083 AGTAAATTT
1 AGTAAATTT
1103092 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 79 0.28
92 116 0.41
93 87 0.31
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1103175 original size:19 final size:19
Alignment explanation
Indices: 1103135--1103263 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1103125 TAGTTTACTT
* *
1103135 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1103155 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1103174 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1103193 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
1103207 TCGCAACGCGAAACTAAAA
1 TCGCAACGCGAAACCAAAA
*
1103226 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1103240 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1103259 TCGCA
1 TCGCA
1103264 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1103214 original size:33 final size:31
Alignment explanation
Indices: 1103171--1103263 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 31
1103161 CGCGAAACCA
1103171 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAAT-AAAATCGCAACGAC
1103203 AGAATCGCAACGCGAAACTAAAATCGCAACGAC
1 A-AATCGCAACGCGAAA-TAAAATCGCAACGAC
*
1103236 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAA-TAAAATCGCA
1103264 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
32 2 0.04
33 54 0.95
34 1 0.02
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (31 bp):
AAATCGCAACGCGAAATAAAATCGCAACGAC
Found at i:1103261 original size:52 final size:52
Alignment explanation
Indices: 1103135--1103263 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
1103125 TAGTTTACTT
**
1103135 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * * *
1103187 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACTAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1103240 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1103264 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1103281 original size:19 final size:18
Alignment explanation
Indices: 1103259--1103377 Score: 101
Period size: 19 Copynumber: 6.8 Consensus size: 18
1103249 GAAACCAAAA
*
1103259 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
1103278 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
1103294 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
* *
1103311 TCGCATTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
1103327 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
1103344 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
1103363 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1103378 AAGTTTCGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
14 15 0.19
16 10 0.12
17 10 0.12
19 46 0.57
ACGTcount: A:0.09, C:0.19, G:0.24, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:1103300 original size:14 final size:14
Alignment explanation
Indices: 1103281--1103337 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1103271 TTTCATTTCG
1103281 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
1103295 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
1103312 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1103328 CGTTGCGATT
1 CGTTGCGATT
1103338 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 7 0.20
19 6 0.17
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1103306 original size:33 final size:33
Alignment explanation
Indices: 1103264--1103356 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1103254 CAAAATCGCA
*
1103264 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
** *
1103297 TTGCGATTTTGGTTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1103330 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1103357 TTGGTTTCGC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1103385 original size:20 final size:19
Alignment explanation
Indices: 1103259--1103393 Score: 96
Period size: 19 Copynumber: 7.6 Consensus size: 19
1103249 GAAACCAAAA
*
1103259 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
1103278 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAGTT
*
1103294 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
* *
1103311 TCGCATTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
1103327 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
1103344 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
1103363 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
1103383 TCGTGTTGCGA
1 TCGCGTTGCGA
1103394 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
14 18 0.19
16 6 0.06
17 6 0.06
18 1 0.01
19 49 0.53
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:1105305 original size:14 final size:14
Alignment explanation
Indices: 1105286--1105321 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1105276 ATTGTTTAAT
1105286 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1105300 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1105314 TGATTTGT
1 TGATTTGT
1105322 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1105443 original size:19 final size:17
Alignment explanation
Indices: 1105427--1105503 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 17
1105417 AAAAATGACT
1105427 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1105446 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
1105460 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1105479 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
1105493 ATCGCAATGCG
1 ATCGCAATGCG
1105504 TTTATAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
14 16 0.33
16 8 0.17
17 9 0.19
19 15 0.31
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:1105517 original size:33 final size:33
Alignment explanation
Indices: 1105427--1105503 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
1105417 AAAAATGACT
1105427 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1105460 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1105493 ATCGCAATGCG
1 ATCGCAATGCG
1105504 TTTATAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1105547 original size:33 final size:33
Alignment explanation
Indices: 1105510--1105906 Score: 303
Period size: 33 Copynumber: 11.5 Consensus size: 33
1105500 TGCGTTTATA
1105510 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
1105543 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
1105579 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
1105614 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT--ATCTCG--TTGCGATTTTC
*
1105652 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
1105692 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
1105723 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
1105756 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
1105790 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
1105823 ATTTCCGCATTGCGATTTTCAT-GTTGCGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
* *
1105857 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
1105891 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
1105907 GTATTTTCCG
Statistics
Matches: 322, Mismatches: 19, Indels: 46
0.83 0.05 0.12
Matches are distributed among these distances:
31 9 0.03
32 6 0.02
33 105 0.33
34 92 0.29
35 14 0.04
36 13 0.04
37 5 0.02
38 63 0.20
39 6 0.02
40 9 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:1105556 original size:19 final size:19
Alignment explanation
Indices: 1105532--1105906 Score: 415
Period size: 19 Copynumber: 21.4 Consensus size: 19
1105522 GATTATCTCG
1105532 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1105551 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1105570 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1105584 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1105603 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1105622 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1105641 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1105660 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1105679 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1105693 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1105712 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1105731 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1105745 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1105765 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1105779 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1105798 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1105812 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1105832 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
1105846 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1105866 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1105880 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1105899 TTGCGATT
1 TTGCGATT
1105907 GTATTTTCCG
Statistics
Matches: 306, Mismatches: 12, Indels: 76
0.78 0.03 0.19
Matches are distributed among these distances:
14 58 0.19
16 35 0.11
17 27 0.09
18 8 0.03
19 142 0.46
20 36 0.12
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1105566 original size:52 final size:52
Alignment explanation
Indices: 1105510--1105878 Score: 493
Period size: 52 Copynumber: 7.0 Consensus size: 52
1105500 TGCGTTTATA
*
1105510 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1105562 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1105614 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1105671 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1105723 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
* * * * * *
1105776 ATGTTGGGATTTTC-ATT-TCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 AT-TTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1105823 ATTTCCGCATTGCGATTTTCAT-GTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1105877 AT
1 AT
1105879 GTTGGGATTT
Statistics
Matches: 284, Mismatches: 15, Indels: 34
0.85 0.05 0.10
Matches are distributed among these distances:
46 5 0.02
47 18 0.06
48 8 0.03
49 2 0.01
50 5 0.02
51 5 0.02
52 133 0.47
53 28 0.10
54 25 0.09
55 9 0.03
56 2 0.01
57 44 0.15
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1105849 original size:14 final size:14
Alignment explanation
Indices: 1105832--1105892 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 14
1105822 CATTTCCGCA
1105832 TTGCGATTTTCATG
1 TTGCGATTTTCATG
1105846 TTGCGATTTTCATTTCCG
1 TTGCGATTTTCA--T--G
1105864 CATTGCGATTTTCATG
1 --TTGCGATTTTCATG
*
1105880 TTGGGATTTTCAT
1 TTGCGATTTTCAT
1105893 TTCGCGTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 24 0.60
16 2 0.05
18 2 0.05
20 12 0.30
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTCATG
Found at i:1108413 original size:24 final size:24
Alignment explanation
Indices: 1108379--1108425 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1108369 CTGAAACATC
1108379 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1108403 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1108426 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1109130 original size:20 final size:20
Alignment explanation
Indices: 1109102--1109492 Score: 450
Period size: 20 Copynumber: 19.4 Consensus size: 20
1109092 AAATTTCAGT
* * * *
1109102 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1109122 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1109142 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1109162 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1109182 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1109202 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1109222 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1109242 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1109262 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1109282 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1109302 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
1109322 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
1109343 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1109363 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1109383 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1109403 GTTGCGATTTTACGGATACAC
1 GTTGCGA-TTTACGGATACGC
1109424 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1109444 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1109464 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1109484 GTTGCGATT
1 GTTGCGATT
1109493 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 24
0.84 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 278 0.86
21 36 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1109511 original size:81 final size:81
Alignment explanation
Indices: 1109107--1109511 Score: 398
Period size: 81 Copynumber: 5.0 Consensus size: 81
1109097 TCAGTGTTGT
* * * * * * *
1109107 GATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTGCGATT
1 GATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
1109171 TACGGATTATCG--TTGC
65 TA-TGAATATCGCATTGC
*
1109187 GATTTACGGATACGCGTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACGCGTTGCGATT
1 GATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
1109251 TACGGATA-CGCATTGC
65 TATGAATATCGCATTGC
*
1109267 GATTTACGGATACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTT
1 GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TT
*
1109332 TATGTATTATCG--TTGC
65 TATG-AATATCGCATTGC
* * **
1109348 GATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTT
1 GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TT
* * * *
1109413 TACGGATA-CACGTTGC
65 TATGAATATCGCATTGC
* * * ** *
1109429 GATTTACGGATACGCGTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGA-T
1 GATTTACGGATACGCGTTGCGATTTACG-GATACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
1109492 TATTGAAAATCGCAATGC
65 TA-TGAATATCGCATTGC
1109510 GA
1 GA
1109512 ATTTGTACTA
Statistics
Matches: 278, Mismatches: 36, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
78 2 0.01
79 9 0.03
80 127 0.46
81 135 0.49
82 3 0.01
83 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (81 bp):
GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTT
ATGAATATCGCATTGC
Found at i:1110096 original size:126 final size:125
Alignment explanation
Indices: 1109931--1110170 Score: 437
Period size: 126 Copynumber: 1.9 Consensus size: 125
1109921 TCTCTGCATA
1109931 TATTTATGAGCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATATT
1 TATTTATGAGCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATATT
* *
1109996 TTT-AAAATAAATATTTAAAATATATTATAAATATTTATTTTTTTTAAAAAAAGTAAATAT
66 TTTAAAAATAAATATTTAAAATATATTATAAATATATA-ATTTTTTAAAAAAAGTAAATAT
1110056 TATTTATGAGCCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATAT
1 TATTTATGAG-CTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATAT
1110121 TTTTAAAAATAAATATTTAAAATATATTATAAATATATAATTTTTTAAAA
65 TTTTAAAAATAAATATTTAAAATATATTATAAATATATAATTTTTTAAAA
1110171 GTAATATTTA
Statistics
Matches: 111, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
125 10 0.09
126 68 0.61
127 33 0.30
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.48
Consensus pattern (125 bp):
TATTTATGAGCTTTGTCTCTTGAGATATGATGATGTTAGGTTTTGTTTAAATTATATAGTATATT
TTTAAAAATAAATATTTAAAATATATTATAAATATATAATTTTTTAAAAAAAGTAAATAT
Found at i:1110167 original size:28 final size:29
Alignment explanation
Indices: 1110136--1110206 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
1110126 AAAATAAATA
1110136 TTTAAAA-T-ATATTATA-AATATATAATTT
1 TTTAAAAGTAATATT-TAGAAT-TATAATTT
*
1110164 TTTAAAAGTAATATTTAGAATTATCATTT
1 TTTAAAAGTAATATTTAGAATTATAATTT
1110193 TTTAAGAAG-AATAT
1 TTTAA-AAGTAATAT
1110207 AGATGGTGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 7 0.18
29 20 0.53
30 11 0.29
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (29 bp):
TTTAAAAGTAATATTTAGAATTATAATTT
Found at i:1116134 original size:63 final size:63
Alignment explanation
Indices: 1116049--1116236 Score: 313
Period size: 63 Copynumber: 3.0 Consensus size: 63
1116039 TCAAATTACC
* *
1116049 TTGTAGAGTGAAGTTTTGGCTGATCTCACACGAGGACAACTCCAAATACTTTAAAGAAGAAAG
1 TTGTAGAGTGAAGTTTTGGCTGATCTCACACGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
*
1116112 TTGTAGAGTGAAGTTTTGGCTGATCTCACATGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
1 TTGTAGAGTGAAGTTTTGGCTGATCTCACACGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
** * *
1116175 TTGTAGAGTGAAGTTTTGGCTGATCTCACACCCGAACAACCCCAAATGCTTCAAAGAAGAAA
1 TTGTAGAGTGAAGTTTTGGCTGATCTCACACGAGGACAACTCCAAATGCTTCAAAGAAGAAA
1116237 ATTCTCTTGG
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 117 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (63 bp):
TTGTAGAGTGAAGTTTTGGCTGATCTCACACGAGGACAACTCCAAATGCTTCAAAGAAGAAAG
Found at i:1116532 original size:22 final size:21
Alignment explanation
Indices: 1116507--1116549 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1116497 ATTACATTTT
1116507 TTAAA-AACAACATTTCAAATTA
1 TTAAACAACAA-ATTT-AAATTA
1116529 TTAAACTAACAAATTTAAATT
1 TTAAAC-AACAAATTTAAATT
1116550 TATGTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAAACAACAAATTTAAATTA
Found at i:1120344 original size:2 final size:2
Alignment explanation
Indices: 1120337--1120366 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1120327 AGTAATTTTA
1120337 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
1120367 TAGTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1123797 original size:21 final size:21
Alignment explanation
Indices: 1123757--1123797 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1123747 TAATAATATA
*
1123757 TTTTATAATTATAAATAAATT
1 TTTTATAATTATAAAAAAATT
1123778 TTTTATAATGTA-AAAAAAAT
1 TTTTATAAT-TATAAAAAAAT
1123798 ACTCGCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTATAATTATAAAAAAATT
Found at i:1130071 original size:2 final size:2
Alignment explanation
Indices: 1130059--1130089 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1130049 TTAAATAAAC
1130059 AT AT A- 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
1130090 TGAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1131259 original size:14 final size:14
Alignment explanation
Indices: 1131240--1131303 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
1131230 TTTAGAAATA
1131240 TACATTTGAGTATT
1 TACATTTGAGTATT
*
1131254 TACATTTGATTTTAAATT
1 TACATTTGA--GT--ATT
*
1131272 TA-ATTT-ATTATT
1 TACATTTGAGTATT
1131284 TACATTTGAGTATT
1 TACATTTGAGTATT
1131298 TACATT
1 TACATT
1131304 CGATTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 22 0.52
16 2 0.05
17 4 0.10
18 5 0.12
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (14 bp):
TACATTTGAGTATT
Found at i:1131854 original size:33 final size:33
Alignment explanation
Indices: 1131817--1131893 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
1131807 TGTTTTGTGT
*
1131817 TTTTGATA-TTGTTTGTTCACTGTAAAT-ATTCCA
1 TTTTGATAGTTG-TAGTTCACTGTAAATGATT-CA
* *
1131850 TTTTGACAGTTGTAGTTCACTGTAATTGATTCA
1 TTTTGATAGTTGTAGTTCACTGTAAATGATTCA
1131883 TTTTGATAGTT
1 TTTTGATAGTT
1131894 TTTCTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 32 0.84
34 6 0.16
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (33 bp):
TTTTGATAGTTGTAGTTCACTGTAAATGATTCA
Found at i:1140985 original size:32 final size:29
Alignment explanation
Indices: 1140945--1141008 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
1140935 TACCATGTTT
* *
1140945 TTATTTTATTTTTTATTTTTTATTTATTACTA
1 TTATTTTA--TTTTATTTTTCATTT-TTAATA
1140977 TTATTTTATTTTATTTTTCATTTTTAATA
1 TTATTTTATTTTATTTTTCATTTTTAATA
1141006 TTA
1 TTA
1141009 AAAACTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 8 0.27
30 14 0.47
32 8 0.27
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (29 bp):
TTATTTTATTTTATTTTTCATTTTTAATA
Found at i:1143220 original size:19 final size:19
Alignment explanation
Indices: 1143188--1143236 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1143178 TTGATACGCA
*
1143188 AATTTTAATATTGATCCTT
1 AATTTTAATTTTGATCCTT
* *
1143207 AATTTAAATTTTGATGCTT
1 AATTTTAATTTTGATCCTT
*
1143226 ATTTTTAATTT
1 AATTTTAATTT
1143237 GATATTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (19 bp):
AATTTTAATTTTGATCCTT
Found at i:1143237 original size:18 final size:18
Alignment explanation
Indices: 1143190--1143250 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1143180 GATACGCAAA
* *
1143190 TTTTAATATTGATCCTTAA
1 TTTTAAT-TTGATACTTAT
* *
1143209 TTTAAATTTTGATGCTTAT
1 TTTTAA-TTTGATACTTAT
*
1143228 TTTTAATTTGATATTTAT
1 TTTTAATTTGATACTTAT
1143246 TTTTA
1 TTTTA
1143251 TCATTGCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 15 0.43
19 19 0.54
20 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.61
Consensus pattern (18 bp):
TTTTAATTTGATACTTAT
Found at i:1143879 original size:17 final size:18
Alignment explanation
Indices: 1143854--1143887 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1143844 TAAAATTATA
1143854 ATTAATTTT-AATAAATT
1 ATTAATTTTAAATAAATT
*
1143871 ATTACTTTTAAATAAAT
1 ATTAATTTTAAATAAAT
1143888 CCTTATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAATTTTAAATAAATT
Found at i:1144020 original size:2 final size:2
Alignment explanation
Indices: 1144015--1144043 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1144005 ACACACACAC
1144015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1144044 AATGCGTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1144233 original size:15 final size:15
Alignment explanation
Indices: 1144213--1144249 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1144203 GGTAAGATCA
*
1144213 CAAGATGCATTACTT
1 CAAGATGCATTACTG
1144228 CAAGATGCATTACTG
1 CAAGATGCATTACTG
1144243 CAAGATG
1 CAAGATG
1144250 AAAATACTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (15 bp):
CAAGATGCATTACTG
Found at i:1149001 original size:22 final size:21
Alignment explanation
Indices: 1148976--1149018 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1148966 CAATTACATT
1148976 TTAAA-AACAATATTTCAAATTA
1 TTAAACAACAA-ATTT-AAATTA
1148998 TTAAACTAACAAATTTAAATT
1 TTAAAC-AACAAATTTAAATT
1149019 TATGTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAAACAACAAATTTAAATTA
Found at i:1165706 original size:21 final size:21
Alignment explanation
Indices: 1165680--1165721 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1165670 AAAAGTTTGG
1165680 GACCGTGAACC-GACCTAATTC
1 GACCGTG-ACCGGACCTAATTC
*
1165701 GACCGTGACCGGCCCTAATTC
1 GACCGTGACCGGACCTAATTC
1165722 CCAGTGCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
GACCGTGACCGGACCTAATTC
Found at i:1165891 original size:14 final size:14
Alignment explanation
Indices: 1165832--1165895 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
1165822 TTTAGAAATA
1165832 TACATTTGAGTATT
1 TACATTTGAGTATT
* *
1165846 TATATTTGATTTTAAATT
1 TACATTTGA--GT--ATT
*
1165864 TA-ATTT-ATTATT
1 TACATTTGAGTATT
1165876 TACATTTGAGTATT
1 TACATTTGAGTATT
1165890 TACATT
1 TACATT
1165896 CGATTTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 21 0.51
16 2 0.05
17 4 0.10
18 5 0.12
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (14 bp):
TACATTTGAGTATT
Found at i:1166444 original size:33 final size:33
Alignment explanation
Indices: 1166407--1166483 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 33
1166397 TGTTTTGTGT
*
1166407 TTTTGATA-TTGTTTGTTCACTGTAAAT-ATTCCA
1 TTTTGATAGTTG-TAGTTCACTGTAAATGATT-CA
*
1166440 TTTTGACAGTTGTAGTTCACTGTAAATGATTCA
1 TTTTGATAGTTGTAGTTCACTGTAAATGATTCA
1166473 TTTTGATAGTT
1 TTTTGATAGTT
1166484 CTTCTAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 33 0.85
34 6 0.15
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (33 bp):
TTTTGATAGTTGTAGTTCACTGTAAATGATTCA
Found at i:1179722 original size:11 final size:11
Alignment explanation
Indices: 1179706--1179731 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1179696 AAATCTACTG
1179706 TTATTTATTTA
1 TTATTTATTTA
1179717 TTATTTATTTA
1 TTATTTATTTA
1179728 TTAT
1 TTAT
1179732 AATAACAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:1185631 original size:15 final size:16
Alignment explanation
Indices: 1185611--1185640 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1185601 CTTCCAAATA
1185611 TTTGAATATA-ATTAT
1 TTTGAATATACATTAT
1185626 TTTGAATATACATTA
1 TTTGAATATACATTA
1185641 ATTTAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (16 bp):
TTTGAATATACATTAT
Found at i:1196588 original size:2 final size:2
Alignment explanation
Indices: 1196581--1196609 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1196571 TCATTTTGGA
1196581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1196610 ATGATGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1212260 original size:21 final size:21
Alignment explanation
Indices: 1212236--1212288 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1212226 AATTTGGAAA
1212236 ATCGCAACGCGAATT-TCAACT
1 ATCGCAACGCGAATTCT-AACT
* *
1212257 ATCGTAACGCG-ATTCTGACT
1 ATCGCAACGCGAATTCTAACT
1212277 ATCGCAACGCGA
1 ATCGCAACGCGA
1212289 TTTTTCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGAATTCTAACT
Found at i:1212395 original size:21 final size:21
Alignment explanation
Indices: 1212296--1212388 Score: 132
Period size: 21 Copynumber: 4.4 Consensus size: 21
1212286 CGATTTTTCT
* * *
1212296 CGTTGCGATAGTTCAAGTTCA
1 CGTTGCGATAATCCAAGTTCG
* *
1212317 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAATCCAAGTTCG
1212338 CGTTGCGATAATCCAAGTTCG
1 CGTTGCGATAATCCAAGTTCG
1212359 CGTTGCGATAATCCAAGTTCG
1 CGTTGCGATAATCCAAGTTCG
*
1212380 CATTGCGAT
1 CGTTGCGAT
1212389 TTTCCAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
CGTTGCGATAATCCAAGTTCG
Found at i:1212812 original size:19 final size:19
Alignment explanation
Indices: 1212784--1212826 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1212774 CTTATTTTGG
*
1212784 ATTTTCACTATCGCAACAC
1 ATTTTAACTATCGCAACAC
1212803 ATTTTAACTATCGCAACAC
1 ATTTTAACTATCGCAACAC
1212822 ATTTT
1 ATTTT
1212827 TCAAAATCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTTTAACTATCGCAACAC
Found at i:1214862 original size:6 final size:6
Alignment explanation
Indices: 1214797--1214850 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
1214787 TTTTATTCCG
1214797 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
1 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
*
1214845 GAAGAA
1 GGAGAA
1214851 AGAAGAAGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GGAGAA
Found at i:1215174 original size:171 final size:167
Alignment explanation
Indices: 1214873--1215186 Score: 445
Period size: 171 Copynumber: 1.9 Consensus size: 167
1214863 CGACACCTGG
* * *
1214873 ATTTTGGATTTTGATTTTTTTTTTAATTTTTTTAATTTTCACTTCAGAATTTCGTTTAGGGGTTA
1 ATTTTGGATTTTGATTTTTTTTATAATTTTTTTAATTGTCACTTCAGAATTTCGTTGAGGGGTTA
* * * * *
1214938 ACGAAAGTTAGAAAAATTTAAACCGGTTGGATCGACAAGTTAGTGACTTAAATCGGATGGACCGA
66 ACGAAAGTTAAAAAAATTTAAACCGGTCGGATCGACAAATTAGTGACTTAAATCAGATAGACCGA
1215003 TAACGTTAAGTACAAGAAGAAGACACGTGGGTTCTGA
131 TAACGTTAAGTACAAGAAGAAGACACGTGGGTTCTGA
1215040 ATTTTGGATTTTGA-TTTTTTTATAATTTTTTT-ATTGTCACTTCAGAATTTCGTTGAGGGGTTA
1 ATTTTGGATTTTGATTTTTTTTATAATTTTTTTAATTGTCACTTCAGAATTTCGTTGAGGGGTTA
* * *
1215103 GCGGAAGTTAATAACAGAGAGATTTAAACCGGTCGGATCGATAAATTAGTGACTTAAA-CTAGAT
66 ACGAAAGTT-A-AA-A-A-A-ATTTAAACCGGTCGGATCGACAAATTAGTGACTTAAATC-AGAT
1215167 AGACCGATAACGTTAAGTAC
124 AGACCGATAACGTTAAGTAC
1215187 CATTTGCCTT
Statistics
Matches: 129, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
165 36 0.28
166 18 0.14
167 15 0.12
168 1 0.01
169 1 0.01
170 2 0.02
171 56 0.43
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (167 bp):
ATTTTGGATTTTGATTTTTTTTATAATTTTTTTAATTGTCACTTCAGAATTTCGTTGAGGGGTTA
ACGAAAGTTAAAAAAATTTAAACCGGTCGGATCGACAAATTAGTGACTTAAATCAGATAGACCGA
TAACGTTAAGTACAAGAAGAAGACACGTGGGTTCTGA
Found at i:1220947 original size:2 final size:2
Alignment explanation
Indices: 1220940--1220980 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1220930 AATAAACGTT
1220940 TA TA TA TA TA 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 TA TA TA TA TA T
1220981 GTGTGTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1221390 original size:17 final size:17
Alignment explanation
Indices: 1221369--1221408 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1221359 GAAATCATCA
*
1221369 AATTGTTACATTATAAT
1 AATTGTGACATTATAAT
* *
1221386 CATTGTGACGTTATAAT
1 AATTGTGACATTATAAT
1221403 AATTGT
1 AATTGT
1221409 AATATTTCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (17 bp):
AATTGTGACATTATAAT
Found at i:1222678 original size:21 final size:22
Alignment explanation
Indices: 1222654--1222694 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1222644 TTGAGTTTTC
*
1222654 TTTATATAACAA-ATATTTGAT
1 TTTAAATAACAATATATTTGAT
*
1222675 TTTAAATAATAATATATTTG
1 TTTAAATAACAATATATTTG
1222695 TTCCTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTAAATAACAATATATTTGAT
Found at i:1223192 original size:3 final size:3
Alignment explanation
Indices: 1223184--1223208 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1223174 CAAAGTTATC
1223184 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1223209 AAGCGGCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1224479 original size:11 final size:11
Alignment explanation
Indices: 1224463--1224504 Score: 84
Period size: 11 Copynumber: 3.8 Consensus size: 11
1224453 AGAGATTACA
1224463 ATGAGTTAATG
1 ATGAGTTAATG
1224474 ATGAGTTAATG
1 ATGAGTTAATG
1224485 ATGAGTTAATG
1 ATGAGTTAATG
1224496 ATGAGTTAA
1 ATGAGTTAA
1224505 ATTGTAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (11 bp):
ATGAGTTAATG
Found at i:1228047 original size:22 final size:24
Alignment explanation
Indices: 1228003--1228047 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1227993 CTCCATGTAA
*
1228003 TTAAAAGAAATGAGATTACATTAT
1 TTAAAAGAAATGAGATTAAATTAT
1228027 TTAAAA-AAATG-GATTAAATTA
1 TTAAAAGAAATGAGATTAAATTA
1228048 AATAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.33
Consensus pattern (24 bp):
TTAAAAGAAATGAGATTAAATTAT
Found at i:1228910 original size:2 final size:2
Alignment explanation
Indices: 1228903--1228935 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1228893 AGAATTTGTA
1228903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1228936 ATTTTTTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1257951 original size:31 final size:31
Alignment explanation
Indices: 1257927--1258037 Score: 195
Period size: 31 Copynumber: 3.6 Consensus size: 31
1257917 CCATAGATTT
* *
1257927 CGAAGAACCTAGGTAATCAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
1257958 CGAAGGACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
1257989 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
1258020 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
1258038 CCTCGACCCT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:1258864 original size:21 final size:21
Alignment explanation
Indices: 1258840--1258884 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1258830 TGTTGTTCGT
* *
1258840 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1258861 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1258882 TTG
1 TTG
1258885 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1261610 original size:13 final size:13
Alignment explanation
Indices: 1261594--1261620 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1261584 TCGAAACCTA
1261594 CGTGTGAAACAAT
1 CGTGTGAAACAAT
1261607 CGTGTGAAACAAT
1 CGTGTGAAACAAT
1261620 C
1 C
1261621 ACACGCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (13 bp):
CGTGTGAAACAAT
Found at i:1262086 original size:31 final size:31
Alignment explanation
Indices: 1262048--1262172 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
1262038 CCCGAAGGAC
* * *
1262048 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1262079 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1262110 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1262141 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1262172 C
1 C
1262173 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1262998 original size:21 final size:21
Alignment explanation
Indices: 1262974--1263018 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1262964 TGTTGTTCGT
* *
1262974 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1262995 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1263016 TTG
1 TTG
1263019 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1265102 original size:26 final size:26
Alignment explanation
Indices: 1265071--1265127 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1265061 TGGGAAACCT
1265071 TTTCTTCTCAACTGTTTCCATGAAAA
1 TTTCTTCTCAACTGTTTCCATGAAAA
1265097 TTTCTTCTCAACTGTTTCCATGAAAA
1 TTTCTTCTCAACTGTTTCCATGAAAA
1265123 TTTCT
1 TTTCT
1265128 CATACAACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.46
Consensus pattern (26 bp):
TTTCTTCTCAACTGTTTCCATGAAAA
Found at i:1269411 original size:15 final size:16
Alignment explanation
Indices: 1269391--1269420 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1269381 TTAAAAAAAC
1269391 ATTAAA-GATAAATTT
1 ATTAAATGATAAATTT
1269406 ATTAAATGATAAATT
1 ATTAAATGATAAATT
1269421 GTGTATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTAAATGATAAATTT
Found at i:1270532 original size:21 final size:22
Alignment explanation
Indices: 1270501--1270542 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1270491 ATGCATATGG
1270501 TCGGATAAAAAATTGATCTGGA
1 TCGGATAAAAAATTGATCTGGA
1270523 TCGGAT-AAAAATTGATCTGG
1 TCGGATAAAAAATTGATCTGG
1270543 TTTTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (22 bp):
TCGGATAAAAAATTGATCTGGA
Found at i:1270817 original size:20 final size:20
Alignment explanation
Indices: 1270780--1270819 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1270770 TTATACTATC
*
1270780 CGGTTTTAAAATATCCGATT
1 CGGTTTTAAAATAACCGATT
1270800 CGGTTTT-AAATAAACCGATT
1 CGGTTTTAAAAT-AACCGATT
1270820 TTTCCCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
CGGTTTTAAAATAACCGATT
Found at i:1276787 original size:61 final size:61
Alignment explanation
Indices: 1276669--1276788 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 61
1276659 ATCACTAAAT
* * * *
1276669 ATTCAATGATTCATCACTACAGTTAAGCATCCAACCTACAATCAGTTGGCAATAGGTGGAAG
1 ATTCAATGATTCATCACTACA-TTAAGCATCCAACCCACAAACAATCGGCAATAGGTGGAAG
* *
1276731 ATTCAATGATTCATTACTAC-TTCAAGCATCCAACACCA-AAACAATCGGTAATAGGTGG
1 ATTCAATGATTCATCACTACATT-AAGCATCCAAC-CCACAAACAATCGGCAATAGGTGG
1276789 GTTCAACTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
60 2 0.04
61 27 0.54
62 21 0.42
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (61 bp):
ATTCAATGATTCATCACTACATTAAGCATCCAACCCACAAACAATCGGCAATAGGTGGAAG
Found at i:1283349 original size:8 final size:8
Alignment explanation
Indices: 1283336--1283367 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
1283326 GCAAATAGTT
1283336 AAAAAAAG
1 AAAAAAAG
1283344 -AAAAAAG
1 AAAAAAAG
1283351 -AAAAAAG
1 AAAAAAAG
1283358 AAAAAAAG
1 AAAAAAAG
1283366 AA
1 AA
1283368 CAAGTAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.61
8 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1283354 original size:6 final size:7
Alignment explanation
Indices: 1283337--1283363 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1283327 CAAATAGTTA
1283337 AAAAAAG
1 AAAAAAG
1283344 AAAAAAG
1 AAAAAAG
1283351 AAAAAAG
1 AAAAAAG
1283358 AAAAAA
1 AAAAAA
1283364 AGAACAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1285396 original size:2 final size:2
Alignment explanation
Indices: 1285391--1285419 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1285381 TCTCTCTTTC
1285391 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 T
1285420 TGGACCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1288230 original size:29 final size:28
Alignment explanation
Indices: 1288180--1288234 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
1288170 CGATTTGATA
1288180 TTAAATTTTAAATCAAATAAATACAAAGG
1 TTAAATTTTAAATCAAATAAAT-CAAAGG
1288209 TTAAATTTATAAAAT-AAA-AAATCAAA
1 TTAAATTT-T-AAATCAAATAAATCAAA
1288235 AATAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 4 0.17
29 12 0.50
30 4 0.17
31 4 0.17
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (28 bp):
TTAAATTTTAAATCAAATAAATCAAAGG
Found at i:1291419 original size:16 final size:15
Alignment explanation
Indices: 1291398--1291428 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1291388 CTAAATAAGT
1291398 TTACTTAATTGAATAA
1 TTACTTAATT-AATAA
1291414 TTACTTAATTAATAA
1 TTACTTAATTAATAA
1291429 AGACAACTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (15 bp):
TTACTTAATTAATAA
Found at i:1291970 original size:2 final size:2
Alignment explanation
Indices: 1291965--1291994 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1291955 ACACACATAC
1291965 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
1291995 TACAATCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1294489 original size:14 final size:13
Alignment explanation
Indices: 1294458--1294496 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1294448 TTTCGGATAA
1294458 AAACCGGTTTTTT
1 AAACCGGTTTTTT
*
1294471 TAACCGGTTTTTT
1 AAACCGGTTTTTT
*
1294484 CAAACCGATTTTT
1 -AAACCGGTTTTT
1294497 ATCCGATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (13 bp):
AAACCGGTTTTTT
Found at i:1294575 original size:19 final size:20
Alignment explanation
Indices: 1294546--1294584 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1294536 GTTAAAATAA
*
1294546 CCGATTTAAAAAAATTCGAT
1 CCGATTTAAAAAAAATCGAT
1294566 CCGA-TTAAAAAAAATCGAT
1 CCGATTTAAAAAAAATCGAT
1294585 TTTTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (20 bp):
CCGATTTAAAAAAAATCGAT
Found at i:1295194 original size:95 final size:95
Alignment explanation
Indices: 1295083--1295276 Score: 388
Period size: 95 Copynumber: 2.0 Consensus size: 95
1295073 TTACAAAATT
1295083 TTAATAGTATTAAATTAGATCATCAATAAAAAATACAAAGAAAATATCTAAATTAAATGAAAATT
1 TTAATAGTATTAAATTAGATCATCAATAAAAAATACAAAGAAAATATCTAAATTAAATGAAAATT
1295148 TAGAATTTAAAATAGGTATTAAGATAGAAA
66 TAGAATTTAAAATAGGTATTAAGATAGAAA
1295178 TTAATAGTATTAAATTAGATCATCAATAAAAAATACAAAGAAAATATCTAAATTAAATGAAAATT
1 TTAATAGTATTAAATTAGATCATCAATAAAAAATACAAAGAAAATATCTAAATTAAATGAAAATT
1295243 TAGAATTTAAAATAGGTATTAAGATAGAAA
66 TAGAATTTAAAATAGGTATTAAGATAGAAA
1295273 TTAA
1 TTAA
1295277 CGGTGGAGAT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 99 1.00
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (95 bp):
TTAATAGTATTAAATTAGATCATCAATAAAAAATACAAAGAAAATATCTAAATTAAATGAAAATT
TAGAATTTAAAATAGGTATTAAGATAGAAA
Found at i:1300235 original size:27 final size:28
Alignment explanation
Indices: 1300180--1300237 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 28
1300170 TCGATATTGA
1300180 AAAATAAATATTAAAATAATTTATATAT
1 AAAATAAATATTAAAATAATTTATATAT
1300208 AAAA-AAATA-TAAAATATTATTTATTATAT
1 AAAATAAATATTAAAATA--ATTTA-TATAT
1300237 A
1 A
1300238 TATATTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 7 0.26
27 5 0.19
28 9 0.33
29 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAATAAATATTAAAATAATTTATATAT
Found at i:1301791 original size:3 final size:3
Alignment explanation
Indices: 1301785--1301839 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
1301775 TAATATTTAT
1301785 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1301831 TAAA TAA TA
1 T-AA TAA TA
1301840 TTTAAATGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.08
3 43 0.88
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1302376 original size:116 final size:116
Alignment explanation
Indices: 1302093--1302996 Score: 1126
Period size: 113 Copynumber: 7.9 Consensus size: 116
1302083 CTCCTCTTTA
* * * * * * * * ** *
1302093 GATGAGTTCTTCTTATTATGAACTCT-TTCTAGCAATATTGATCCATCGAATGATAAAATCGAGC
1 GATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGTTGATCCATCAAATGATGAATTTAAAC
** * *
1302157 AAAAATTTGAACAAATTCTTCTCATTATGAATTCCTTCTTTCTTCTTC--A-
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
* * * * * * *
1302206 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACA
*
1302271 AAAGGTTGACCAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
* * *
1302322 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATTTTAATCCATCAAATGATGAATTCAAAC
1 GATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGTTGATCCATCAAATGATGAATTTAAAC
* * *
1302386 AAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTC--A-
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
* * * * *
1302435 GATGAGTTCTTCTCATTGTGAACTTTCTCTGG-AATAGCTGATCCATCAAATGATGAATTCAAGC
1 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAAT-GTTGATCCATCAAATGATGAATTTAAAC
*
1302499 AAAAAGTTGAACAAATTCTTCTCATTATGAATTT-TCTCTTCCTTCTTCAGAT
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCT-TCTTCCTTCTTCAGAT
*
1302551 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGTTAATCCATCAAATGATGAATTTAAAC
1 GATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGTTGATCCATCAAATGATGAATTTAAAC
*
1302615 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
* * *
1302667 GACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAAC
1 GATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGTTGATCCATCAAATGATGAATTTAAAC
*
1302731 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
* * * * * *
1302783 GA--A-TTCTTCTCATTACGAACTTCCTCTGGAAAAGTTGATCCATCAAATGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACA
1302845 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
* * * ** *
1302896 GA--A-TTCTTCTCATTACGAACTTCCTCTGGAAA-GTTTGATCCATCAAGTGATGGTTTTGAAC
1 GATGAGTTCTTCTCATTATGAACTTACTCTGGAAATG-TTGATCCATCAAATGATGAATTTAAAC
*
1302957 AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT
1302997 TCAGATGAGT
Statistics
Matches: 710, Mismatches: 65, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
112 10 0.01
113 378 0.53
114 2 0.00
115 2 0.00
116 310 0.44
117 8 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (116 bp):
GATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACA
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
Found at i:1302502 original size:229 final size:229
Alignment explanation
Indices: 1302093--1302996 Score: 1207
Period size: 229 Copynumber: 3.9 Consensus size: 229
1302083 CTCCTCTTTA
* ** * * * * * * * * *
1302093 GATGAGTTCTTCTTATTATGAACTCTTTCTAGCAATATTGATCCATCGAATGATAAAATCGAGCA
1 GATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTAATCCATCAAATGATGAATTCAAACA
** *
1302158 AAAATTTGAACAAATTCTTCTCATTATGAA-TTCCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTT-CTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
1302222 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGACCAAATT
130 TATGAACTTTCTCTGGAATAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAATT
1302287 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
195 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
*
1302322 GATGAGTTCTTCTCATTATGAACTCTACCTGGAAATTTTAATCCATCAAATGATGAATTCAAACA
1 GATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTAATCCATCAAATGATGAATTCAAACA
* *
1302387 AAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1302452 GTGAACTTTCTCTGGAATAGCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTC
131 ATGAACTTTCTCTGGAATAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAATTC
1302517 TTCTCATTATGAATTT-TCTCTTCCTTCTTCAGAT
196 TTCTCATTATGAATTTCT-TCTTCCTTCTTCAGAT
*
1302551 GATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTAATCCATCAAATGATGAATTTAAACA
1 GATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTAATCCATCAAATGATGAATTCAAACA
1302616 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTC
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTC
* * * * *
1302681 ATTATGAACTCTAC-CTGGCAAT-GTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACA
128 ATTATGAACT-TTCTCTGG-AATAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACA
*
1302744 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
191 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
* * * * * ** *
1302783 GA--A-TTCTTCTCATTACGAACT-TCCTCTGGAAAAGTTGATCCATCAAATGATGGATTTGAGC
1 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGTTAATCCATCAAATGATGAATTCAAAC
* *
1302844 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCAT
65 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * **
1302909 TACGAACTTCCTCTGGAA-AGTTTGATCCATCAAGTGATGGTTTTGAA-CAAAAAGTTGAACAAA
130 TATGAACTTTCTCTGGAATAG-CTGATCCATCAAATGATGAATTT-AAGCAAAAAGTTGAACAAA
1302972 TTCTTCTCATTATGAATTTCTTCTT
193 TTCTTCTCATTATGAATTTCTTCTT
1302997 TCAGATGAGT
Statistics
Matches: 608, Mismatches: 54, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
225 5 0.01
226 81 0.13
227 2 0.00
228 3 0.00
229 410 0.67
230 3 0.00
232 98 0.16
233 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (229 bp):
GATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTAATCCATCAAATGATGAATTCAAACA
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAATAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAATTC
TTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
Found at i:1302994 original size:17 final size:17
Alignment explanation
Indices: 1302972--1303060 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
1302962 GTTGAACAAA
*
1302972 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAC
* *
1302989 TTCTTCTTTCA-GATG-AG
1 TTCTTC--TCATTATGAAC
1303006 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
1303023 TTCTTCTTC-TTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
1303042 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
1303059 TT
1 TT
1303061 TCTCTGGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
15 3 0.05
16 3 0.05
17 27 0.48
18 9 0.16
19 14 0.25
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:1303015 original size:34 final size:36
Alignment explanation
Indices: 1302972--1303063 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
1302962 GTTGAACAAA
1302972 TTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
*
1303006 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
1303042 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
1303064 CTGGAAAAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
36 26 0.49
37 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
Found at i:1303060 original size:143 final size:149
Alignment explanation
Indices: 1302859--1303173 Score: 473
Period size: 143 Copynumber: 2.1 Consensus size: 149
1302849 GTTGAACAAA
1302859 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTG
1 TTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTG
* *
1302924 G-AAAGTTTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
63 GAAAAG-GTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
1302988 -T-TTCTT-C-T-TTCAGATGAG
127 CTCTTCTTCCTTCTTCAGATGAG
* * *
1303006 TTCTTCTCATTATGAACTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGAA
* *
1303070 AAGGTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTC
66 AAGGTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC-TC
1303135 TTCTTCCTTCTTCAGATGAG
130 TTCTTCCTTCTTCAGATGAG
1303155 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
1303174 TCTCTGGAAA
Statistics
Matches: 154, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
143 91 0.59
144 10 0.06
145 1 0.01
146 5 0.03
147 17 0.11
148 1 0.01
149 29 0.19
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (149 bp):
TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGAA
AAGGTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTCT
TCTTCCTTCTTCAGATGAG
Found at i:1303203 original size:113 final size:109
Alignment explanation
Indices: 1303004--1303208 Score: 347
Period size: 113 Copynumber: 1.8 Consensus size: 109
1302994 CTTTCAGATG
1303004 AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* *
1303069 AAAGGTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
66 AAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACA
*
1303113 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1303178 TGGAAAAGCTGATCCATCAAATGATGGATTT
62 TGGAAAAGCTGATCCATCAAATGATGGATTT
1303209 TAATCTTTGC
Statistics
Matches: 89, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
109 17 0.19
112 6 0.07
113 66 0.74
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (109 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACA
Found at i:1304057 original size:93 final size:93
Alignment explanation
Indices: 1303909--1304266 Score: 558
Period size: 93 Copynumber: 3.9 Consensus size: 93
1303899 ATCCTTTAAT
* * * * * *
1303909 TCCAATAATTGGTTCTGT-GGTTCCTATCGAACCAGATCAGATAACTTAAAGAACACTTCCAGAA
1 TCCAATGATTGGTTCTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
1303973 GATGCTATGAGCACATTCATCTTCCAAA
66 GATGCTATGAGCACATTCATCTTCCAAA
* *
1304001 TCCAATGATTGGTTCTATGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
1 TCCAATGATTGGTTCTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
* *
1304066 GATGTTATGAGCACATTCATCTTCTAAA
66 GATGCTATGAGCACATTCATCTTCCAAA
**
1304094 TTTAATGATTGGTT-TTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 TCCAATGATTGGTTCTTT-GGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1304158 AGATGCTATGAGCACATTCATCTTCCAAA
65 AGATGCTATGAGCACATTCATCTTCCAAA
* * *
1304187 TTCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCATATAACTCAAAGAACACTTCCAGAA
1 TCCAATGATTGGTTCTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
1304252 GATGCTATGAGCACA
66 GATGCTATGAGCACA
1304267 CGGCACTTGT
Statistics
Matches: 246, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
92 18 0.07
93 225 0.91
94 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (93 bp):
TCCAATGATTGGTTCTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
GATGCTATGAGCACATTCATCTTCCAAA
Found at i:1305245 original size:6 final size:6
Alignment explanation
Indices: 1305234--1305298 Score: 80
Period size: 6 Copynumber: 11.0 Consensus size: 6
1305224 TCTTGACCCC
* *
1305234 CTTTTT CTTTTT CTTTTT CTTTTT -TCTGTT CTATTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT CTTTTT CTTTTT
*
1305282 CTTTTT -TGTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT
1305299 TGTTCTTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
5 5 0.10
6 44 0.88
7 1 0.02
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:1305271 original size:30 final size:28
Alignment explanation
Indices: 1305236--1305312 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 28
1305226 TTGACCCCCT
1305236 TTTTCTTTTTCTTTTTCTTTTTTCTGTTC
1 TTTTCTTTTTCTTTTTCTTTTTTCT-TTC
*
1305265 TATTTCTTTTTCTTTTTCTTTTTTGTTTC
1 T-TTTCTTTTTCTTTTTCTTTTTTCTTTC
*
1305294 TTTT-TTGTTCTTTTCTCTT
1 TTTTCTTTTTCTTTT-TCTT
1305313 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 9 0.20
28 7 0.16
29 5 0.11
30 23 0.52
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (28 bp):
TTTTCTTTTTCTTTTTCTTTTTTCTTTC
Found at i:1305304 original size:10 final size:11
Alignment explanation
Indices: 1305267--1305307 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1305257 TTCTGTTCTA
*
1305267 TTTCTTTTTCTT
1 TTTCTTTTT-TG
1305279 TTTCTTTTTTG
1 TTTCTTTTTTG
1305290 TTTCTTTTTTG
1 TTTCTTTTTTG
1305301 -TTCTTTT
1 TTTCTTTT
1305308 CTCTTCAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 7 0.25
11 12 0.43
12 9 0.32
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTTG
Found at i:1312655 original size:15 final size:15
Alignment explanation
Indices: 1312632--1312663 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1312622 TGAAATGAAT
1312632 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1312647 AATGTATGTATGCAA
1 AATGAATGTATGCAA
1312662 AA
1 AA
1312664 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1315982 original size:19 final size:18
Alignment explanation
Indices: 1315960--1316001 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
1315950 TATTAATAAG
1315960 AAAATATATAA-ATACTATA
1 AAAATA-ATAAGATA-TATA
1315979 AAAATAATAAGTATATATA
1 AAAATAATAAG-ATATATA
1315998 AAAA
1 AAAA
1316002 ATTTGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.19
19 14 0.67
20 3 0.14
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAATAATAAGATATATA
Found at i:1316506 original size:28 final size:25
Alignment explanation
Indices: 1316475--1316526 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
1316465 ATTTCAAAAT
1316475 TATAATTATGAGAAAAAAATAATTTATA
1 TATAATTAT-A-AAAAAAAT-ATTTATA
* *
1316503 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
1316527 TTATTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 1 0.05
28 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATA
Found at i:1316533 original size:23 final size:26
Alignment explanation
Indices: 1316485--1316539 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
1316475 TATAATTATG
1316485 AGAAA-AAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
1316510 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
1316533 AGAAATA
1 AGAAATA
1316540 TCAGTAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 10 0.37
26 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:1316613 original size:23 final size:22
Alignment explanation
Indices: 1316589--1316633 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1316579 CTTCGATATT
1316589 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
1316613 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
1316634 TTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:1318271 original size:16 final size:15
Alignment explanation
Indices: 1318252--1318304 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1318242 TTGGGCCTAA
*
1318252 AATAATAGTTATTAAT
1 AATAATAATTATT-AT
1318268 AATAATAATTATTAT
1 AATAATAATTATTAT
*
1318283 AATAATAA-TAATAT
1 AATAATAATTATTAT
1318297 AAATAATA
1 -AATAATA
1318305 TTTAAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 5 0.15
15 17 0.50
16 12 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AATAATAATTATTAT
Found at i:1318675 original size:6 final size:6
Alignment explanation
Indices: 1318664--1318704 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
1318654 TCCCTCTCGG
1318664 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAAT
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAAT
1318705 TATAAGTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTAATA
Found at i:1324506 original size:15 final size:16
Alignment explanation
Indices: 1324481--1324513 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1324471 TATCGCCGAC
1324481 CGAATTTCACTATTCA
1 CGAATTTCACTATTCA
1324497 CGAA-TTCACTATTCA
1 CGAATTTCACTATTCA
1324512 CG
1 CG
1324514 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.33
Consensus pattern (16 bp):
CGAATTTCACTATTCA
Found at i:1327471 original size:16 final size:17
Alignment explanation
Indices: 1327444--1327481 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1327434 GCTCCCAAAA
1327444 ATTTTAAATTTTCATAT
1 ATTTTAAATTTTCATAT
**
1327461 ATTTT-AATTTTTTTAT
1 ATTTTAAATTTTCATAT
1327477 ATTTT
1 ATTTT
1327482 TCTATGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTAAATTTTCATAT
Found at i:1327958 original size:102 final size:102
Alignment explanation
Indices: 1327782--1328019 Score: 325
Period size: 102 Copynumber: 2.3 Consensus size: 102
1327772 ACCGGAAGAA
* * * ** *
1327782 CATCATCGATAGCAGTGTTTCTCTGCT-GGGGAAATCAGCCTGTTAGGGTGTTGCGCCGTTATAT
1 CATCATCAATATCAGTGTTTCTTTGCTAGGGG-AATCAGCCTGTTACAGTGTTGCGCCGTTACAT
*
1327846 ATAAGGGTGAATAAAACTCGATCGATGCCGACCATAAG
65 ATAAGAGTGAATAAAACTCGATCGATGCCGACCATAAG
* * *
1327884 CATCATCAATATCAGTGTTTCTTTGCTAGAGGAATCAGCCTGTTACAGTGTTGTGCCGTTACATT
1 CATCATCAATATCAGTGTTTCTTTGCTAGGGGAATCAGCCTGTTACAGTGTTGCGCCGTTACATA
* **
1327949 TAAGAGTGAATAAAACTCGATCGGTGTTGACCATAAG
66 TAAGAGTGAATAAAACTCGATCGATGCCGACCATAAG
**
1327986 CATCATCAATATCAACGTTTCTTTGCTAGGGGAA
1 CATCATCAATATCAGTGTTTCTTTGCTAGGGGAA
1328020 CTGTTACGGT
Statistics
Matches: 119, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
102 116 0.97
103 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (102 bp):
CATCATCAATATCAGTGTTTCTTTGCTAGGGGAATCAGCCTGTTACAGTGTTGCGCCGTTACATA
TAAGAGTGAATAAAACTCGATCGATGCCGACCATAAG
Found at i:1332042 original size:25 final size:26
Alignment explanation
Indices: 1331992--1332043 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1331982 TAGCGACGGG
1331992 CATACCGCATGCTGATCCCATCTTAA
1 CATACCGCATGCTGATCCCATCTTAA
*
1332018 CATACCGCATGCTTA-CCCATCTTAA
1 CATACCGCATGCTGATCCCATCTTAA
1332043 C
1 C
1332044 GAGTTTTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.27
Consensus pattern (26 bp):
CATACCGCATGCTGATCCCATCTTAA
Done.