Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002449.1 Hibiscus syriacus cultivar Beakdansim tig00005019_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: 52088
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Found at i:2051 original size:100 final size:100
Alignment explanation
Indices: 1865--2104 Score: 273
Period size: 100 Copynumber: 2.3 Consensus size: 100
1855 AAATTGTTCT
* * ** * * *
1865 GAGTCCAATATCCTCTGCCGTGAAGTTGAAATTGGTTCTGGAACTAGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGACTAT-TAA-T--GAAA-T-TTTGTTGACAA
*
1930 CCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGCGCTGTCTC
60 CCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGCGCTGTCTC
* * * *
1971 GAGTCTAATATCTTTTGTTGTGAAGTTGAAATTGACTATTAATGAAATTTTGTTGACAATCAGCC
1 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGACTATTAATGAAATTTTGTTGACAACCAGCC
* * * *
2036 GCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
66 GCCCCTTCGCTGTGAAGTTGAGCTTGCGCTGTCTC
*
2071 GGGTCCAATATCCTTTGCTGTGAAGTTGAAATTG
1 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTG
2105 GCACTGAAAT
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
100 75 0.66
101 1 0.01
102 4 0.04
104 1 0.01
105 2 0.02
106 31 0.27
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (100 bp):
GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGACTATTAATGAAATTTTGTTGACAACCAGCC
GCCCCTTCGCTGTGAAGTTGAGCTTGCGCTGTCTC
Found at i:3337 original size:17 final size:17
Alignment explanation
Indices: 3312--3347 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3302 ACCCTAAACG
3312 TTTT-TTTTTT-CTTTT
1 TTTTGTTTTTTCCTTTT
3327 TTTTGTTTTTTCCTTTT
1 TTTTGTTTTTTCCTTTT
3344 TTTT
1 TTTT
3348 CGAGTTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 6 0.32
17 9 0.47
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (17 bp):
TTTTGTTTTTTCCTTTT
Found at i:3362 original size:73 final size:71
Alignment explanation
Indices: 3246--3381 Score: 184
Period size: 73 Copynumber: 1.9 Consensus size: 71
3236 CTTATCTTTC
* *
3246 TTTTTCTTTTTTGTTCTTTTTTCTTTTTTCAATTTAAGGCGCCCTTTCGGGTCTTCACCCTAAAC
1 TTTTTCTTTTTTGTTCTTTTTTCTTTTTTCAAGTTAAGACGCCCTTTCGGGTCTTCACCCTAAAC
3311 GTTTTT
66 GTTTTT
* * * *
3317 TTTTTCTTTTTT-TTGTTTTTTCCTTTTTTTTCGAGTTAAGACGCCCTTTCGGGTTTTCATCCTA
1 TTTTTCTTTTTTGTTCTTTTTT-C--TTTTTTCAAGTTAAGACGCCCTTTCGGGTCTTCACCCTA
3381 A
63 A
3382 GTGAAGTACT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
70 8 0.14
71 13 0.23
73 35 0.62
ACGTcount: A:0.11, C:0.20, G:0.12, T:0.57
Consensus pattern (71 bp):
TTTTTCTTTTTTGTTCTTTTTTCTTTTTTCAAGTTAAGACGCCCTTTCGGGTCTTCACCCTAAAC
GTTTTT
Found at i:13675 original size:6 final size:6
Alignment explanation
Indices: 13666--13735 Score: 68
Period size: 6 Copynumber: 11.3 Consensus size: 6
13656 AAAGACGAAG
* * * * *
13666 AAAATA AAAATA GAAATA AAAATA GAAATA AAATTA AAACTA AAACTA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
13714 AAAACA TAAAATA ATAAATA AA
1 AAAATA -AAAATA A-AAATA AA
13736 GTAGTACTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
6 42 0.79
7 11 0.21
ACGTcount: A:0.74, C:0.04, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:15476 original size:17 final size:17
Alignment explanation
Indices: 15454--15504 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
15444 TCTTGAAATT
15454 TTTAAATTTTTATATAA
1 TTTAAATTTTTATATAA
15471 TTTAAATATTTTTATTGATAA
1 TTT-AA-ATTTTTA-T-ATAA
15492 TTT-AA-TTTTATAT
1 TTTAAATTTTTATAT
15505 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.07
16 1 0.03
17 8 0.27
18 3 0.10
19 8 0.27
20 1 0.03
21 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTAAATTTTTATATAA
Found at i:16486 original size:38 final size:36
Alignment explanation
Indices: 16416--16486 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
16406 ATATTTTCAA
* *
16416 TTTTGTAAAAAATTATATAAATTTTATGAATTTAAT
1 TTTTGTAAAAAAATATATAAATTTTATCAATTTAAT
* *
16452 TTTTTTAAAGAAAATATATAAATATTTTTCAATTT
1 TTTTGTAAA-AAAATATATAAAT-TTTATCAATTT
16487 GTTAAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 8 0.28
37 12 0.41
38 9 0.31
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (36 bp):
TTTTGTAAAAAAATATATAAATTTTATCAATTTAAT
Found at i:16947 original size:22 final size:21
Alignment explanation
Indices: 16913--16952 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16903 AGCGCTACCG
16913 GTTTTGTTATTTTTTCTACAT
1 GTTTTGTTATTTTTTCTACAT
*
16934 GTTTTTTTATTTTTTCTAC
1 GTTTTGTTATTTTTTCTAC
16953 CGGAAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.70
Consensus pattern (21 bp):
GTTTTGTTATTTTTTCTACAT
Found at i:19500 original size:18 final size:18
Alignment explanation
Indices: 19477--19545 Score: 129
Period size: 18 Copynumber: 3.8 Consensus size: 18
19467 AGGTTGACTT
19477 AGTCAAGTTGACTCAACC
1 AGTCAAGTTGACTCAACC
19495 AGTCAAGTTGACTCAACC
1 AGTCAAGTTGACTCAACC
19513 AGTCAAGTTGACTCAACC
1 AGTCAAGTTGACTCAACC
*
19531 AGTCGAGTTGACTCA
1 AGTCAAGTTGACTCA
19546 GTTCGGTGTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (18 bp):
AGTCAAGTTGACTCAACC
Found at i:20349 original size:21 final size:20
Alignment explanation
Indices: 20264--20420 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
20254 AATGACCAAT
** *
20264 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
20283 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
20303 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
20323 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
20344 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
20365 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
20386 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
20406 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
20421 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:20449 original size:20 final size:20
Alignment explanation
Indices: 20387--20580 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
20377 CGATTTTCCA
* ** *
20387 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
20407 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
20427 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
20447 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
20467 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
20487 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
20507 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * * *
20527 AAATCACAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
*
20547 AAAATCGCAACGCGTATTCGT
1 -AAATCGCAACGCGTATCCGT
20568 AAATCGCAACGCG
1 AAATCGCAACGCG
20581 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:20471 original size:60 final size:60
Alignment explanation
Indices: 20387--20580 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
20377 CGATTTTCCA
* ** * *
20387 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
20447 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * ** *
20507 ATATCGCAACGCGTATCCGTAAATCACAACGATAATACATAAAATCGCAACGCGTATTCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
20568 AAATCGCAACGCG
1 AAATCGCAACGCG
20581 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 80 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:21137 original size:41 final size:41
Alignment explanation
Indices: 21079--21156 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
21069 TTGCAGAAGA
* *
21079 GTCGCAACGAGATAAATGAAAATCGTAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
21120 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
21157 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.45, C:0.15, G:0.26, T:0.14
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:21153 original size:21 final size:21
Alignment explanation
Indices: 21080--21155 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
21070 TGCAGAAGAG
*
21080 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* ***
21101 TCGTAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
21121 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
21142 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
21156 TCGCAACGCG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.46, C:0.16, G:0.25, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:21159 original size:14 final size:14
Alignment explanation
Indices: 21140--21196 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
21130 GAGAAATGAA
21140 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
21154 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
21173 AATCTCAACGAGAG
1 AATCGCAACGAGAG
21187 AATCGCAACG
1 AATCGCAACG
21197 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:21172 original size:33 final size:33
Alignment explanation
Indices: 21132--21212 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
21122 CGCAACGAGA
21132 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
21165 GAAATGAAAATCTCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
21198 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
21213 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:21230 original size:19 final size:19
Alignment explanation
Indices: 21208--21305 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
21198 GAAACCAAAA
*
21208 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21227 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
21241 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21260 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
21274 TCTCGTTGCGCTTGTCATT
1 TCGCGTTGCGATTTTCATT
21293 TCGCGTTGCGATT
1 TCGCGTTGCGATT
21306 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
16 5 0.08
17 6 0.10
19 31 0.51
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:21249 original size:14 final size:14
Alignment explanation
Indices: 21230--21319 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
21220 TTTCATTTCG
21230 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21244 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
21263 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
21277 CGTTGCGCTTGTCATTTCG
1 CGTTGCG-AT-TC---TCT
21296 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
21310 CGTTGCGATT
1 CGTTGCGATT
21320 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 19 0.32
ACGTcount: A:0.08, C:0.26, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:21255 original size:33 final size:33
Alignment explanation
Indices: 21213--21327 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
21203 CAAAATCGCA
21213 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
21246 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
21279 TTGCGCTTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
21312 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
21328 AACCCAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:23003 original size:14 final size:14
Alignment explanation
Indices: 22984--23041 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
22974 ATAAATTTAC
22984 TCGTTGCGATTCTT
1 TCGTTGCGATTCTT
*
22998 TCGTTGCGATTTTGGTT
1 TCGTTGCGA--TT-CTT
*
23015 TCGCGTTGCGATTCTG
1 T--CGTTGCGATTCTT
23031 TCGTTGCGATT
1 TCGTTGCGATT
23042 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 19 0.53
16 4 0.11
17 5 0.14
19 8 0.22
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.47
Consensus pattern (14 bp):
TCGTTGCGATTCTT
Found at i:23023 original size:19 final size:19
Alignment explanation
Indices: 22999--23097 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
22989 GCGATTCTTT
22999 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
23018 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTGGTTTCG
**
23032 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCG
23051 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
23070 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
23090 TGTTGCGA
1 CGTTGCGA
23098 AAGTAAACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.16
16 1 0.01
17 1 0.01
18 1 0.01
19 40 0.60
20 13 0.19
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:23027 original size:33 final size:33
Alignment explanation
Indices: 22985--23060 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
22975 TAAATTTACT
* **
22985 CGTTGCGATTCTTTCGTTGCGATTTTGGTTTCG
1 CGTTGCGATTCTGTCGTTGCGATTTTCATTTCG
23018 CGTTGCGATTCTGTCGTTGCGATTTTCATTTCG
1 CGTTGCGATTCTGTCGTTGCGATTTTCATTTCG
23051 CGTTGCGATT
1 CGTTGCGATT
23061 TTGGTTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.08, C:0.20, G:0.26, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTCTGTCGTTGCGATTTTCATTTCG
Found at i:25039 original size:14 final size:14
Alignment explanation
Indices: 25020--25055 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
25010 ATTGTTTAAT
25020 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
25034 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
25048 TGATTTGT
1 TGATTTGT
25056 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:25178 original size:19 final size:19
Alignment explanation
Indices: 25162--25259 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
25152 AAAAATGACT
25162 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
25181 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25200 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
25214 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
25233 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
25253 ATCGCAA
1 ATCGCAA
25260 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:25291 original size:53 final size:53
Alignment explanation
Indices: 25162--25278 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
25152 AAAAATGACT
25162 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
25214 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
25267 ATCGCAATGCGA
1 ATCGCAATGCGA
25279 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:25296 original size:19 final size:19
Alignment explanation
Indices: 25268--25468 Score: 176
Period size: 19 Copynumber: 11.7 Consensus size: 19
25258 AACGAGAGAA
*
25268 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
25287 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
25306 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
25322 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
25339 TTGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
25357 TCGCA-TGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
25372 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
25389 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
25405 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
25422 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
25440 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
25456 TCGCATTGCGATT
1 TCGCATTGCGATT
25469 CTCTCGTTGC
Statistics
Matches: 147, Mismatches: 13, Indels: 44
0.72 0.06 0.22
Matches are distributed among these distances:
14 28 0.19
15 4 0.03
16 21 0.14
17 21 0.14
18 14 0.10
19 48 0.33
20 11 0.07
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:25381 original size:14 final size:14
Alignment explanation
Indices: 25362--25415 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
25352 TCATTTCGCA
25362 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
*
25376 TGCGATTTTCATTTCGCAT
1 TGCGA--TTC-TCTCG--T
25395 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
25409 TGCGATT
1 TGCGATT
25416 TTTATTTCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TGCGATTCTCTCGT
Found at i:25387 original size:50 final size:51
Alignment explanation
Indices: 25274--25482 Score: 222
Period size: 50 Copynumber: 4.1 Consensus size: 51
25264 AGAATCGCAA
25274 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTATCTCGT
* *
25326 TGCGATTTTCATTTTGCATTGCGATTTCATTTCGCA-TGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTATCTCGT
* *
25376 TGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTTATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGA---TTATCT-CG--T
* *
25429 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTATCTCGT
25476 TGCGATT
1 TGCGATT
25483 GTAATTTCCG
Statistics
Matches: 135, Mismatches: 10, Indels: 29
0.78 0.06 0.17
Matches are distributed among these distances:
47 13 0.10
48 9 0.07
49 5 0.04
50 48 0.36
51 19 0.14
52 23 0.17
53 18 0.13
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (51 bp):
TGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTATCTCGT
Found at i:25450 original size:67 final size:67
Alignment explanation
Indices: 25344--25501 Score: 216
Period size: 67 Copynumber: 2.4 Consensus size: 67
25334 TCATTTTGCA
*
25344 TTGCGA-TTTCATTT-CGCA-TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 TTGCGATTTTAATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
25406 CG
66 CG
* * *
25408 TTGCGATTTTTATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATTCTC
1 TTGCGATTTTAATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
25472 TCG
65 TCG
* **
25475 TTGCGATTGTAATTTCCGTGTTGCGAT
1 TTGCGATTTTAATTTCCGCATTGCGAT
25502 AGTCAAATGC
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
64 6 0.07
65 7 0.08
66 4 0.05
67 65 0.78
68 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (67 bp):
TTGCGATTTTAATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
CG
Found at i:25490 original size:33 final size:33
Alignment explanation
Indices: 25344--25482 Score: 212
Period size: 33 Copynumber: 4.2 Consensus size: 33
25334 TCATTTTGCA
25344 TTGCGA-TTTCATTTCGCA-TGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
25375 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
25408 TTGCGATTTTTATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
25442 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
25475 TTGCGATT
1 TTGCGATT
25483 GTAATTTCCG
Statistics
Matches: 97, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
31 6 0.06
32 13 0.13
33 49 0.51
34 28 0.29
35 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:28736 original size:20 final size:20
Alignment explanation
Indices: 28708--28957 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
28698 AAATTTCAGT
* * *
28708 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28728 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
**
28748 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
28768 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28788 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
28808 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
28828 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
28848 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
28868 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
28888 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
28908 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
28928 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
28948 GTTGCGATTT
1 GTTGCGATTT
28958 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:28974 original size:21 final size:21
Alignment explanation
Indices: 28944--29026 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
28934 ATTTTCATAT
*
28944 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
28965 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
28986 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
29007 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
29027 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:29017 original size:42 final size:43
Alignment explanation
Indices: 28924--29022 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
28914 ATTTATGTGT
* *
28924 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
28965 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
29007 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
29023 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:32491 original size:137 final size:137
Alignment explanation
Indices: 32236--32530 Score: 360
Period size: 137 Copynumber: 2.1 Consensus size: 137
32226 TCCATCGTCC
* * *
32236 ATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCATATTTA
1 ATAATTGATTAAAATTAATTAGAATTAATATTAGAGCATCCATCTTAGGCCTAATTTCACATTTA
* ** * * * *
32301 ATCCTTAAATTAGGTGAATTCTTAATTTGGTCCTCGCTTGTGCTCGAGGTTCCAATTTAATTATT
66 ATACTTAAATTAGAAGAATTCTTAATTTGGTCCTCGCTTGTACTCAAGATTCCAATTCAATTATT
32366 CGAATCA
131 CGAATCA
* * * *
32373 ATAATTGATT-AAATGTGATTATAATTAATATTAGATCATCCATCTTAGGCCTAATTTCACCTTT
1 ATAATTGATTAAAAT-TAATTAGAATTAATATTAGAGCATCCATCTTAGGCCTAATTTCACATTT
* * * * *
32437 AGTATTTAAATTAGAAGAATTCTTAATTTGGTTCTCGCTTTTACTCAAGATTCCACTTCAATTAT
65 AATACTTAAATTAGAAGAATTCTTAATTTGGTCCTCGCTTGTACTCAAGATTCCAATTCAATTAT
* *
32502 TTGAATTGTA
130 TCGAA-T-CA
32512 AT-ATTGATTAAAATTAATT
1 ATAATTGATTAAAATTAATT
32531 TAAGTTAATG
Statistics
Matches: 132, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
136 4 0.03
137 109 0.83
138 12 0.09
139 7 0.05
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (137 bp):
ATAATTGATTAAAATTAATTAGAATTAATATTAGAGCATCCATCTTAGGCCTAATTTCACATTTA
ATACTTAAATTAGAAGAATTCTTAATTTGGTCCTCGCTTGTACTCAAGATTCCAATTCAATTATT
CGAATCA
Found at i:34398 original size:203 final size:203
Alignment explanation
Indices: 33803--34562 Score: 1077
Period size: 203 Copynumber: 3.8 Consensus size: 203
33793 ACCCTTTACT
* * *
33803 AGAATAAGTTCATAATGATAAGAACTTGTTAAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
* * *
33868 AACAGCACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATCGTCACTTTGTTTGA
66 AACAACACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTCGA
* * *
33933 TTCCATCACAGAAGGAGGTGGATCAATATTTCCAATGTAGAGTTCATAATGAGAAGAACTCATCC
131 TTCCATCACAAAAGGAGGTGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC
33998 GATGAGGG
196 GATGAGGG
* * * *
34006 ATAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTTCATCACATAAGGAGGTGG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
* * * * *
34071 AACAACATCGA-CCTTAGCTCATCCATCGCATATGGAGTTGGATCAACATCATCACTTTGTTCGA
66 AACAACACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTCGA
* * *
34135 TTCCATCACAGAAA-GAGGTGGATCAACATTACCAGTAGAGAGTTCATAATGAGAAGAACTCATC
131 TTCCATCACA-AAAGGAGGTGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATC
*
34199 CGAAGAGGG
195 CGATGAGGG
34208 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
* * *
34273 AACATCACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATAATCACTTTGTTCAA
66 AACAACACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTCGA
* *
34338 TTCCATCACAAAAGGAGGTGGATCAACATTTCCAACGGAGAGTTCATAATTAGAAGAACTCATCC
131 TTCCATCACAAAAGGAGGTGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC
34403 GATGAGGG
196 GATGAGGG
* * * * *
34411 AGAAGAAGTACATAATAAGAAGAACTTGTTCAACATTAGCTCATTTCCATCATATAAAGAGTTGG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
* * * * * *
34476 AGCAACACC--TACCTTGGCTCATCCATCGTATAAGGAGTTAGATCAGCAACATCA-TTTCGCTC
66 AACAACACCAATA-CTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTT-GTTC
*
34538 G--TCCATCA-AATAAGGAGTTGGATCA
129 GATTCCATCACAA-AAGGAGGTGGATCA
34563 GCATCACCTT
Statistics
Matches: 498, Mismatches: 53, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
199 2 0.00
200 20 0.04
201 5 0.01
202 223 0.45
203 248 0.50
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (203 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
AACAACACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATCATCACTTTGTTCGA
TTCCATCACAAAAGGAGGTGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC
GATGAGGG
Found at i:34645 original size:405 final size:403
Alignment explanation
Indices: 33803--34570 Score: 1126
Period size: 405 Copynumber: 1.9 Consensus size: 403
33793 ACCCTTTACT
* *
33803 AGAATAAGTTCATAATGATAAGAACTTGTTAAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
1 AGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
** **
33868 AACAGCACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATCGTCACTTTGTTTGA
66 AACAGCACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATAATCACTTTGTTCAA
* * * *
33933 TTCCATCACAGAAGGAGGTGGATCAATATTTCCAATGTAGAGTTCATAATGAGAAGAACTCATCC
131 TTCCATCACAAAAGGAGGTGGATCAACATTTCCAACGGAGAGTTCATAATGAGAAGAACTCATCC
* * * * * *
33998 GATGAGGGATAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTTCATCACATAA
196 GATGAGGGAGAAGAAGTACATAATAAGAAGAACTTGTTCAACATTAGCTCATTTCCATCACATAA
* * * * *
34063 GGAGGTGGAACAACATCGACCTTAGCTCATCCATCGCATATGGAGTTGGATCAACATCATCACTT
261 AGAGGTGGAACAACACCGACCTTAGCTCATCCATCGCATAAGGAGTTAGATCAACAACATCACTT
* * * * *
34128 TGTTCGATTCCATCACAGAAAGAGGTGGATCAACATTACCAGTAGAGAGTTCATAATGAGAAGAA
326 TGCTCGA-TCCATCAAAGAAAGAGGTGGATCAACATCACCA-TAGAGAGTTCATAATCAAAAGAA
*
34193 CTCATCCGAAGAGGG
389 CTCATCCGAAGAGAG
*
34208 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
1 AGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
*
34273 AACATCACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATAATCACTTTGTTCAA
66 AACAGCACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATAATCACTTTGTTCAA
*
34338 TTCCATCACAAAAGGAGGTGGATCAACATTTCCAACGGAGAGTTCATAATTAGAAGAACTCATCC
131 TTCCATCACAAAAGGAGGTGGATCAACATTTCCAACGGAGAGTTCATAATGAGAAGAACTCATCC
*
34403 GATGAGGGAGAAGAAGTACATAATAAGAAGAACTTGTTCAACATTAGCTCATTTCCATCATATAA
196 GATGAGGGAGAAGAAGTACATAATAAGAAGAACTTGTTCAACATTAGCTCATTTCCATCACATAA
* * * * * *
34468 AGAGTTGGAGCAACACCTACCTTGGCTCATCCATCGTATAAGGAGTTAGATCAGCAACATCA-TT
261 AGAGGTGGAACAACACCGACCTTAGCTCATCCATCGCATAAGGAGTTAGATCAACAACATCACTT
* * * *
34532 TCGCTCG-TCCATCAAATAAGGAGTTGGATCAGCATCACC
326 T-GCTCGATCCATCAAAGAAAGAGGTGGATCAACATCACC
34571 TTGGGTCAAC
Statistics
Matches: 324, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
403 26 0.08
404 3 0.01
405 295 0.91
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (403 bp):
AGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCACATAAGGAGTTGG
AACAGCACCAATACTTGGCTCATCCATCGCATATGGAGTTGGATCAGCATAATCACTTTGTTCAA
TTCCATCACAAAAGGAGGTGGATCAACATTTCCAACGGAGAGTTCATAATGAGAAGAACTCATCC
GATGAGGGAGAAGAAGTACATAATAAGAAGAACTTGTTCAACATTAGCTCATTTCCATCACATAA
AGAGGTGGAACAACACCGACCTTAGCTCATCCATCGCATAAGGAGTTAGATCAACAACATCACTT
TGCTCGATCCATCAAAGAAAGAGGTGGATCAACATCACCATAGAGAGTTCATAATCAAAAGAACT
CATCCGAAGAGAG
Found at i:36448 original size:27 final size:26
Alignment explanation
Indices: 36405--36458 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
36395 GTATCTTCTT
*
36405 TTTTATTTATTTTAATTTTGGCACTA
1 TTTTATTTATTTTAATTTAGGCACTA
* *
36431 TTTTATTTCTTTTAAATTTAGTCACTA
1 TTTTATTTATTTT-AATTTAGGCACTA
36458 T
1 T
36459 GTTGTTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTTATTTATTTTAATTTAGGCACTA
Found at i:36834 original size:14 final size:14
Alignment explanation
Indices: 36817--36859 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
36807 TTTAATTTAT
*
36817 GCATTTACTTTTCA
1 GCATTTACATTTCA
*
36831 GCATGTACATTTCA
1 GCATTTACATTTCA
*
36845 GCATTTGCATTTCA
1 GCATTTACATTTCA
36859 G
1 G
36860 TCCTTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (14 bp):
GCATTTACATTTCA
Found at i:37438 original size:137 final size:139
Alignment explanation
Indices: 37183--37520 Score: 441
Period size: 137 Copynumber: 2.4 Consensus size: 139
37173 CCTTAAATGT
* * * * *
37183 TTAATTTAGGAGAATTTTTGATTTGGTCCTTGCTTATGCTCTAGGTTCCGAA-TTAATTATTCGA
1 TTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTCGAGGTTCC-AATTTAATTATTCGA
*
37247 TAGTACATAATTGATTAAAATTAATTAGGATTAATATTAAAGCCTCCATCTTAGGCCTAATTTCA
65 TAGTACATAATTGATTAAAATTAATTAGAATTAATATTAAAGCCTCCATCTTAGGCCTAATTTCA
*
37312 TATTTAATCC
130 CATTTAATCC
* * *
37322 TTAAATTAGGTGAATTCTTAATTTGGTCCTCGCTTGTGCTCGAGGTTCCAATTTAATTATTTGA-
1 TTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCAATTTAATTATTCGAT
* * * *
37386 A-T-CAATAATTGATTAAAGTTGATTAGAATTAATATTAGATCCTCCATCTTAGGCCTAATTTCA
66 AGTAC-ATAATTGATTAAAATTAATTAGAATTAATATTAAAGCCTCCATCTTAGGCCTAATTTCA
* *
37449 CCTTTAGTCC
130 CATTTAATCC
* * * * *
37459 TTAAATTAGAAGAATTCTTAATTTGGTCATCGCTTTTGCTCGAGATTCCACTTTAATTATTC
1 TTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCAATTTAATTATTC
37521 CAATTGCAAT
Statistics
Matches: 174, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
136 1 0.01
137 117 0.67
138 3 0.02
139 53 0.30
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (139 bp):
TTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCAATTTAATTATTCGAT
AGTACATAATTGATTAAAATTAATTAGAATTAATATTAAAGCCTCCATCTTAGGCCTAATTTCAC
ATTTAATCC
Found at i:40876 original size:15 final size:15
Alignment explanation
Indices: 40858--40887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40848 CCTATAAAAT
*
40858 TACAAGTTATAATTA
1 TACAAATTATAATTA
40873 TACAAATTATAATTA
1 TACAAATTATAATTA
40888 GACGTTCATG
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:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (15 bp):
TACAAATTATAATTA
Found at i:45194 original size:23 final size:22
Alignment explanation
Indices: 45168--45210 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
45158 TACTTTATGG
45168 CACATCTTCTTCTGTCTTTATAA
1 CACATCTTCTT-TGTCTTTATAA
* *
45191 CACATTTTCTTTGTTTTTAT
1 CACATCTTCTTTGTCTTTAT
45211 GGCACATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.56
Consensus pattern (22 bp):
CACATCTTCTTTGTCTTTATAA
Found at i:45216 original size:22 final size:23
Alignment explanation
Indices: 45160--45221 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
45150 ATAATTTTTA
*
45160 CTTTATGGCACATCTTCTTCTGT
1 CTTTATGGCACATTTTCTTCTGT
**
45183 CTTTATAACACATTTTCTT-TGT
1 CTTTATGGCACATTTTCTTCTGT
*
45205 TTTTATGGCACATTTTC
1 CTTTATGGCACATTTTC
45222 GGTCGTTTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.18, C:0.21, G:0.10, T:0.52
Consensus pattern (23 bp):
CTTTATGGCACATTTTCTTCTGT
Found at i:45766 original size:4 final size:4
Alignment explanation
Indices: 45757--45781 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
45747 ACACAAAAGA
45757 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
45782 GTTCAGTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:46693 original size:23 final size:23
Alignment explanation
Indices: 46637--46693 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
46627 GTTAGTAAAT
**
46637 ATGTTCGTTTAATGTTTGTGAAC
1 ATGTTCGTTTAATGTTTACGAAC
* * *
46660 GTGTGCATTTAATGTTTACGAAC
1 ATGTTCGTTTAATGTTTACGAAC
46683 ATGTTCGTTTA
1 ATGTTCGTTTA
46694 GCATTCTTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.46
Consensus pattern (23 bp):
ATGTTCGTTTAATGTTTACGAAC
Found at i:46715 original size:11 final size:11
Alignment explanation
Indices: 46701--46748 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
46691 TTAGCATTCT
*
46701 TTTAGTGTTTA
1 TTTAGTGTTTG
*
46712 TTTAGTGTTCG
1 TTTAGTGTTTG
* *
46723 TGTAGCGTTTG
1 TTTAGTGTTTG
46734 TTTAGTGTTTG
1 TTTAGTGTTTG
46745 TTTA
1 TTTA
46749 TCTTTCTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.12, C:0.04, G:0.25, T:0.58
Consensus pattern (11 bp):
TTTAGTGTTTG
Found at i:46722 original size:33 final size:33
Alignment explanation
Indices: 46684--46748 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
46674 TTTACGAACA
*
46684 TGTTCGTTTAGCATTCT-TTTAGTGTTTATTTAG
1 TGTTCGTGTAGCATT-TGTTTAGTGTTTATTTAG
* *
46717 TGTTCGTGTAGCGTTTGTTTAGTGTTTGTTTA
1 TGTTCGTGTAGCATTTGTTTAGTGTTTATTTA
46749 TCTTTCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.12, C:0.08, G:0.23, T:0.57
Consensus pattern (33 bp):
TGTTCGTGTAGCATTTGTTTAGTGTTTATTTAG
Found at i:48305 original size:47 final size:47
Alignment explanation
Indices: 48236--48449 Score: 214
Period size: 47 Copynumber: 4.6 Consensus size: 47
48226 TATCCTCGGA
* * * * *
48236 TGAGACCTAGGGTCACATAGCATTAGGAACGTACATTCGACATCGAG
1 TGAGGCCTGGGGTCACATAGCATCAGGAACATACACTCGACATCGAG
* * * * *
48283 TGAGACCTGGGGTCACATAGCATCAAGAACGTACACTCAATATCGAG
1 TGAGGCCTGGGGTCACATAGCATCAGGAACATACACTCGACATCGAG
* * *
48330 TGAGGCTTGAGATCACATAGCATCAGGAACATACAC-CTGACATCGAG
1 TGAGGCCTGGGGTCACATAGCATCAGGAACATACACTC-GACATCGAG
* * * * * * * *
48377 TAAGGCATGGGATAACATAACATCAGGAAAATACACTCTACATCGAA
1 TGAGGCCTGGGGTCACATAGCATCAGGAACATACACTCGACATCGAG
*
48424 TGAGGCCCGGGGTCACATAGCATCAG
1 TGAGGCCTGGGGTCACATAGCATCAG
48450 AAATGTACAT
Statistics
Matches: 137, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
46 1 0.01
47 135 0.99
48 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (47 bp):
TGAGGCCTGGGGTCACATAGCATCAGGAACATACACTCGACATCGAG
Done.