Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 30
Found at i:1730266 original size:44 final size:43
Alignment explanation
Indices: 1730200--1730316 Score: 105
Period size: 42 Copynumber: 2.7 Consensus size: 43
1730190 CCGCGTAGAA
* * * * *
1730200 ATGTCCCAAAGGACTACGTATATTTATCCC-ATATGACTACATAT
1 ATGTTCCAAAGGACCACATATA-TTATCCCGA-AGGACCACATAT
* * *
1730244 ATGTTCCAAAGGACCAAATATA-TGTCCCGAAGGACCGCATAT
1 ATGTTCCAAAGGACCACATATATTATCCCGAAGGACCACATAT
* *
1730286 ATGTTCCAAAAGACCACATATA-TGTCCCGAA
1 ATGTTCCAAAGGACCACATATATTATCCCGAA
1730317 TGACTGCATA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 43 0.69
43 1 0.02
44 18 0.29
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (43 bp):
ATGTTCCAAAGGACCACATATATTATCCCGAAGGACCACATAT
Found at i:1730294 original size:42 final size:42
Alignment explanation
Indices: 1730239--1730326 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
1730229 CATATGACTA
*
1730239 CATATATGTTCCAAAGGACCAAATATATGTCCCGAAGGACCG
1 CATATATGTTCCAAAAGACCAAATATATGTCCCGAAGGACCG
* * *
1730281 CATATATGTTCCAAAAGACCACATATATGTCCCGAATGACTG
1 CATATATGTTCCAAAAGACCAAATATATGTCCCGAAGGACCG
1730323 CATA
1 CATA
1730327 GACCCTCAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (42 bp):
CATATATGTTCCAAAAGACCAAATATATGTCCCGAAGGACCG
Found at i:1730326 original size:21 final size:21
Alignment explanation
Indices: 1730239--1730326 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
1730229 CATATGACTA
* *
1730239 CATATATGTTCC-AAAGGACCA
1 CATATATGTCCCGAAA-GACCG
* *
1730260 AATATATGTCCCGAAGGACCG
1 CATATATGTCCCGAAAGACCG
* * *
1730281 CATATATGTTCCAAAAGACCA
1 CATATATGTCCCGAAAGACCG
* *
1730302 CATATATGTCCCGAATGACTG
1 CATATATGTCCCGAAAGACCG
1730323 CATA
1 CATA
1730327 GACCCTCAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
21 50 0.96
22 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (21 bp):
CATATATGTCCCGAAAGACCG
Found at i:1738527 original size:90 final size:90
Alignment explanation
Indices: 1738413--1738590 Score: 304
Period size: 90 Copynumber: 2.0 Consensus size: 90
1738403 TAATCCCGAA
* * *
1738413 TATTTAATTTTAATTAATTAAATATAGATTTAATTCATTTGAAATAATAAAATA-CCTAATATGA
1 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-ACCCTAATATGA
1738477 TTAGGGTAACTTGGATATAAAAGGAT
65 TTAGGGTAACTTGGATATAAAAGGAT
1738503 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
1738568 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
1738591 GTGTGTTAGT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
89 1 0.01
90 82 0.99
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:1745283 original size:90 final size:89
Alignment explanation
Indices: 1745164--1745340 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
1745154 TAATCCCAAA
* **
1745164 TATTTAATTTCAATTAATAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAACATGATT
1 TATTAAATTTCAATTAATAAATATAGATTTAATTAATTTAAAATAATAAAAAACCTAACATGATT
1745229 AGGGTAACCTGGATATAAAAGGAT
66 AGGGTAACCTGGATATAAAAGGAT
*
1745253 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAAACCTAATATGAT
1 TATTAAATTTCAATTAA-TAAATATAGATTTAATTAATTTAAAATAATAAAAAACCTAACATGAT
* *
1745318 TAGGGTAACTTGGCTATAAAAGG
65 TAGGGTAACCTGGATATAAAAGG
1745341 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 16 0.20
90 65 0.80
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (89 bp):
TATTAAATTTCAATTAATAAATATAGATTTAATTAATTTAAAATAATAAAAAACCTAACATGATT
AGGGTAACCTGGATATAAAAGGAT
Found at i:1745851 original size:31 final size:31
Alignment explanation
Indices: 1745813--1745923 Score: 195
Period size: 31 Copynumber: 3.5 Consensus size: 31
1745803 AGGTTCGAGG
*
1745813 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1745844 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1745875 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1745906 GATTTACCTAGGTTCTTC
1 G-TTTACCTATGTTCTTC
1745924 AGAATCTATG
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 62 0.81
32 15 0.19
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1748441 original size:3 final size:3
Alignment explanation
Indices: 1748433--1748488 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
1748423 AATTTTTTCA
* *
1748433 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1748481 TAT TAT TA
1 TAT TAT TA
1748489 AATATATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1749210 original size:23 final size:22
Alignment explanation
Indices: 1749184--1749247 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
1749174 CAGCTCATAT
1749184 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
1749207 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
1749230 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
1749248 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:1749432 original size:102 final size:103
Alignment explanation
Indices: 1749267--1749582 Score: 564
Period size: 103 Copynumber: 3.1 Consensus size: 103
1749257 GTCCATAAGG
*
1749267 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
*
1749332 TCACACATATTCCAAAGAATACATATATGTCCCGAAGT
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGT
1749370 ACCACATATCATTCCTTAAGAAT-ATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
*
1749434 TCACACATGTTCCAAAGAATACATATATATCCCGAA-T
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGT
1749471 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1 -ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
* *
1749536 CTCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
65 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAGT
1749575 ACCACATA
1 ACCACATA
1749583 GACCCTCTAC
Statistics
Matches: 204, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
101 1 0.00
102 97 0.48
103 106 0.52
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGT
Found at i:1750101 original size:19 final size:20
Alignment explanation
Indices: 1750064--1750101 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1750054 TTTTTTATTA
*
1750064 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1750084 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1750102 TATAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1750145 original size:19 final size:19
Alignment explanation
Indices: 1750123--1750166 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1750113 GGAAATTCAT
* *
1750123 ATTCGTTGAGGGGGTATCG
1 ATTCCTTGAAGGGGTATCG
*
1750142 ATTCCCTTGAATGGGTATCG
1 ATT-CCTTGAAGGGGTATCG
1750162 ATTCC
1 ATTCC
1750167 CTAGCCCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (19 bp):
ATTCCTTGAAGGGGTATCG
Found at i:1756239 original size:23 final size:23
Alignment explanation
Indices: 1756213--1756276 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1756203 CAGCTCATAT
*
1756213 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1756236 AATTGCATCGGAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1756259 AATTGCATCGGAGTGCCA
1 AATTGCACCGAAGTGCCA
1756277 TATAATAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1756421 original size:103 final size:103
Alignment explanation
Indices: 1756292--1756612 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
1756282 TAATGTCCAT
*
1756292 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1756357 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1756395 AAGAACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1756460 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1756498 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1756563 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1756601 AAGGACCACATA
1 AAGGACCACATA
1756613 GACCCTCTAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1757182 original size:21 final size:21
Alignment explanation
Indices: 1757158--1757197 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1757148 TCATATTCGT
*
1757158 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
1757179 TTGAATGGGTATCGATTCC
1 TTGAAGGGGTATCGATTCC
1757198 TCTAGCCCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:1759237 original size:17 final size:17
Alignment explanation
Indices: 1759211--1759244 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1759201 TTCAGTCACT
1759211 ATTTATTTA-TATTTTA
1 ATTTATTTATTATTTTA
1759227 ATTTAATTTATTATTTTA
1 ATTT-ATTTATTATTTTA
1759245 TATGTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTATTTATTATTTTA
Found at i:1759478 original size:19 final size:20
Alignment explanation
Indices: 1759438--1759480 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1759428 GATATTTCTA
*
1759438 AATAAATAAATATATTGTTT
1 AATAAATAAATATATTGATT
1759458 AATAAA-AAATATATAT-ATT
1 AATAAATAAATATAT-TGATT
1759477 AATA
1 AATA
1759481 TATTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATAAATAAATATATTGATT
Found at i:1762239 original size:15 final size:14
Alignment explanation
Indices: 1762198--1762238 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1762188 ATTTTAAATA
1762198 ATTTACATTTTTGC
1 ATTTACATTTTTGC
1762212 ATTTATGCA-TTTTGC
1 ATTTA--CATTTTTGC
1762227 ATTTACATTTTT
1 ATTTACATTTTT
1762239 TTATTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (14 bp):
ATTTACATTTTTGC
Found at i:1768946 original size:46 final size:46
Alignment explanation
Indices: 1768894--1769769 Score: 1444
Period size: 46 Copynumber: 19.2 Consensus size: 46
1768884 GGGAGATTTT
* *
1768894 TGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1768940 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
1768985 TGATGTTTTCAAAAACCTTTGGGTCATCTGTAAGTCCTTTAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
1769031 TGATGTTATC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1769076 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
1769122 TGATGTTATC-AAAACCTTCGGGTCATCTGTAAGTCCTTTAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
1769167 TGATGTTATC-AAAACCTTCGGTTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
1769212 TGATGTTATC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
1769257 TGATGTTATC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
1769302 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1769348 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1769394 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* * *
1769440 TGATGTTATC-AAAATCTTCAGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* * *
1769485 TGATGTTATC-AAAACCTTCGGGTCATCTGTAAGTCTTTTAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
1769530 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
1769576 TGATGTTTTCAAAACCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
1769622 TGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTC-AAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
1769669 TGATGTTTTCAAAACCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* * *
1769715 TGATGTTTTCAAAACCCTTCGGGTCACCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1769761 TGATGTTTT
1 TGATGTTTT
1769770 AAACATTTCC
Statistics
Matches: 794, Mismatches: 31, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
45 343 0.43
46 406 0.51
47 45 0.06
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (46 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:1769049 original size:91 final size:91
Alignment explanation
Indices: 1768894--1769769 Score: 1461
Period size: 91 Copynumber: 9.6 Consensus size: 91
1768884 GGGAGATTTT
* *
1768894 TGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC
1768959 GGGTCATCTGTAAGTCCTTCAGTGCA
66 GGGTCATCTGTAAGTCCTTCAGTGCA
* * *
1768985 TGATGTTTTCAAAAACCTTTGGGTCATCTGTAAGTCCTTTAGTGCATGATGTTATCAAAACCTTC
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC
1769050 GGGTCATCTGTAAGTCCTTCAGTGCA
66 GGGTCATCTGTAAGTCCTTCAGTGCA
*
1769076 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAACCTTC
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC
*
1769141 GGGTCATCTGTAAGTCCTTTAGTGCA
66 GGGTCATCTGTAAGTCCTTCAGTGCA
* * *
1769167 TGATGTTATC-AAAACCTTCGGTTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAACCTTC
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC
1769231 GGGTCATCTGTAAGTCCTTCAGTGCA
66 GGGTCATCTGTAAGTCCTTCAGTGCA
*
1769257 TGATGTTATC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTT
*
1769321 CGGGTCATCTGTAAGCCCTTCAGTGCA
65 CGGGTCATCTGTAAGTCCTTCAGTGCA
1769348 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTT
1769413 CGGGTCATCTGTAAGTCCTTCAGTGCA
65 CGGGTCATCTGTAAGTCCTTCAGTGCA
* * * *
1769440 TGATGTTATC-AAAATCTTCAGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAACCTTC
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC
* *
1769504 GGGTCATCTGTAAGTCTTTTAGTGCA
66 GGGTCATCTGTAAGTCCTTCAGTGCA
*
1769530 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA-CCTT
*
1769595 CGGGTCATCTGTAAGCCCTTCAGTGCA
65 CGGGTCATCTGTAAGTCCTTCAGTGCA
*
1769622 TGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCCT
1 TGATGTTTTC-AAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA-CCT
*
1769687 TCGGGTCATCTGTAAGCCCTTCAGTGCA
64 TCGGGTCATCTGTAAGTCCTTCAGTGCA
* * *
1769715 TGATGTTTTCAAAACCCTTCGGGTCACCTGTAAGCCCTTCAGTGCATGATGTTTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
1769770 AAACATTTCC
Statistics
Matches: 748, Mismatches: 32, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
90 173 0.23
91 313 0.42
92 170 0.23
93 92 0.12
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (91 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC
GGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:1769932 original size:2 final size:2
Alignment explanation
Indices: 1769925--1769949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1769915 TTATTATTAA
1769925 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 A
1769950 CAAGGCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1771346 original size:17 final size:17
Alignment explanation
Indices: 1771320--1771353 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1771310 TTCAGTCACT
1771320 ATTTATTTA-TATTTTA
1 ATTTATTTATTATTTTA
1771336 ATTTAATTTATTATTTTA
1 ATTT-ATTTATTATTTTA
1771354 TATGTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTATTTATTATTTTA
Found at i:1774947 original size:26 final size:26
Alignment explanation
Indices: 1774876--1774948 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
1774866 TTAAAACGAT
*
1774876 ATAATAAAAAAATTAAAAAAC-AGTAA
1 ATAAT-AAAAAATTAACAAACAAGTAA
* *
1774902 ATAATAAAAACATT--CGAACAATTAA
1 ATAATAAAAA-ATTAACAAACAAGTAA
*
1774927 GTAATAAAAAATTAACAAACAA
1 ATAATAAAAAATTAACAAACAA
1774949 AATAAATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
24 6 0.16
25 18 0.47
26 14 0.37
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (26 bp):
ATAATAAAAAATTAACAAACAAGTAA
Found at i:1774967 original size:17 final size:16
Alignment explanation
Indices: 1774921--1774968 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
1774911 ACATTCGAAC
1774921 AATTAAGTAAT-AAAA
1 AATTAAGTAATAAAAA
** *
1774936 AATTAACAAACAAAATA
1 AATTAAGTAATAAAA-A
1774953 AATTAAGTAATAAAAA
1 AATTAAGTAATAAAAA
1774969 GTAAATAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
15 8 0.32
16 4 0.16
17 13 0.52
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (16 bp):
AATTAAGTAATAAAAA
Found at i:1777321 original size:26 final size:25
Alignment explanation
Indices: 1777242--1777340 Score: 73
Period size: 26 Copynumber: 3.9 Consensus size: 25
1777232 TAACTTTTAT
*
1777242 TAATAATAT-ATTA-TATATTATTAAAA
1 TAATAATATAATTAGTATATTATT---G
*
1777268 TAAGAATATAA-TAGTATCA-TATAT-
1 TAATAATATAATTAGTAT-ATTAT-TG
1777292 TAATAATATAATTGAGTATATTATTG
1 TAATAATATAATT-AGTATATTATTG
* *
1777318 TAATAATATTATTATTATATTAT
1 TAATAATATAATTAGTATATTAT
1777341 ATTATTAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
24 10 0.16
25 12 0.20
26 30 0.49
27 7 0.11
28 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (25 bp):
TAATAATATAATTAGTATATTATTG
Found at i:1780654 original size:51 final size:51
Alignment explanation
Indices: 1780599--1780761 Score: 168
Period size: 51 Copynumber: 3.0 Consensus size: 51
1780589 TGAGGCTTAG
1780599 TCACTCACTAATTTAAGATTTTGGTTACATTCTTATAAAAATAATATACAA
1 TCACTCACTAATTTAAGATTTTGGTTACATTCTTATAAAAATAATATACAA
** *
1780650 TCACTCACTAATTTAAGATTTTGGTTACATTAGACCTT-TGGAAACAA-AGGATGAGGCTTAG
1 TCACTCACTAATTTAAGATTTTGGTTACATT----CTTAT--AAA-AATA--AT-ATAC--AA
*
1780711 TCACTCACTAATGTAAGATTTTGGTTACATTCTTATAAAAATAATATACAA
1 TCACTCACTAATTTAAGATTTTGGTTACATTCTTATAAAAATAATATACAA
1780762 ATATATTCTT
Statistics
Matches: 91, Mismatches: 7, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
51 32 0.35
53 2 0.02
54 3 0.03
55 5 0.05
56 8 0.09
57 5 0.05
58 3 0.03
59 2 0.02
61 31 0.34
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (51 bp):
TCACTCACTAATTTAAGATTTTGGTTACATTCTTATAAAAATAATATACAA
Found at i:1782666 original size:3 final size:3
Alignment explanation
Indices: 1782658--1782731 Score: 87
Period size: 3 Copynumber: 24.0 Consensus size: 3
1782648 TCGTTTTTGT
* *
1782658 TTA TTA TTA TTA TTA TT- TTA TTTA TTTA TTA CTA TTA TTA TTTA TTT
1 TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA -TTA TTA
*
1782705 TTA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1782732 CAAACAGGTC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 50 0.81
4 10 0.16
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1782676 original size:22 final size:21
Alignment explanation
Indices: 1782651--1782732 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 21
1782641 CTCCATTTCG
*
1782651 TTTTTGTTTATTATTATTATTA
1 TTTTT-TTTATTACTATTATTA
1782673 TTTTATTTATTTATTACTATTATTA
1 --TT-TTT-TTTATTACTATTATTA
1782698 TTTATTTTTATTACTATTATTA
1 TTT-TTTTTATTACTATTATTA
* *
1782720 TTATTATTATTAC
1 TTTTTTTTATTAC
1782733 AAACAGGTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.17
22 19 0.37
23 4 0.08
24 2 0.04
25 18 0.35
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (21 bp):
TTTTTTTTATTACTATTATTA
Found at i:1782685 original size:25 final size:26
Alignment explanation
Indices: 1782657--1782727 Score: 99
Period size: 25 Copynumber: 2.7 Consensus size: 26
1782647 TTCGTTTTTG
1782657 TTTATTATTATTATTATTT-TATTTA
1 TTTATTATTATTATTATTTATATTTA
* *
1782682 TTTATTACTATTATTATTTATTTTTA
1 TTTATTATTATTATTATTTATATTTA
1782708 TTACTATTATTATTATTATT
1 TT--TATTATTATTATTATT
1782728 ATTACAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 18 0.45
26 7 0.17
28 15 0.38
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTATTATTATTATTATTTATATTTA
Found at i:1783916 original size:28 final size:26
Alignment explanation
Indices: 1783885--1783947 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
1783875 TTTAATACTA
1783885 TAGTTTTAATTTT-ATTTTAGTCACTGTT
1 TAGTTTTAATTTTAATTTTA-T-A-TGTT
*
1783913 TAGTTAT-ATTTTAATTTTATATGTT
1 TAGTTTTAATTTTAATTTTATATGTT
*
1783938 TATTTTTAAT
1 TAGTTTTAAT
1783948 ATATTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 9 0.30
26 3 0.10
27 6 0.20
28 12 0.40
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.63
Consensus pattern (26 bp):
TAGTTTTAATTTTAATTTTATATGTT
Found at i:1783954 original size:15 final size:14
Alignment explanation
Indices: 1783916--1783966 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1783906 CACTGTTTAG
1783916 TTATAT-TTTAATT
1 TTATATATTTAATT
* *
1783929 TTATATGTTTATTT
1 TTATATATTTAATT
1783943 TTAATATATTTAATT
1 TT-ATATATTTAATT
1783958 ATTAT-TATT
1 -TTATATATT
1783967 ATTATTATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 6 0.19
14 12 0.38
15 12 0.38
16 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:1784093 original size:16 final size:15
Alignment explanation
Indices: 1784070--1784102 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1784060 TTTAATCCTA
1784070 TTTATA-AAATTAAT
1 TTTATATAAATTAAT
*
1784084 TTTATATAAATTACT
1 TTTATATAAATTAAT
1784099 TTTA
1 TTTA
1784103 GGAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATAAATTAAT
Found at i:1788222 original size:15 final size:15
Alignment explanation
Indices: 1788202--1788233 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1788192 GATCAATACC
1788202 TTTTGCATACATTCA
1 TTTTGCATACATTCA
1788217 TTTTGCATACATTCA
1 TTTTGCATACATTCA
1788232 TT
1 TT
1788234 GCATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:1789894 original size:18 final size:18
Alignment explanation
Indices: 1789850--1789909 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
1789840 ATAATACTAC
1789850 TAATAATAATTATAATTTTA
1 TAATAATAATTATAA--TTA
** *
1789870 TTGTAATAATTATGATTA
1 TAATAATAATTATAATTA
*
1789888 TAATAATAATTATTATTA
1 TAATAATAATTATAATTA
1789906 TAAT
1 TAAT
1789910 GTAATATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 22 0.65
20 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATAATAATTATAATTA
Found at i:1790967 original size:15 final size:15
Alignment explanation
Indices: 1790947--1790978 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1790937 AAAATAATAC
1790947 AATGAATGTATACAA
1 AATGAATGTATACAA
*
1790962 AATGAATGTATGCAA
1 AATGAATGTATACAA
1790977 AA
1 AA
1790979 GGTTTTGATC
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:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AATGAATGTATACAA
Found at i:1795870 original size:3 final size:3
Alignment explanation
Indices: 1795849--1795904 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
1795839 TATGCTTGAC
* *
1795849 GAA GAA AAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1795897 GAA -AA GAA
1 GAA GAA GAA
1795905 AACAAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1796302 original size:18 final size:18
Alignment explanation
Indices: 1796275--1796311 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1796265 CAAGTTTATC
*
1796275 TTTTCGAAATTCAATTTA
1 TTTTCAAAATTCAATTTA
1796293 TTTTCAAAATTCAATTTA
1 TTTTCAAAATTCAATTTA
1796311 T
1 T
1796312 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTCAAAATTCAATTTA
Found at i:1797552 original size:123 final size:123
Alignment explanation
Indices: 1797326--1797900 Score: 935
Period size: 123 Copynumber: 4.7 Consensus size: 123
1797316 CACTCGATGG
*
1797326 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGACGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* *
1797391 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTATATCACAGAAGGAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* * * *
1797449 ATAAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTGTCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
1797514 ATGAGAAGATCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
*
1797572 ATCAACTTTTCCAGAGAATGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
1797637 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTTTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
*
1797695 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAACAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
1797760 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAAATAGATCAGC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* * *
1797818 ATCAA-TATTTCC-G-GAAGAGTTCATAATGATAAGAACTCATCT-AAGAAGG-AGAAGAATTTC
1 ATCAACT-TTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTC
**
1797878 ATAATGAGAAGAATTTGTTCAAC
63 ATAATGAGAAGAGCTTGTTCAAC
1797901 TTTGCCTTAA
Statistics
Matches: 424, Mismatches: 25, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
121 36 0.08
122 28 0.07
123 360 0.85
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:1798282 original size:3 final size:3
Alignment explanation
Indices: 1798274--1798361 Score: 94
Period size: 3 Copynumber: 30.0 Consensus size: 3
1798264 TTTTTGTTTT
*
1798274 TTA TTA TTA TTA TT- TTA TT- TGT- TTA TTA CTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* * *
1798316 TTA TTA TTA TTTA TTT TTA TTA CTA TTA TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1798362 ATACAAACAA
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
2 6 0.08
3 63 0.88
4 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1798289 original size:22 final size:22
Alignment explanation
Indices: 1798265--1798314 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1798255 TCATTTCGCT
* *
1798265 TTTTGTTT-TTTATTATTATTA
1 TTTTATTTGTTTATTACTATTA
1798286 TTTTATTTGTTTATTACTATTA
1 TTTTATTTGTTTATTACTATTA
1798308 TTATTAT
1 TT-TTAT
1798315 ATTATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
22 14 0.56
23 4 0.16
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTTATTTGTTTATTACTATTA
Found at i:1798294 original size:25 final size:25
Alignment explanation
Indices: 1798266--1798361 Score: 85
Period size: 25 Copynumber: 3.9 Consensus size: 25
1798256 CATTTCGCTT
* * *
1798266 TTTGTTTTTTATTATTATTATTTTA
1 TTTGTTTATTACTATTATTATTATA
1798291 TTTGTTTATTACTATTATTATTATA
1 TTTGTTTATTACTATTATTATTATA
*
1798316 TTAT-TATTATT--TATTTTTATTACTA
1 TT-TGT-TTATTACTATTATTATTA-TA
*
1798341 -TT-ATTATTACTATTATTATTA
1 TTTGTTTATTACTATTATTATTA
1798362 ATACAAACAA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.08
23 1 0.02
24 21 0.35
25 27 0.45
26 6 0.10
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTGTTTATTACTATTATTATTATA
Found at i:1798320 original size:36 final size:37
Alignment explanation
Indices: 1798275--1798361 Score: 140
Period size: 36 Copynumber: 2.3 Consensus size: 37
1798265 TTTTGTTTTT
1798275 TATTATTATTATTTTATTTGTTTATTACTATTATTATTA-
1 TATTATTATTA-TTTA-TT-TTTATTACTATTATTATTAC
1798314 TATTATTATTATTTATTTTTATTACTATTATTATTAC
1 TATTATTATTATTTATTTTTATTACTATTATTATTAC
1798351 TATTATTATTA
1 TATTATTATTA
1798362 ATACAAACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
36 19 0.40
37 13 0.28
38 4 0.09
39 11 0.23
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (37 bp):
TATTATTATTATTTATTTTTATTACTATTATTATTAC
Found at i:1798346 original size:39 final size:40
Alignment explanation
Indices: 1798274--1798361 Score: 117
Period size: 39 Copynumber: 2.2 Consensus size: 40
1798264 TTTTTGTTTT
* *
1798274 TTATTATTATTATTTTATTTGTTTATTACTATTATTATTA
1 TTATTATTATTATTTTATTTGTTTACTACTATTATTACTA
* *
1798314 -TATTATTATTA-TTTATTTTTATTACTATTATTATTACTA
1 TTATTATTATTATTTTATTTGT-TTACTACTATTATTACTA
1798353 TTATTATTA
1 TTATTATTA
1798362 ATACAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 8 0.19
39 26 0.62
40 8 0.19
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (40 bp):
TTATTATTATTATTTTATTTGTTTACTACTATTATTACTA
Found at i:1799778 original size:13 final size:13
Alignment explanation
Indices: 1799743--1799793 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1799733 CACTGTTTAG
*
1799743 TTATATTTTA-AT
1 TTATATTTTATTT
1799755 TTATATGTTTATTT
1 TTATAT-TTTATTT
*
1799769 TTATATTTTATTA
1 TTATATTTTATTT
1799782 TTATATTATTAT
1 TTATATT-TTAT
1799794 GTAGTCATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 6 0.18
13 17 0.50
14 11 0.32
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTATATTTTATTT
Found at i:1799848 original size:19 final size:19
Alignment explanation
Indices: 1799800--1799850 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1799790 TTATGTAGTC
*
1799800 ATATAATATATAAATATAT
1 ATATAATATATAAATACAT
* *
1799819 -TTTAGTCATATAAATACAT
1 ATATAAT-ATATAAATACAT
1799838 ATATAATATATAA
1 ATATAATATATAA
1799851 TATTTATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATAATATATAAATACAT
Found at i:1801036 original size:17 final size:17
Alignment explanation
Indices: 1800958--1801040 Score: 53
Period size: 17 Copynumber: 4.9 Consensus size: 17
1800948 GCATTTAAAT
*
1800958 CATCTAGTTCATTTAGG
1 CATCTAGTTCATTTATG
* ** *
1800975 GAAGTTGTTCATTTATG
1 CATCTAGTTCATTTATG
*
1800992 CATTTAGATT-ATTTA-G
1 CATCTAG-TTCATTTATG
* * *
1801008 TAAGCTACTTCATTTATG
1 -CATCTAGTTCATTTATG
1801026 CATCTAGTTCATTTA
1 CATCTAGTTCATTTA
1801041 ATAAAGTTAG
Statistics
Matches: 46, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
16 3 0.07
17 40 0.87
18 3 0.07
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (17 bp):
CATCTAGTTCATTTATG
Found at i:1801040 original size:34 final size:34
Alignment explanation
Indices: 1800958--1801040 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
1800948 GCATTTAAAT
**
1800958 CATCTAGTTCATTTAGGGAAGTTGTTCATTTATG
1 CATCTAGTTCATTTAGGGAAGTACTTCATTTATG
* *
1800992 CATTTAGATT-ATTTA-GTAAGCTACTTCATTTATG
1 CATCTAG-TTCATTTAGGGAAG-TACTTCATTTATG
1801026 CATCTAGTTCATTTA
1 CATCTAGTTCATTTA
1801041 ATAAAGTTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
33 6 0.15
34 33 0.80
35 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (34 bp):
CATCTAGTTCATTTAGGGAAGTACTTCATTTATG
Found at i:1801072 original size:17 final size:17
Alignment explanation
Indices: 1801029--1801100 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
1801019 ATTTATGCAT
1801029 CTAGTTCATTTAA-TAAA
1 CTAGTTCA-TTAATTAAA
* *
1801046 GTTAGCTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
1801064 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
1801081 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
1801098 CTA
1 CTA
1801101 ACTCTTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
17 35 0.78
18 10 0.22
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1802642 original size:20 final size:20
Alignment explanation
Indices: 1802601--1802654 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1802591 CCGGGTTAGT
* *
1802601 AAAAAAATTAAAAAAATCAG
1 AAAAAAATGAAAAAAATAAG
1802621 AAAAAAATCGAAAAAAA-AAG
1 AAAAAAAT-GAAAAAAATAAG
*
1802641 AAAAGAAAAGAAAA
1 AAAA-AAATGAAAA
1802655 TTTTAAAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07
Consensus pattern (20 bp):
AAAAAAATGAAAAAAATAAG
Found at i:1808204 original size:29 final size:29
Alignment explanation
Indices: 1808170--1808228 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1808160 CCTAAATTAA
1808170 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1808199 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1808228 T
1 T
1808229 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1820369 original size:16 final size:15
Alignment explanation
Indices: 1820322--1820361 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
1820312 CGAGACAGTG
1820322 CTGAAACATCAAATAC
1 CTGAAAC-TCAAATAC
*
1820338 CTGAAGACCCAAATAC
1 CTGAA-ACTCAAATAC
1820354 CTGAAACT
1 CTGAAACT
1820362 TCATATACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 17 0.81
17 2 0.10
ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17
Consensus pattern (15 bp):
CTGAAACTCAAATAC
Found at i:1820898 original size:60 final size:59
Alignment explanation
Indices: 1820833--1821010 Score: 189
Period size: 60 Copynumber: 3.0 Consensus size: 59
1820823 TACATGTTTA
* * *
1820833 GATGAAATTGGAATATTCAAAAGTTTGGGAACTAATTTAGAAAGAGGGTTATAGTTTAGG
1 GATGAAATTAGAATATTCAAAAGTTTAGGAACTAATTTA-AAAGAGAGTTATAGTTTAGG
* * * * *
1820893 GATGAAATTAGAATGTTCAAAATTTTAAGG-ATTAATTTAAAATGTGAGTCA-AGGTTTAGG
1 GATGAAATTAGAATATTCAAAAGTTT-AGGAACTAATTTAAAA-GAGAGTTATA-GTTTAGG
* ** * *
1820953 GATGAAATTAAAATATTCAAAAGTTTAAAAACTAATTTAAATGAAAGTTATAGTTTAG
1 GATGAAATTAGAATATTCAAAAGTTTAGGAACTAATTTAAAAGAGAGTTATAGTTTAG
1821011 AGACATATTA
Statistics
Matches: 95, Mismatches: 18, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
59 16 0.17
60 77 0.81
61 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (59 bp):
GATGAAATTAGAATATTCAAAAGTTTAGGAACTAATTTAAAAGAGAGTTATAGTTTAGG
Found at i:1820964 original size:31 final size:29
Alignment explanation
Indices: 1820885--1820979 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
1820875 AGAGGGTTAT
*
1820885 AGTTTAGGGATGAAATTAGAATGTTCAAA
1 AGTTTAGGGATGAAATTAAAATGTTCAAA
* * * *
1820914 ATTTTAAGGATTAATTTAAAATGTGAGTC-AA
1 AGTTTAGGGATGAAATTAAAATGT---TCAAA
* *
1820945 GGTTTAGGGATGAAATTAAAATATTCAAA
1 AGTTTAGGGATGAAATTAAAATGTTCAAA
1820974 AGTTTA
1 AGTTTA
1820980 AAAACTAATT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
28 2 0.04
29 26 0.52
31 20 0.40
32 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (29 bp):
AGTTTAGGGATGAAATTAAAATGTTCAAA
Found at i:1822519 original size:15 final size:15
Alignment explanation
Indices: 1822499--1822528 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1822489 ACCAGTTTAG
*
1822499 AGCAAAGGGCAAGCT
1 AGCAAAGAGCAAGCT
1822514 AGCAAAGAGCAAGCT
1 AGCAAAGAGCAAGCT
1822529 TACAGTTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.30, T:0.07
Consensus pattern (15 bp):
AGCAAAGAGCAAGCT
Found at i:1835731 original size:21 final size:21
Alignment explanation
Indices: 1835706--1835749 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1835696 CGGAATATTA
*
1835706 AAAAACATTAATATTTTAGGT
1 AAAAACAATAATATTTTAGGT
*
1835727 AAAAATAATAATATTTTAGGT
1 AAAAACAATAATATTTTAGGT
1835748 AA
1 AA
1835750 TTTTTACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (21 bp):
AAAAACAATAATATTTTAGGT
Found at i:1838498 original size:14 final size:14
Alignment explanation
Indices: 1838479--1838507 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1838469 GGAAATGTCC
1838479 ATGCTGCGGTCGAG
1 ATGCTGCGGTCGAG
1838493 ATGCTGCGGTCGAG
1 ATGCTGCGGTCGAG
1838507 A
1 A
1838508 GACTTCGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.21, G:0.41, T:0.21
Consensus pattern (14 bp):
ATGCTGCGGTCGAG
Found at i:1839676 original size:20 final size:21
Alignment explanation
Indices: 1839615--1839687 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 21
1839605 ATATAGAATT
* *
1839615 TGTCCCGAAGGACCACGTAGAAA
1 TGTCCCGACGGACCACATAG--A
* * *
1839638 TATCCCGAAGGACCACATATA
1 TGTCCCGACGGACCACATAGA
1839659 TGTCCCGACGGA-CACATAGA
1 TGTCCCGACGGACCACATAGA
1839679 TGTCCCGAC
1 TGTCCCGAC
1839688 TCTCAAACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.36
21 11 0.25
23 17 0.39
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.16
Consensus pattern (21 bp):
TGTCCCGACGGACCACATAGA
Found at i:1842840 original size:13 final size:13
Alignment explanation
Indices: 1842806--1842844 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1842796 GTGACCACCA
1842806 ATAGATATTTTTT
1 ATAGATATTTTTT
* *
1842819 AAATCATATTTTTT
1 ATA-GATATTTTTT
1842833 ATAGATATTTTT
1 ATAGATATTTTT
1842845 GATTGATCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (13 bp):
ATAGATATTTTTT
Found at i:1848574 original size:19 final size:19
Alignment explanation
Indices: 1848535--1848574 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1848525 ACGTGACCTT
*
1848535 CACACTAGCATAAAATTTC
1 CACACTAGCATAAAATGTC
* *
1848554 CACATTAGCATAAACTGTC
1 CACACTAGCATAAAATGTC
1848573 CA
1 CA
1848575 TATCACTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (19 bp):
CACACTAGCATAAAATGTC
Found at i:1849966 original size:137 final size:136
Alignment explanation
Indices: 1849718--1850003 Score: 448
Period size: 137 Copynumber: 2.1 Consensus size: 136
1849708 GTGAAAAAAT
* *
1849718 AAAATAAAAATTGAAGTTACATAGGTATTCTACAGTGGCATATGACAAGTGGTTCAAATTTGATA
1 AAAATAAAAACTGAAGTTACATAGGTATTCTACAGTGGCATATGACAACTGGTTCAAATTTGAT-
* * *
1849783 AAAAAAAGAACTTGAAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAATTGAAGAACT
65 AAAAAAAGAACTTGAAATAAAGGATGAATTGAAAAAATAAGAAAATTATGAAAAATTGAAGAACT
* *
1849848 AAATTGA
130 AAAGTAA
*
1849855 AAAATAGAAAACTGAAGTTACATAGGTATTCTATAGTGGCATATGAGCAACTGGTTCAAATTTGA
1 AAAATA-AAAACTGAAGTTACATAGGTATTCTACAGTGGCATATGA-CAACTGGTTCAAATTTGA
* *
1849920 T-AAAAATGAACTTGAAATAAAGGATGAATTGAAAAAATAAGAAAATTATGAAAAATTGAAGGAC
64 TAAAAAAAGAACTTGAAATAAAGGATGAATTGAAAAAATAAGAAAATTATGAAAAATTGAAGAAC
1849984 TAAAGTAA
129 TAAAGTAA
1849992 AAAATAAAAACT
1 AAAATAAAAACT
1850004 TGTTATCGAA
Statistics
Matches: 137, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
136 6 0.04
137 76 0.55
138 37 0.27
139 18 0.13
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (136 bp):
AAAATAAAAACTGAAGTTACATAGGTATTCTACAGTGGCATATGACAACTGGTTCAAATTTGATA
AAAAAAGAACTTGAAATAAAGGATGAATTGAAAAAATAAGAAAATTATGAAAAATTGAAGAACTA
AAGTAA
Found at i:1850402 original size:2 final size:2
Alignment explanation
Indices: 1850395--1850433 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1850385 ACATATTACA
1850395 AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1850434 TTAACTCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1850421 original size:24 final size:23
Alignment explanation
Indices: 1850387--1850433 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
1850377 CTGATGTTAC
1850387 ATATTACAATATATATATATATAT
1 ATATTACAATATATATAT-TATAT
*
1850411 ATATTATAATATATATATTATAT
1 ATATTACAATATATATATTATAT
1850434 TTAACTCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTACAATATATATATTATAT
Found at i:1857447 original size:23 final size:20
Alignment explanation
Indices: 1857410--1857462 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
1857400 CGGTTCAACC
1857410 TAAATTTTTT-GATTTTTTAT
1 TAAATTTTTTAGA-TTTTTAT
1857430 TAAATGTTTTTAGTATTTTTAT
1 TAAAT-TTTTTAG-ATTTTTAT
*
1857452 TTAATTTTTTA
1 TAAATTTTTTA
1857463 AATAATTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 11 0.38
22 12 0.41
23 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (20 bp):
TAAATTTTTTAGATTTTTAT
Found at i:1859646 original size:3 final size:3
Alignment explanation
Indices: 1859640--1859708 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
1859630 TTTTCATTTG
1859640 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1859688 ATT ATT ATT ATT A-T ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
1859709 CTAACTAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1866936 original size:45 final size:45
Alignment explanation
Indices: 1866872--1866961 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1866862 CTGAGATTAA
1866872 ATCTCCTTTTGGTTGGATATTTCAACAACTCTCCTTATCCGGTAT
1 ATCTCCTTTTGGTTGGATATTTCAACAACTCTCCTTATCCGGTAT
1866917 ATCTCCTTTTGGTTGGATATTTCAACAACTCTCCTTATCCGGTAT
1 ATCTCCTTTTGGTTGGATATTTCAACAACTCTCCTTATCCGGTAT
1866962 GATTCCACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.42
Consensus pattern (45 bp):
ATCTCCTTTTGGTTGGATATTTCAACAACTCTCCTTATCCGGTAT
Found at i:1868984 original size:17 final size:16
Alignment explanation
Indices: 1868962--1868996 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1868952 ACAATCATTC
*
1868962 TTTACATTCTTTATATT
1 TTTACATTCATTAT-TT
1868979 TTTACATTCATTATTT
1 TTTACATTCATTATTT
1868995 TT
1 TT
1868997 CATTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTACATTCATTATTT
Found at i:1870383 original size:59 final size:61
Alignment explanation
Indices: 1870319--1870438 Score: 226
Period size: 59 Copynumber: 2.0 Consensus size: 61
1870309 TCACCAGCTT
1870319 TGACAGGCAAAATGGCTAGATGGCAGATGTTATTATCCGAG-TTGATA-TGTATATGTCAA
1 TGACAGGCAAAATGGCTAGATGGCAGATGTTATTATCCGAGTTTGATATTGTATATGTCAA
1870378 TGACAGGCAAAATGGCTAGATGGCAGATGTTATTATCCGAGTTTGATATTGTATATGTCAA
1 TGACAGGCAAAATGGCTAGATGGCAGATGTTATTATCCGAGTTTGATATTGTATATGTCAA
1870439 CCAAAAGCAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 41 0.69
60 6 0.10
61 12 0.20
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (61 bp):
TGACAGGCAAAATGGCTAGATGGCAGATGTTATTATCCGAGTTTGATATTGTATATGTCAA
Found at i:1871257 original size:30 final size:30
Alignment explanation
Indices: 1871221--1871280 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1871211 TGTTTAGATA
1871221 CTAGCGAAGCCAGAATCATCATTGAGGAAG
1 CTAGCGAAGCCAGAATCATCATTGAGGAAG
1871251 CTAGCGAAGCCAGAATCATCATTGAGGAAG
1 CTAGCGAAGCCAGAATCATCATTGAGGAAG
1871281 TCCATAGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (30 bp):
CTAGCGAAGCCAGAATCATCATTGAGGAAG
Found at i:1872350 original size:9 final size:10
Alignment explanation
Indices: 1872335--1872390 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
1872325 GCTTGAAGGA
1872335 AAAAAAAAAT
1 AAAAAAAAAT
1872345 AAAAAAAAAT
1 AAAAAAAAAT
1872355 AAAAAAAATGAT
1 AAAAAAAA--AT
* ** *
1872367 GATGAAAAAG
1 AAAAAAAAAT
1872377 AAAAAAAAAT
1 AAAAAAAAAT
1872387 AAAA
1 AAAA
1872391 TAGAAAATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 29 0.81
12 7 0.19
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:1874113 original size:113 final size:113
Alignment explanation
Indices: 1873913--1874723 Score: 688
Period size: 113 Copynumber: 7.0 Consensus size: 113
1873903 TACCAAAGAT
* * *
1873913 TCGAATCCATCATTCGATG-GATCAACATTT-CTG-GAAGAGTTCATAATGAGAAGAACTCATAT
1 TCGAATCCATCATTTGA-GAGATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCT
* * * * *
1873975 GAAAAAGGAAAAAGAAGTTCATAATGTGAAGAACTTGTTTAACCTTTTAC
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTAAACCTTTTAC
* ** ** * *
1874025 TCAAATCCATCACTTTTTG-GATCAACATTGACAGATAGAGTTCATAATGAGAAGAACTCATCTG
1 TCGAATCCATCA-TTTGAGAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * **
1874089 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTCTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT-AAACCTTTTAC
* * * * *
1874139 TTGAATTCATCATTCGAGAGATCAAC-TTTTCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCGAATCCATCATTTGAGAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* ** * *
1874203 AGAAGGAAGAAGAAGGTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTAAACCTTTTAC
* * ** *
1874251 AT-GACTCTATCA-CAGAAGGAGATATATCAACATCAACTTTTCCAGAGAAAGTTTATAATGAGA
1 -TCGAATCCATCATTTG-A-GAG----ATC-A-A-C-A--TTTCCAGAGAAAGTTCATAATGAGA
* * *
1874314 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTCTTGC
53 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT-AAACCTTTTAC
* * *
1874376 TTGAATTCATCATTTGAGAGATCAA-ATTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
1 TCGAATCCATCATTTGAGAGATCAACA-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * *
1874440 AAGAAGGAAGAAGAAGTTCATAATGAGAAAAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTAAACCTTTTAC
* * ***
1874489 AT-GACTCTATCACAGAAGGAGATAGATCATCATCAACTTTTCCAGAGAAAGTTCATAATGAGAA
1 -TCGAATCCAT--CA-TTTGAG--AGATCA--A-C-A--TTTCCAGAGAAAGTTCATAATGAGAA
* * **
1874553 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTCTTGT
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT-AAACCTTTTAC
* * * * * * * * *
1874614 TTGAATTCATCATTCGAGGGATTAACTTTTCTAGAGAAAATTCATAATAAGAAGAACTCATCTGA
1 TCGAATCCATCATTTGAGAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
1874679 AGAA-GAACAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTAAACCTTTT
1874724 GTATGATCTA
Statistics
Matches: 573, Mismatches: 90, Indels: 72
0.78 0.12 0.10
Matches are distributed among these distances:
111 1 0.00
112 45 0.08
113 178 0.31
114 136 0.24
115 3 0.01
116 3 0.01
117 4 0.01
118 9 0.02
119 2 0.00
120 9 0.02
122 3 0.01
123 3 0.01
124 146 0.25
125 30 0.05
126 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (113 bp):
TCGAATCCATCATTTGAGAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTAAACCTTTTAC
Found at i:1874315 original size:124 final size:122
Alignment explanation
Indices: 1874159--1874804 Score: 718
Period size: 124 Copynumber: 5.4 Consensus size: 122
1874149 CATTCGAGAG
*
1874159 ATCAACTTTT-CAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGGTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
** *
1874223 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATATATCAAC
66 AATGAGAAGAATTTGTTCAACCTTTTGCATGAATCTATCACAGAAGGAGATA-ATC-AC
* * *
1874282 ATCAACTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * **
1874347 AATGAGAAGAATTTGTTCAAACCTCTTGCTTGAAT-TCATCATTTG-A-GAG---AT--C
66 AATGAGAAGAATTTGTTC-AACCTTTTGCATGAATCT-ATCA-CAGAAGGAGATAATCAC
1874399 A--AA-TTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
1874461 AATGAGAAAAATTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATC
66 AATGAGAAGAATTTGTTCAACCTTTTGCATGAATCTATCACAGAAGGAGATA-ATCA-C
* *
1874520 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* **
1874585 AATGAGAAGAATTTGTTCAAACCTCTTGTTTGAAT-TCATCATTC-G-AGG-G---AT---
66 AATGAGAAGAATTTGTTC-AACCTTTTGCATGAATCT-ATCA--CAGAAGGAGATAATCAC
* * *
1874636 -T-AACTTTTCTAGAGAAAATTCATAATAAGAAGAACTCATCTGAAGAA-GAACAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * *
1874698 AATGAGAAGAGTTTGTTCAACCTTTTGTATG-ATCTATCACAAAAGGAGATAGATCAGT
66 AATGAGAAGAATTTGTTCAACCTTTTGCATGAATCTATCACAGAAGGAGATA-ATCA-C
** *
1874756 ATCAACATTTT-CAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 ATCAAC-TTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAG
1874805 AAGGAGCAAA
Statistics
Matches: 445, Mismatches: 41, Indels: 75
0.79 0.07 0.13
Matches are distributed among these distances:
109 1 0.00
111 9 0.02
112 14 0.03
113 48 0.11
114 120 0.27
115 3 0.01
116 2 0.00
117 2 0.00
118 2 0.00
120 4 0.01
121 32 0.07
122 6 0.01
123 16 0.04
124 146 0.33
125 37 0.08
126 2 0.00
127 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (122 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAATTTGTTCAACCTTTTGCATGAATCTATCACAGAAGGAGATAATCAC
Found at i:1874505 original size:238 final size:238
Alignment explanation
Indices: 1874063--1874804 Score: 1251
Period size: 238 Copynumber: 3.1 Consensus size: 238
1874053 TGACAGATAG
1874063 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1874128 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTT-CAGAGAAAGTTCATAATAAGAAG
66 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAG
* *
1874192 AACTCATCTGAAGAAGGAAGAAGAAGGTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACT
131 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCATGACT
*
1874257 CTATCACAGAAGGAGATATATCAACATCAACTTTTCCAGAGAA
196 CTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
*
1874300 AGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * *
1874365 AAACCTCTTGCTTGAATTCATCATTTGAGAGATCAAATTTTCCAGAGAAAGTTCATAATAAGAAG
66 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAG
* *
1874430 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAAATTTGTTCAACCTTTTGCATGACT
131 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCATGACT
*
1874495 CTATCACAGAAGGAGATAGATCATCATCAACTTTTCCAGAGAA
196 CTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
1874538 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
1874603 AAACCTCTTGTTTGAATTCATCATTCGAGGGATTAACTTTTCTAGAGAAAATTCATAATAAGAAG
66 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAG
* *
1874668 AACTCATCTGAAGAA-GAACAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGTATGA-T
131 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCATGACT
* ** *
1874731 CTATCACAAAAGGAGATAGATCAGTATCAACATTTT-CAGA-AG
196 CTATCACAGAAGGAGATAGATCAACATCAAC-TTTTCCAGAGAA
*
1874773 TGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAG
1874805 AAGGAGCAAA
Statistics
Matches: 476, Mismatches: 27, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
235 32 0.07
236 33 0.07
237 149 0.31
238 262 0.55
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (238 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAG
AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCATGACT
CTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
Found at i:1875039 original size:3 final size:3
Alignment explanation
Indices: 1875033--1875080 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1875023 TTTTTATTTG
*
1875033 ATT ATT ATT ATT ATT GTT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1875080 A
1 A
1875081 CTAAATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1877592 original size:24 final size:24
Alignment explanation
Indices: 1877565--1877615 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1877555 TAAATCAAAA
* * *
1877565 ATCAAAACATAGTCCATGTCAAGT
1 ATCAAAACAAAATCCAAGTCAAGT
* *
1877589 ATCAGATCAAAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAAGTCAAGT
1877613 ATC
1 ATC
1877616 CATTTAGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAAGTCAAGT
Found at i:1883553 original size:11 final size:13
Alignment explanation
Indices: 1883521--1883550 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1883511 TGGCCAAAGA
1883521 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1883534 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1883546 TGAAA
1 TGAAA
1883551 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1890935 original size:17 final size:16
Alignment explanation
Indices: 1890895--1890967 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 16
1890885 TCATTCAAAT
* *
1890895 CATGTACTTCATTTAG
1 CATGTAGTTCATTAAG
*
1890911 CATTTAGTTCATTAAAG
1 CATGTAGTTCATT-AAG
1890928 CATGTAGTTCATCTAAG
1 CATGTAGTTCAT-TAAG
* *
1890945 CAAGCTATTTCATTTAAG
1 CATG-TAGTTCA-TTAAG
1890963 CATGT
1 CATGT
1890968 TGAATCATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
16 11 0.24
17 20 0.43
18 14 0.30
19 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (16 bp):
CATGTAGTTCATTAAG
Found at i:1890994 original size:18 final size:18
Alignment explanation
Indices: 1890973--1891019 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1890963 CATGTTGAAT
1890973 CATTCAA-TAAAGCTAGTC
1 CATTCAATTAAA-CTAGTC
1890991 CATT-AATTAAACTAGTC
1 CATTCAATTAAACTAGTC
*
1891008 CATTCATTTAAA
1 CATTCAATTAAA
1891020 TTGATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.34
Consensus pattern (18 bp):
CATTCAATTAAACTAGTC
Found at i:1897721 original size:20 final size:20
Alignment explanation
Indices: 1897705--1897757 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1897695 TTAATGTTAT
*
1897705 AATGTTAAATTTGATGTCAG
1 AATGTGAAATTTGATGTCAG
1897725 AATGTGAAATTTGATGTCAG
1 AATGTGAAATTTGATGTCAG
1897745 AATGTGAAATTTG
1 AATGTGAAATTTG
1897758 GACTATTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (20 bp):
AATGTGAAATTTGATGTCAG
Found at i:1899331 original size:50 final size:49
Alignment explanation
Indices: 1899262--1899406 Score: 218
Period size: 50 Copynumber: 2.9 Consensus size: 49
1899252 ATAGTGTATA
**
1899262 TAAAGGACACTTAACGCATATGGTGGGCACATCCTTATGTGTATTAGCAC
1 TAAAGGACACTTAGTGCATATGGTGGGCACA-CCTTATGTGTATTAGCAC
*
1899312 TAAAGGACACTTAGTGCATATGGTGGGCATGACCTTATGTGTATTAGCAC
1 TAAAGGACACTTAGTGCATATGGTGGGCA-CACCTTATGTGTATTAGCAC
* *
1899362 TAAAGGACACTTAGTGCATATGGTAGGCACGACCTTATCTGTATT
1 TAAAGGACACTTAGTGCATATGGTGGGCAC-ACCTTATGTGTATT
1899407 GACACTTCAG
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
50 86 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (49 bp):
TAAAGGACACTTAGTGCATATGGTGGGCACACCTTATGTGTATTAGCAC
Found at i:1899943 original size:22 final size:24
Alignment explanation
Indices: 1899901--1899947 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
1899891 AAATGAATAC
1899901 TATTATATTAAATTATGTTTTAAA
1 TATTATATTAAATTATGTTTTAAA
1899925 TATTA-ATT-AATTA-GATTTTAAA
1 TATTATATTAAATTATG-TTTTAAA
1899947 T
1 T
1899948 TAGAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.05
22 13 0.59
23 3 0.14
24 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TATTATATTAAATTATGTTTTAAA
Found at i:1904780 original size:23 final size:23
Alignment explanation
Indices: 1904717--1904780 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
1904707 TGTATTGATA
*
1904717 CACATTCAAGGAATGCATCGGTG
1 CACATTCAAGGAATGCATCGATG
* * *
1904740 TACTTTCATA-G--TGTATCGATG
1 CACATTCA-AGGAATGCATCGATG
1904761 CACATTCAAGGAATGCATCG
1 CACATTCAAGGAATGCATCG
1904781 GTACACTTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
23 13 0.43
24 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (23 bp):
CACATTCAAGGAATGCATCGATG
Found at i:1904791 original size:23 final size:23
Alignment explanation
Indices: 1904715--1904791 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 23
1904705 AGTGTATTGA
1904715 TACACATTCAAGGAATGCATCGG
1 TACACATTCAAGGAATGCATCGG
** * * *
1904738 TGTACTTTCATA-G--TGTATCGA
1 TACACATTCA-AGGAATGCATCGG
*
1904759 TGCACATTCAAGGAATGCATCGG
1 TACACATTCAAGGAATGCATCGG
*
1904782 TACACTTTCA
1 TACACATTCA
1904792 TAGTGTAATG
Statistics
Matches: 39, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
23 22 0.56
24 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (23 bp):
TACACATTCAAGGAATGCATCGG
Found at i:1904805 original size:44 final size:44
Alignment explanation
Indices: 1904705--1904807 Score: 154
Period size: 44 Copynumber: 2.3 Consensus size: 44
1904695 TACACTCTTG
* * **
1904705 AGTGTATTGATACACATTCAAGGAATGCATCGGTGTACTTTCAT
1 AGTGTAATGATGCACATTCAAGGAATGCATCGGTACACTTTCAT
1904749 AGTGT-ATCGATGCACATTCAAGGAATGCATCGGTACACTTTCAT
1 AGTGTAAT-GATGCACATTCAAGGAATGCATCGGTACACTTTCAT
1904793 AGTGTAATGATGCAC
1 AGTGTAATGATGCAC
1904808 TTTGCACAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 1 0.02
44 50 0.94
45 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (44 bp):
AGTGTAATGATGCACATTCAAGGAATGCATCGGTACACTTTCAT
Found at i:1911372 original size:14 final size:12
Alignment explanation
Indices: 1911337--1911367 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1911327 TTATTCTTTT
1911337 TTTAAAATATTA
1 TTTAAAATATTA
*
1911349 TTTAAAATATTT
1 TTTAAAATATTA
1911361 TTTAAAA
1 TTTAAAA
1911368 AATATGAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAAATATTA
Found at i:1912927 original size:27 final size:30
Alignment explanation
Indices: 1912860--1912927 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
1912850 ATGTCATTAA
*
1912860 TAATTTAT-AAAATGTTTTTATATTTATTG
1 TAATTTATAAAAAAGTTTTTATATTTATTG
*
1912889 TAATTTATAAAAAAG-TTTTCT-TTTATT-
1 TAATTTATAAAAAAGTTTTTATATTTATTG
1912916 TAATTTATAAAA
1 TAATTTATAAAA
1912928 GTATGTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 12 0.33
28 6 0.17
29 13 0.36
30 5 0.14
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (30 bp):
TAATTTATAAAAAAGTTTTTATATTTATTG
Found at i:1912991 original size:80 final size:80
Alignment explanation
Indices: 1912850--1913005 Score: 217
Period size: 80 Copynumber: 1.9 Consensus size: 80
1912840 CTCACCCCTA
** * *
1912850 ATGTCATTAATAATTTATAAAATGTTTTTATATTTATTGTAATTTATAAAAAAGTTTTCTTTTAT
1 ATGTCATTAATAATTTATAAAATGTTTAAACATTTATTGAAATTTATAAAAAAGTTTTCTTTTAT
*
1912915 TTAATTTATAAAAGT
66 ATAATTTATAAAAGT
* *
1912930 ATGTCATTAATAATTTATGAGATGTTTAAACATTTATT-AAATTTAT-AAAAAGATTTGTCTTTT
1 ATGTCATTAATAATTTATAAAATGTTTAAACATTTATTGAAATTTATAAAAAAG-TTT-TCTTTT
1912993 ATATAATTTATAA
64 ATATAATTTATAA
1913006 GTGTTATCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 6 0.09
79 10 0.15
80 51 0.76
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (80 bp):
ATGTCATTAATAATTTATAAAATGTTTAAACATTTATTGAAATTTATAAAAAAGTTTTCTTTTAT
ATAATTTATAAAAGT
Found at i:1913866 original size:42 final size:42
Alignment explanation
Indices: 1913776--1913873 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
1913766 ATGCTCAGAG
*
1913776 CCTAATTTTTTAAATCTTACTTTTTACATTTATAATTGATGT
1 CCTAATTTTTTAAATCTTACTTTTTACATTTATAATTGATGC
** * * *
1913818 TGTAATTTTTTCAAT-TTCATTTTTTACCTTTATAATTG-TGCC
1 CCTAATTTTTTAAATCTT-ACTTTTTACATTTATAATTGATG-C
1913860 CCTAA-TTTTTAAAT
1 CCTAATTTTTTAAAT
1913874 TTATAATTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
41 12 0.27
42 33 0.73
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.55
Consensus pattern (42 bp):
CCTAATTTTTTAAATCTTACTTTTTACATTTATAATTGATGC
Found at i:1917711 original size:29 final size:29
Alignment explanation
Indices: 1917668--1917750 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
1917658 CTCACCTAAC
*
1917668 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1917698 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
1917727 TAAATGATATAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1917751 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1922477 original size:29 final size:29
Alignment explanation
Indices: 1922435--1922515 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
1922425 CACCTAACTA
* *
1922435 AATTAATGTAAGCAATGACATCATTACTT
1 AATTGATGTAAGCAATGACATCATTAATT
*
1922464 AATTGATGTAAGCAATGACATCTTTAATT
1 AATTGATGTAAGCAATGACATCATTAATT
* *
1922493 AAATGATGTAAGTAATGACATCA
1 AATTGATGTAAGCAATGACATCA
1922516 ATTTAGTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
AATTGATGTAAGCAATGACATCATTAATT
Found at i:1926650 original size:16 final size:16
Alignment explanation
Indices: 1926629--1926659 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1926619 ACTATTCACG
*
1926629 TGAATAGTGAATTTCA
1 TGAATAGTAAATTTCA
1926645 TGAATAGTAAATTTC
1 TGAATAGTAAATTTC
1926660 GGTTGCCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (16 bp):
TGAATAGTAAATTTCA
Found at i:1936911 original size:13 final size:13
Alignment explanation
Indices: 1936895--1936964 Score: 81
Period size: 13 Copynumber: 5.4 Consensus size: 13
1936885 TCAATGCGTT
1936895 TCATAAATGAGCG
1 TCATAAATGAGCG
1936908 TCATAAATGAGCG
1 TCATAAATGAGCG
* *
1936921 TCATAAATGTGTG
1 TCATAAATGAGCG
*
1936934 TCATAAAT-ACGTG
1 TCATAAATGA-GCG
1936947 TCATAAATGCA-CG
1 TCATAAATG-AGCG
1936960 TCATA
1 TCATA
1936965 GATTTATTAC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
13 49 0.98
15 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (13 bp):
TCATAAATGAGCG
Found at i:1937294 original size:6 final size:7
Alignment explanation
Indices: 1937277--1937302 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1937267 CAAAATTGTA
1937277 AAAAAAG
1 AAAAAAG
1937284 AAAAAAG
1 AAAAAAG
1937291 AAAAAAG
1 AAAAAAG
1937298 AAAAA
1 AAAAA
1937303 TAGATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1939687 original size:985 final size:985
Alignment explanation
Indices: 1937777--1939734 Score: 3889
Period size: 985 Copynumber: 2.0 Consensus size: 985
1937767 GTCGATTTAC
1937777 GACGTTATAACCTCTCTATAGTCTCTGTCAAAGTGAAACGGGAAGTTAAGAGAAGAAATGAGAGA
1 GACGTTATAACCTCTCTATAGTCTCTGTCAAAGTGAAACGGGAAGTTAAGAGAAGAAATGAGAGA
*
1937842 TTTTGGGTTCATATATGTTGAAAGTCAAATGCACTTTCGGTCCATTGTAGAAAACAATGGTAGGC
66 TTTCGGGTTCATATATGTTGAAAGTCAAATGCACTTTCGGTCCATTGTAGAAAACAATGGTAGGC
1937907 ACCGAATTAGGTGTAGATTTAGTCATTGTACTTTAGGGTATTTATAAGAATAGTCCTTAAGCTTC
131 ACCGAATTAGGTGTAGATTTAGTCATTGTACTTTAGGGTATTTATAAGAATAGTCCTTAAGCTTC
1937972 AACAATAAATACCCTAACCCATTTATCTTCAAAACCATCCCAAATCATTCTAGCTTTCTCCCAAA
196 AACAATAAATACCCTAACCCATTTATCTTCAAAACCATCCCAAATCATTCTAGCTTTCTCCCAAA
*
1938037 AAATAGAGAGTTTCTTGAGAGTCATTTTTCTCCTTTTTATCAAGAGAGAATTGTCATTGTTTTCT
261 AAATAGAGAGTTTCTTGAGAGTCATTTTTCTCCTTTTTATCAAGAGAGAATTGTCATGGTTTTCT
1938102 CCTTGGCAGATTGAGAGAATTTTTAATTCTTATTTTCTCATAGTAAAATTCTTCTACCATTACCC
326 CCTTGGCAGATTGAGAGAATTTTTAATTCTTATTTTCTCATAGTAAAATTCTTCTACCATTACCC
*
1938167 GTGGTTTTTACCCTATATTATTTAGGGTTTTTCCACGTAAATTTATGTGTCTTCTTTATCTTCAT
391 GTGGTTTTTACCCTATATTATTTAGGGGTTTTCCACGTAAATTTATGTGTCTTCTTTATCTTCAT
1938232 TTTTATTTTCTAAAATTATCAGTTGCGATTTTGCTTTATCCGATAGCCATATTCTGCAATAATTG
456 TTTTATTTTCTAAAATTATCAGTTGCGATTTTGCTTTATCCGATAGCCATATTCTGCAATAATTG
1938297 GTATCAAGAGCTAGATTTGAGTGTGTAATATCTACTTATTGTCTTTGTGATTGCCACCAAAAGGT
521 GTATCAAGAGCTAGATTTGAGTGTGTAATATCTACTTATTGTCTTTGTGATTGCCACCAAAAGGT
1938362 GGATCCTCCAACATAATAAAGTAAGAAGTTATTACCAATTCTTTGAAGATTCCAGAGAACTATTC
586 GGATCCTCCAACATAATAAAGTAAGAAGTTATTACCAATTCTTTGAAGATTCCAGAGAACTATTC
1938427 ACGATAGTGAAATAGTGGGAACTATCCGTAATAGAAGCTATGGCAATGAAATTTGATATTGAAAA
651 ACGATAGTGAAATAGTGGGAACTATCCGTAATAGAAGCTATGGCAATGAAATTTGATATTGAAAA
1938492 GTTCAATGGGAGAAATTTCTCATTGTGAAAATTGAAGATGAAGGTTATCCTGAGGAAAGACGATT
716 GTTCAATGGGAGAAATTTCTCATTGTGAAAATTGAAGATGAAGGTTATCCTGAGGAAAGACGATT
1938557 GTCTAGCAGCTATCAGTGAAAGGCCGGTAGATTTCACAGATGACAACAAATAGATTAAAATGGAT
781 GTCTAGCAGCTATCAGTGAAAGGCCGGTAGATTTCACAGATGACAACAAATAGATTAAAATGGAT
1938622 GGGAATGCTATGGAAAACTTTCATCTAGCATTAGCAGATAAAGTATTGTCAAGCATCGTGGAGAA
846 GGGAATGCTATGGAAAACTTTCATCTAGCATTAGCAGATAAAGTATTGTCAAGCATCGTGGAGAA
1938687 GAAGACAACTAAGGAGATATGACATCATCTCACCAAATTGAACGAGGCCACATCGTTGCACAACT
911 GAAGACAACTAAGGAGATATGACATCATCTCACCAAATTGAACGAGGCCACATCGTTGCACAACT
1938752 AAGGAGATAT
976 AAGGAGATAT
1938762 GACGTTATAACCTCTCTATAGTCTCTGTCAAAGTGAAACGGGAAGTTAAGAGAAGAAATGAGAGA
1 GACGTTATAACCTCTCTATAGTCTCTGTCAAAGTGAAACGGGAAGTTAAGAGAAGAAATGAGAGA
1938827 TTTCGGGTTCATATATGTTGAAAGTCAAATGCACTTTCGGTCCATTGTAGAAAACAATGGTAGGC
66 TTTCGGGTTCATATATGTTGAAAGTCAAATGCACTTTCGGTCCATTGTAGAAAACAATGGTAGGC
1938892 ACCGAATTAGGTGTAGATTTAGTCATTGTACTTTAGGGTATTTATAAGAATAGTCCTTAAGCTTC
131 ACCGAATTAGGTGTAGATTTAGTCATTGTACTTTAGGGTATTTATAAGAATAGTCCTTAAGCTTC
1938957 AACAATAAATACCCTAACCCATTTATCTTCAAAACCATCCCAAATCATTCTAGCTTTCTCCCAAA
196 AACAATAAATACCCTAACCCATTTATCTTCAAAACCATCCCAAATCATTCTAGCTTTCTCCCAAA
1939022 AAATAGAGAGTTTCTTGAGAGTCATTTTTCTCCTTTTTATCAAGAGAGAATTGTCATGGTTTTCT
261 AAATAGAGAGTTTCTTGAGAGTCATTTTTCTCCTTTTTATCAAGAGAGAATTGTCATGGTTTTCT
1939087 CCTTGGCAGATTGAGAGAATTTTTAATTCTTATTTTCTCATAGTAAAATTCTTCTACCATTACCC
326 CCTTGGCAGATTGAGAGAATTTTTAATTCTTATTTTCTCATAGTAAAATTCTTCTACCATTACCC
1939152 GTGGTTTTTACCCTATATTATTTAGGGGTTTTCCACGTAAATTTATGTGTCTTCTTTATCTTCAT
391 GTGGTTTTTACCCTATATTATTTAGGGGTTTTCCACGTAAATTTATGTGTCTTCTTTATCTTCAT
1939217 TTTTATTTTCTAAAATTATCAGTTGCGATTTTGCTTTATCCGATAGCCATATTCTGCAATAATTG
456 TTTTATTTTCTAAAATTATCAGTTGCGATTTTGCTTTATCCGATAGCCATATTCTGCAATAATTG
1939282 GTATCAAGAGCTAGATTTGAGTGTGTAATATCTACTTATTGTCTTTGTGATTGCCACCAAAAGGT
521 GTATCAAGAGCTAGATTTGAGTGTGTAATATCTACTTATTGTCTTTGTGATTGCCACCAAAAGGT
1939347 GGATCCTCCAACATAATAAAGTAAGAAGTTATTACCAATTCTTTGAAGATTCCAGAGAACTATTC
586 GGATCCTCCAACATAATAAAGTAAGAAGTTATTACCAATTCTTTGAAGATTCCAGAGAACTATTC
1939412 ACGATAGTGAAATAGTGGGAACTATCCGTAATAGAAGCTATGGCAATGAAATTTGATATTGAAAA
651 ACGATAGTGAAATAGTGGGAACTATCCGTAATAGAAGCTATGGCAATGAAATTTGATATTGAAAA
1939477 GTTCAATGGGAGAAATTTCTCATTGTGAAAATTGAAGATGAAGGTTATCCTGAGGAAAGACGATT
716 GTTCAATGGGAGAAATTTCTCATTGTGAAAATTGAAGATGAAGGTTATCCTGAGGAAAGACGATT
1939542 GTCTAGCAGCTATCAGTGAAAGGCCGGTAGATTTCACAGATGACAACAAATAGATTAAAATGGAT
781 GTCTAGCAGCTATCAGTGAAAGGCCGGTAGATTTCACAGATGACAACAAATAGATTAAAATGGAT
1939607 GGGAATGCTATGGAAAACTTTCATCTAGCATTAGCAGATAAAGTATTGTCAAGCATCGTGGAGAA
846 GGGAATGCTATGGAAAACTTTCATCTAGCATTAGCAGATAAAGTATTGTCAAGCATCGTGGAGAA
1939672 GAAGACAACTAAGGAGATATGACATCATCTCACCAAATTGAACGAGGCCACATCGTTGCACAA
911 GAAGACAACTAAGGAGATATGACATCATCTCACCAAATTGAACGAGGCCACATCGTTGCACAA
1939735 TAAAATTTTC
Statistics
Matches: 970, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
985 970 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (985 bp):
GACGTTATAACCTCTCTATAGTCTCTGTCAAAGTGAAACGGGAAGTTAAGAGAAGAAATGAGAGA
TTTCGGGTTCATATATGTTGAAAGTCAAATGCACTTTCGGTCCATTGTAGAAAACAATGGTAGGC
ACCGAATTAGGTGTAGATTTAGTCATTGTACTTTAGGGTATTTATAAGAATAGTCCTTAAGCTTC
AACAATAAATACCCTAACCCATTTATCTTCAAAACCATCCCAAATCATTCTAGCTTTCTCCCAAA
AAATAGAGAGTTTCTTGAGAGTCATTTTTCTCCTTTTTATCAAGAGAGAATTGTCATGGTTTTCT
CCTTGGCAGATTGAGAGAATTTTTAATTCTTATTTTCTCATAGTAAAATTCTTCTACCATTACCC
GTGGTTTTTACCCTATATTATTTAGGGGTTTTCCACGTAAATTTATGTGTCTTCTTTATCTTCAT
TTTTATTTTCTAAAATTATCAGTTGCGATTTTGCTTTATCCGATAGCCATATTCTGCAATAATTG
GTATCAAGAGCTAGATTTGAGTGTGTAATATCTACTTATTGTCTTTGTGATTGCCACCAAAAGGT
GGATCCTCCAACATAATAAAGTAAGAAGTTATTACCAATTCTTTGAAGATTCCAGAGAACTATTC
ACGATAGTGAAATAGTGGGAACTATCCGTAATAGAAGCTATGGCAATGAAATTTGATATTGAAAA
GTTCAATGGGAGAAATTTCTCATTGTGAAAATTGAAGATGAAGGTTATCCTGAGGAAAGACGATT
GTCTAGCAGCTATCAGTGAAAGGCCGGTAGATTTCACAGATGACAACAAATAGATTAAAATGGAT
GGGAATGCTATGGAAAACTTTCATCTAGCATTAGCAGATAAAGTATTGTCAAGCATCGTGGAGAA
GAAGACAACTAAGGAGATATGACATCATCTCACCAAATTGAACGAGGCCACATCGTTGCACAACT
AAGGAGATAT
Found at i:1953302 original size:16 final size:16
Alignment explanation
Indices: 1953281--1953313 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1953271 TAATAAATAA
1953281 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1953297 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1953313 A
1 A
1953314 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1953394 original size:10 final size:10
Alignment explanation
Indices: 1953379--1953427 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
1953369 CATTTAATAA
1953379 ATAAACGAAC
1 ATAAACGAAC
1953389 ATAAACGAAC
1 ATAAACGAAC
*
1953399 ATAAAC-ATAA
1 ATAAACGA-AC
1953409 ATGAACACGAAC
1 AT-AA-ACGAAC
1953421 ATAAACG
1 ATAAACG
1953428 TTGGAGACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 1 0.03
10 22 0.67
11 4 0.12
12 5 0.15
13 1 0.03
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1953407 original size:16 final size:16
Alignment explanation
Indices: 1953386--1953427 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1953376 TAAATAAACG
*
1953386 AACATAAACGAACATA
1 AACATAAACGAACACA
* *
1953402 AACATAAATGAACACG
1 AACATAAACGAACACA
1953418 AACATAAACG
1 AACATAAACG
1953428 TTGGAGACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.12
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:1954180 original size:10 final size:10
Alignment explanation
Indices: 1954165--1954212 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1954155 ATAAATGAAT
1954165 GAACATAAAC
1 GAACATAAAC
1954175 GAACATTACTGAAC
1 GAACA-TA---AAC
1954189 GAACATAAAC
1 GAACATAAAC
*
1954199 GAACATAACC
1 GAACATAAAC
1954209 GAAC
1 GAAC
1954213 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 21 0.64
11 2 0.06
13 2 0.06
14 8 0.24
ACGTcount: A:0.52, C:0.23, G:0.12, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1954187 original size:24 final size:24
Alignment explanation
Indices: 1954152--1954220 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
1954142 GATTGGGTTA
* *
1954152 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACGAACATAAACG
*
1954176 AACATTACTGAACGAACATAAACG
1 AACATAACTGAACGAACATAAACG
*
1954200 AACATAACCGAACGAACATAA
1 AACATAACTGAACGAACATAA
1954221 CCAAACGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.55, C:0.19, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:1954219 original size:14 final size:14
Alignment explanation
Indices: 1954172--1954227 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1954162 AATGAACATA
* *
1954172 AACGAACATTACTG
1 AACGAACATAACCG
1954186 AACGAACAT-A---
1 AACGAACATAACCG
1954196 AACGAACATAACCG
1 AACGAACATAACCG
*
1954210 AACGAACATAACCA
1 AACGAACATAACCG
1954224 AACG
1 AACG
1954228 TTCATGAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.52, C:0.25, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1964963 original size:19 final size:19
Alignment explanation
Indices: 1964935--1964972 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1964925 AAAAGATCAT
*
1964935 ATTAGGTTAGAATTCATCG
1 ATTAGCTTAGAATTCATCG
1964954 ATTAGCTTAGAATTCATCG
1 ATTAGCTTAGAATTCATCG
1964973 CGTTAGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (19 bp):
ATTAGCTTAGAATTCATCG
Found at i:1965627 original size:16 final size:17
Alignment explanation
Indices: 1965606--1965638 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1965596 CTCAAATAAA
1965606 ATTATTTTATTA-CTTT
1 ATTATTTTATTATCTTT
1965622 ATTATTTTATTATCTTT
1 ATTATTTTATTATCTTT
1965639 CATTTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTATTTTATTATCTTT
Found at i:1967062 original size:27 final size:28
Alignment explanation
Indices: 1966997--1967240 Score: 129
Period size: 27 Copynumber: 8.8 Consensus size: 28
1966987 CCAGAATTTA
*
1966997 GATTGAAGCACAGAGGTGCTCAGTCAT-
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
**
1967024 -ATTTGGCTGCACAGAGGTG-TCAGTCCTC
1 GA-TT-GAAGCACAGAGGTGCTCAGTCCTC
* *
1967052 GATTGAAGCACAGAGGTGCTCAATCGTC
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
*
1967080 --TTAGCTA-CACAGAGGTG-TCAGCTCC-C
1 GATT-G-AAGCACAGAGGTGCTCAG-TCCTC
** * *
1967106 GGCTGAAGCACAGAGGTGCTCAGTCATT
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
* * * *
1967134 TATTTTAACTGCACATAGGTG-TCAGTTCTC
1 GA-TTGAA--GCACAGAGGTGCTCAGTCCTC
*
1967164 GATTGAAGCACAGAGGTGCTCAATCACT-
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
* *
1967192 -TTTGGCTA-CACAGAGGTG-TCAG-CTCTC
1 GATT-G-AAGCACAGAGGTGCTCAGTC-CTC
1967219 GATTGAAGCACAGAGGTGCTCA
1 GATTGAAGCACAGAGGTGCTCA
1967241 ATCGTTAATT
Statistics
Matches: 160, Mismatches: 33, Indels: 47
0.67 0.14 0.20
Matches are distributed among these distances:
26 12 0.08
27 73 0.46
28 47 0.29
29 11 0.07
30 7 0.04
31 10 0.06
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (28 bp):
GATTGAAGCACAGAGGTGCTCAGTCCTC
Found at i:1967064 original size:55 final size:55
Alignment explanation
Indices: 1966997--1967243 Score: 293
Period size: 55 Copynumber: 4.5 Consensus size: 55
1966987 CCAGAATTTA
* * * *
1966997 GATTGAAGCACAGAGGTGCTCAGTCATATTTGGCTGCACAGAGGTGTCAGTCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
* *
1967052 GATTGAAGCACAGAGGTGCTCAATC-GTCTTAGCTACACAGAGGTGTCAGCTCC-C
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC
** * * * * *
1967106 GGCTGAAGCACAGAGGTGCTCAGTCATTTATTTTAACTGCACATAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA--T-TTTTAGCTACACAGAGGTGTCAGTCCTC
* *
1967164 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG-CTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTC-CTC
1967219 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
1967244 GTTAATTCTA
Statistics
Matches: 161, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
54 42 0.26
55 74 0.46
57 2 0.01
58 43 0.27
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
Found at i:1967495 original size:81 final size:81
Alignment explanation
Indices: 1967360--1967516 Score: 244
Period size: 81 Copynumber: 1.9 Consensus size: 81
1967350 CGAGTTACAA
* * *
1967360 AGAATGGTTCGCACACGAAATGGCGGAGTAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTAC
1 AGAATGGTTCACACACGAAATGGCGGAGTAACAAGCTCTCACAGAAGTGTAGAGCAGGAAGATAC
* *
1967425 TGAGCCGGTTGCACCG
66 CGAGCCAGTTGCACCG
*
1967441 AGAATGGTTCACACACGAAATGGCGGA-TCGACAAGCTCTCACAGAAGTGTAGAGCAGGAAGATA
1 AGAATGGTTCACACACGAAATGGCGGAGT-AACAAGCTCTCACAGAAGTGTAGAGCAGGAAGATA
1967505 CCGAGCCAGTTG
65 CCGAGCCAGTTG
1967517 TGCAAGAGAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
80 1 0.01
81 68 0.99
ACGTcount: A:0.32, C:0.21, G:0.31, T:0.17
Consensus pattern (81 bp):
AGAATGGTTCACACACGAAATGGCGGAGTAACAAGCTCTCACAGAAGTGTAGAGCAGGAAGATAC
CGAGCCAGTTGCACCG
Found at i:1975127 original size:13 final size:13
Alignment explanation
Indices: 1975109--1975134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1975099 AGCCCAACTT
1975109 GTCATAAATTTGA
1 GTCATAAATTTGA
1975122 GTCATAAATTTGA
1 GTCATAAATTTGA
1975135 CTCGAAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
GTCATAAATTTGA
Found at i:1980575 original size:23 final size:23
Alignment explanation
Indices: 1980544--1980599 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1980534 GTGCCGATGT
*
1980544 AAGCAGTTAGTTGTGTAGTTAGG
1 AAGCTGTTAGTTGTGTAGTTAGG
*
1980567 AAGTTGTTAGTTGTGTAGTTAGG
1 AAGCTGTTAGTTGTGTAGTTAGG
1980590 AAGCTGTTAG
1 AAGCTGTTAG
1980600 GAGTAGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.04, G:0.34, T:0.38
Consensus pattern (23 bp):
AAGCTGTTAGTTGTGTAGTTAGG
Found at i:1999866 original size:55 final size:55
Alignment explanation
Indices: 1999649--2000271 Score: 841
Period size: 55 Copynumber: 11.6 Consensus size: 55
1999639 ATAGTCCTTT
* *
1999649 AGAGAGTATAAGACTCGAAC-ATCTTTAACAATCGCGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* *
1999703 AGAGAGTATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCC-ATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * * *
1999757 AAAGAGTATAAGACTC--ACAATCTTCATCAATCGCG--TG-CCCCTATTTCGTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
1999807 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * * *
1999862 AGAGAGTATAAGAC-C-CACAATCTTCATCAATCACGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * * * *
1999915 AGAGAGTATAAGACCCAAACAATCTTCAACAATCGTGTATGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
*
1999970 AGGGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* *
2000025 AGGGAGTATAAGACTCGAACAATCTTCAACGAT--CGTC-GTCCCCCTATTTCCTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTC
* * * * * *
2000078 AGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCAGCTCCCTATTTCCTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
2000133 AGAGAGTATAAGACTCG-ACAATCTTCAACGATCGCGTCTG--CCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* *
2000185 AAAGAG-ATAAGACTCGAACAATCTTCAACGATCG-GTCCGCCCCCTATTTCTTC
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* *
2000238 AGAG-GTATGAGACTTGAACAATCTTCAACGATCG
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCG
2000272 TAGGGAACCT
Statistics
Matches: 507, Mismatches: 45, Indels: 35
0.86 0.08 0.06
Matches are distributed among these distances:
49 4 0.01
50 24 0.05
51 14 0.03
52 67 0.13
53 136 0.27
54 67 0.13
55 194 0.38
56 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (55 bp):
AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
Found at i:1999943 original size:108 final size:109
Alignment explanation
Indices: 1999649--2000271 Score: 812
Period size: 108 Copynumber: 5.8 Consensus size: 109
1999639 ATAGTCCTTT
* *
1999649 AGAGAGTATAAGACTCGA-ACATCTTTAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
1 AGAGAGTATAAGACTCCACA-ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
* *
1999713 AGACTCGAACAATCTTCAATGATCACGTCTGCCCCC-ATTTCTTC
65 AGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * *
1999757 AAAGAGTATAAGACT-CACAATCTTCATCAATCGCG--TG-CCCCTATTTCGTCAGAGAGTATAA
1 AGAGAGTATAAGACTCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAA
1999818 GACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
66 GACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* *
1999862 AGAGAGTATAAGAC-CCACAATCTTCATCAATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAA
1 AGAGAGTATAAGACTCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAA
* * * * *
1999926 GACCCAAACAATCTTCAACAATCGTGTATGCCCCCTATTTCTTC
66 GACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * * *
1999970 AGGGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGGGAGTATA
1 AGAGAGTATAAGACTC-CACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
*
2000035 AGACTCGAACAATCTTCAACGAT--CGTC-GTCCCCCTATTTCCTC
65 AGACTCGAACAATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTC
* * * *
2000078 AGAGAGTATAAGAC-CCGAACAATCTTCAACAATCGTGTCAGCTCCCTATTTCCTCAGAGAGTAT
1 AGAGAGTATAAGACTCC--ACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTAT
2000142 AAGACTCG-ACAATCTTCAACGATCGCGTCTG--CCCTATTTCTTC
64 AAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
* * * * *
2000185 AAAGAG-ATAAGACTCGAACAATCTTCAACGATCG-GTCCGCCCCCTATTTCTTCAGAG-GTATG
1 AGAGAGTATAAGACTC-CACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
*
2000247 AGACTTGAACAATCTTCAACGATCG
65 AGACTCGAACAATCTTCAACGATCG
2000272 TAGGGAACCT
Statistics
Matches: 454, Mismatches: 44, Indels: 37
0.85 0.08 0.07
Matches are distributed among these distances:
104 66 0.15
105 79 0.17
106 23 0.05
107 51 0.11
108 166 0.37
109 5 0.01
110 64 0.14
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (109 bp):
AGAGAGTATAAGACTCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAA
GACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTC
Found at i:2000000 original size:163 final size:164
Alignment explanation
Indices: 1999649--2000272 Score: 877
Period size: 163 Copynumber: 3.9 Consensus size: 164
1999639 ATAGTCCTTT
* *
1999649 AGAGAGTATAAGACTCGAAC-ATCTTTAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
* * *
1999713 AGACTCGAACAATCTTCAATGATCACGTCTGCCCCC-ATTTCTTCAAAGAGTATAAGACTC--AC
66 AGACTCGAACAATCTTCAACGATC-CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAAC
* * *
1999775 AATCTTCATCAATCGCG--TG-CCCCTATTTCGTC
130 AATCTTCAACAATCGTGTATGCCCCCTATTTCCTC
1999807 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
* * * *
1999872 AGAC-C-CACAATCTTCATCAATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCAAAC
66 AGACTCGAACAATCTTCAACGATC-CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAAC
*
1999935 AATCTTCAACAATCGTGTATGCCCCCTATTTCTTC
130 AATCTTCAACAATCGTGTATGCCCCCTATTTCCTC
* *
1999970 AGGGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGGGAGTATA
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
*
2000035 AGACTCGAACAATCTTCAACGAT-CGTC-GTCCCCCTATTTCCTCAGAGAGTATAAGACCCGAAC
66 AGACTCGAACAATCTTCAACGATCCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACCCGAAC
*
2000098 AATCTTCAACAATCGTGTCA-GCTCCCTATTTCCTC
130 AATCTTCAACAATCGTGT-ATGCCCCCTATTTCCTC
*
2000133 AGAGAGTATAAGACTCG-ACAATCTTCAACGATCGCGTCTG--CCCTATTTCTTCAAAGAG-ATA
1 AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
* * * **
2000194 AGACTCGAACAATCTTCAACGATCGGTCCGCCCCCTATTTCTTCAGAG-GTATGAGACTTGAACA
66 AGACTCGAACAATCTTCAACGATCCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACA
*
2000258 ATCTTCAACGATCGT
131 ATCTTCAACAATCGT
2000273 AGGGAACCTG
Statistics
Matches: 424, Mismatches: 29, Indels: 25
0.89 0.06 0.05
Matches are distributed among these distances:
157 25 0.06
158 43 0.10
159 99 0.23
160 53 0.12
161 1 0.00
162 26 0.06
163 162 0.38
164 2 0.00
165 13 0.03
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (164 bp):
AGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
AGACTCGAACAATCTTCAACGATCCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACA
ATCTTCAACAATCGTGTATGCCCCCTATTTCCTC
Found at i:2001234 original size:8 final size:8
Alignment explanation
Indices: 2001216--2001251 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
2001206 TTTTTCATTC
2001216 ATTTT-TT
1 ATTTTATT
2001223 ATTTTATT
1 ATTTTATT
2001231 ATTTTATT
1 ATTTTATT
*
2001239 ATTTTATC
1 ATTTTATT
2001247 ATTTT
1 ATTTT
2001252 TTCACTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
7 5 0.19
8 22 0.81
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTATT
Found at i:2001242 original size:16 final size:15
Alignment explanation
Indices: 2001214--2001253 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
2001204 TTTTTTTCAT
2001214 TCATTTTTTATTTTA
1 TCATTTTTTATTTTA
*
2001229 TTATTTTATTATTTTA
1 TCATTTT-TTATTTTA
2001245 TCATTTTTT
1 TCATTTTTT
2001254 CACTCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (15 bp):
TCATTTTTTATTTTA
Found at i:2022143 original size:20 final size:20
Alignment explanation
Indices: 2022118--2022160 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2022108 TCTAAGAGCC
*
2022118 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
2022138 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
2022158 CAT
1 CAT
2022161 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:2022481 original size:18 final size:18
Alignment explanation
Indices: 2022458--2022531 Score: 130
Period size: 18 Copynumber: 4.1 Consensus size: 18
2022448 ATGTCAGATG
2022458 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
*
2022476 CCCATGCTGGATCACTGC
1 CCCATGCTGGACCACTGC
*
2022494 ACCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
2022512 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
2022530 CC
1 CC
2022532 AATCCTCACG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.18
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:2027556 original size:21 final size:19
Alignment explanation
Indices: 2027523--2027563 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2027513 TGCATCAAGG
*
2027523 TATTTGTGGAGGCCATGAAA
1 TATTTGTCGAGGCCAT-AAA
2027543 TATTTCGTCGAGGCCATAAA
1 TATTT-GTCGAGGCCATAAA
2027563 T
1 T
2027564 TCCTGCAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (19 bp):
TATTTGTCGAGGCCATAAA
Found at i:2029265 original size:110 final size:110
Alignment explanation
Indices: 2028982--2029278 Score: 387
Period size: 110 Copynumber: 2.7 Consensus size: 110
2028972 GGGTGGGTCA
* * ** * * *
2028982 CTCCCTTTTCTTTCAAGGAGTATAGGCCTCGAACAATCTTCGGTAAACGAGTCTGCTCCCTTTTC
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGAGTCTGCTCCCTATTC
*
2029047 TTTCAAGGAGTATAGAACTCGAACAATCTTATAAAAATGGGTCCG
66 TTTCAAGGAGTATAGAACTCAAACAATCTTATAAAAATGGGTCCG
* * * *
2029092 CTCCTTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTAAAAACGAGTTTGTTCCCTATTC
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGAGTCTGCTCCCTATTC
* * **
2029157 TTTCAAGGAGTATAGAACTCAAACAATCTTTTGAAAATGGGTTTG
66 TTTCAAGGAGTATAGAACTCAAACAATCTTATAAAAATGGGTCCG
* * * * *
2029202 CTCCCTATTCTTTTAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTCCGCTCTCTATTC
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGAGTCTGCTCCCTATTC
* *
2029267 TTTTAGGGAGTA
66 TTTCAAGGAGTA
2029279 CATGACTCGA
Statistics
Matches: 160, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
110 160 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (110 bp):
CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGAGTCTGCTCCCTATTC
TTTCAAGGAGTATAGAACTCAAACAATCTTATAAAAATGGGTCCG
Found at i:2029288 original size:55 final size:55
Alignment explanation
Indices: 2028982--2029278 Score: 351
Period size: 55 Copynumber: 5.4 Consensus size: 55
2028972 GGGTGGGTCA
* * ** * * * *
2028982 CTCCCTTTTCTTTCAAGGAGTATAGGCCTCGAACAATCTTCGGTAAACGAGTCTG
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTCTG
* * * * *
2029037 CTCCCTTTTCTTTCAAGGAGTATAGAACTCGAACAATCTTATAAAAATGGGTCCG
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTCTG
* * * * *
2029092 CTCCTTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTAAAAACGAGTTTG
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTCTG
* * * * *
2029147 TTCCCTATTCTTTCAAGGAGTATAGAACTCAAACAATCTTTTGAAAATGGGTTTG
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTCTG
* *
2029202 CTCCCTATTCTTTTAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTCCG
1 CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTCTG
* *
2029257 CTCTCTATTCTTTTAGGGAGTA
1 CTCCCTATTCTTTCAGGGAGTA
2029279 CATGACTCGA
Statistics
Matches: 209, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 209 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (55 bp):
CTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTCTG
Found at i:2029387 original size:37 final size:37
Alignment explanation
Indices: 2029300--2029402 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 37
2029290 CTTGATTTTT
* ***
2029300 TTCACTACTC-TTCCTTGAAGGCTTATAGACGATTTGT
1 TTCACTACTCTTTCC-TGAAGGCTTATAGATGATTCAC
* *
2029337 TTCACTACCCTTTCGTGAAGGCTTATAGATGATTCAC
1 TTCACTACTCTTTCCTGAAGGCTTATAGATGATTCAC
* *
2029374 TTCCCTACTCTTTCCCGAAGGCTTA-AGAT
1 TTCACTACTCTTTCCTGAAGGCTTATAGAT
2029403 TGACTTGCTT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
36 4 0.07
37 48 0.87
38 3 0.05
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (37 bp):
TTCACTACTCTTTCCTGAAGGCTTATAGATGATTCAC
Found at i:2030694 original size:11 final size:11
Alignment explanation
Indices: 2030675--2030795 Score: 54
Period size: 11 Copynumber: 10.5 Consensus size: 11
2030665 GAAACCCCCC
*
2030675 TTTTATTTTCT
1 TTTTCTTTTCT
2030686 TTTTCTTTTCT
1 TTTTCTTTTCT
*
2030697 TTTTC-ATT-T
1 TTTTCTTTTCT
*
2030706 TTTTCATTTCT
1 TTTTCTTTTCT
2030717 TTTTCCATTTCTTCCAT
1 TTTT-C--TT-TT-C-T
2030734 TTTTCTTTTCAT
1 TTTTCTTTTC-T
2030746 TTTT-TTTATCTT
1 TTTTCTTT-TC-T
*
2030758 TTTTCATTT-T
1 TTTTCTTTTCT
* *
2030768 TTTCCTCTT-T
1 TTTTCTTTTCT
*
2030778 TTTCCTTTTCAT
1 TTTTCTTTTC-T
2030790 TTTTCT
1 TTTTCT
2030796 CATTTTTAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 23
0.72 0.09 0.19
Matches are distributed among these distances:
9 6 0.07
10 20 0.23
11 23 0.26
12 22 0.25
13 4 0.05
14 3 0.03
15 2 0.02
16 2 0.02
17 5 0.06
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:2030710 original size:9 final size:9
Alignment explanation
Indices: 2030696--2030802 Score: 67
Period size: 9 Copynumber: 11.3 Consensus size: 9
2030686 TTTTCTTTTC
2030696 TTTTTCATT
1 TTTTTCATT
2030705 TTTTTCATTT
1 TTTTTCA-TT
2030715 CTTTTTCCATT
1 -TTTTT-CATT
* *
2030726 TCTTCCATTTT
1 TTTTTCA--TT
2030737 TCTTTTCATT
1 T-TTTTCATT
*
2030747 TTTTTTATCT
1 TTTTTCAT-T
2030757 TTTTTCATT
1 TTTTTCATT
*
2030766 TTTTTCCTCT
1 TTTTTCAT-T
2030776 TTTTTC---
1 TTTTTCATT
*
2030782 CTTTTCATT
1 TTTTTCATT
*
2030791 TTTCTCATT
1 TTTTTCATT
2030800 TTT
1 TTT
2030803 AATTTCTTCT
Statistics
Matches: 77, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
6 5 0.06
9 33 0.43
10 23 0.30
11 10 0.13
12 6 0.08
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCATT
Found at i:2030728 original size:43 final size:42
Alignment explanation
Indices: 2030681--2030800 Score: 104
Period size: 43 Copynumber: 2.8 Consensus size: 42
2030671 CCCCTTTTAT
2030681 TTTCTTTTTCTTTTCTTTTTCATTTTTTTCATTTCTTTTTCCA
1 TTTCTTTTTCTTTTC-TTTTCATTTTTTTCATTTCTTTTTCCA
** * *
2030724 TTTCTTCCAT-TTTTCTTTTCATTTTTTT--TATCTTTTTTCA
1 TTTCTT-TTTCTTTTCTTTTCATTTTTTTCATTTCTTTTTCCA
*
2030764 TTT-TTTTCCTCTTTTTTCCTTTTCATTTTTCTCATTT
1 TTTCTTTT--TC--TTTT-CTTTTCATTTTTTTCATTT
2030801 TTAATTTCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
39 2 0.03
40 14 0.23
42 13 0.22
43 15 0.25
44 14 0.23
46 2 0.03
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.73
Consensus pattern (42 bp):
TTTCTTTTTCTTTTCTTTTCATTTTTTTCATTTCTTTTTCCA
Found at i:2030759 original size:10 final size:10
Alignment explanation
Indices: 2030739--2030781 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
2030729 TCCATTTTTC
2030739 TTTTCAT-TT
1 TTTTCATCTT
*
2030748 TTTTTATCTT
1 TTTTCATCTT
2030758 TTTTCAT-TT
1 TTTTCATCTT
*
2030767 TTTTCCTCTT
1 TTTTCATCTT
2030777 TTTTC
1 TTTTC
2030782 CTTTTCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTCATCTT
Done.