Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004602.1 Hibiscus syriacus cultivar Beakdansim tig00010286_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: 135704
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1654 original size:49 final size:48
Alignment explanation
Indices: 1564--1660 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 48
1554 ATTAATCAAC
*
1564 ATACATCACCAAATTGATCTTATCAAAACATGTCATGTCAAAATTATT
1 ATACATCACCAAATTGATCTTATCAAAACATATCATGTCAAAATTATT
*
1612 ATACATCACCAAATTGATCTTTATCCAAACATATCATGTCAAAATTATT
1 ATACATCACCAAATTGATC-TTATCAAAACATATCATGTCAAAATTATT
1661 TATATGCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 19 0.41
49 27 0.59
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (48 bp):
ATACATCACCAAATTGATCTTATCAAAACATATCATGTCAAAATTATT
Found at i:2293 original size:27 final size:27
Alignment explanation
Indices: 2255--2306 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
2245 GCAACAAGGT
2255 CAAGGATAGTACCACTGTCCACATTTA
1 CAAGGATAGTACCACTGTCCACATTTA
2282 CAAGGATAGTACCACTGTCCACATT
1 CAAGGATAGTACCACTGTCCACATT
2307 GGTCCGACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (27 bp):
CAAGGATAGTACCACTGTCCACATTTA
Found at i:3297 original size:19 final size:19
Alignment explanation
Indices: 3273--3309 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3263 ATAAAGAGAA
3273 TTAACCCTCAACATTTAAT
1 TTAACCCTCAACATTTAAT
* *
3292 TTAACCCTTATCATTTAA
1 TTAACCCTCAACATTTAA
3310 AAAGTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAACCCTCAACATTTAAT
Found at i:9268 original size:17 final size:18
Alignment explanation
Indices: 9237--9270 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9227 AATAAAAATT
*
9237 ATAAAAATCTATTGAAAA
1 ATAAAAATATATTGAAAA
9255 ATAAAAATAT-TTGAAA
1 ATAAAAATATATTGAAA
9271 TTTAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAAAAATATATTGAAAA
Found at i:14115 original size:22 final size:22
Alignment explanation
Indices: 14076--14123 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
14066 TTTTAACTAA
*
14076 TTTATAATTATATGTTTAGTAC-
1 TTTATAATTATATATTTA-TACG
14098 TTTATAATT-TATAATTTATACG
1 TTTATAATTATAT-ATTTATACG
14120 TTTA
1 TTTA
14124 GCATTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTATAATTATATATTTATACG
Found at i:14123 original size:30 final size:29
Alignment explanation
Indices: 14073--14134 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
14063 GATTTTTAAC
* *
14073 TAATTTATAATTATATGTTTAGTACTTTA
1 TAATTTATAATTATACGTTTAGCACTTTA
*
14102 TAATTTATAATTTATACGTTTAGCATTTTA
1 TAATTTATAA-TTATACGTTTAGCACTTTA
14132 TAA
1 TAA
14135 ATTAATTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.53
Consensus pattern (29 bp):
TAATTTATAATTATACGTTTAGCACTTTA
Found at i:14210 original size:2 final size:2
Alignment explanation
Indices: 14203--14248 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
14193 CATCATCCTT
14203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14245 TA TA
1 TA TA
14249 AATAATCTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14786 original size:496 final size:498
Alignment explanation
Indices: 14229--15178 Score: 1807
Period size: 496 Copynumber: 1.9 Consensus size: 498
14219 TATATATATA
14229 TATATATATATATATATATAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTTA
1 TATATATATATATATATATAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTTA
*
14294 ACTCTTGATAATAAATATACTATTAAGACCACTCTATAGATTATCTTATCTATATA-TTATATTA
66 ACTCTTGATAATAAATATACTATTAAGACCACTCAATAGATTATCTTATCTATATATTTATATTA
14358 TGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAGAAAAAAAATAAAATCTTTTGAATGAAAA
131 TGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAG-AAAAAAATAAAATCTTTTGAATGAAAA
14423 ATGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTAAATTAAAAATCAA
195 ATGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTAAATTAAAAATCAA
*
14488 AATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAGTTTTTATCGATTG
260 AATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAATTTTTATCGATTG
**
14553 ATTTATAATTATTTGTTAAATAAAATTTTATAATAATTTACTAATATTAAATATTTTCTTTTATC
325 ATCGATAATTATTTGTTAAATAAAATTTTATAATAATTTACTAATATTAAATATTTTCTTTTATC
14618 TATATTATAAATGTGACTC-GTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAATTTTTTT
390 TATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAATTTTTTT
14682 AACGGTACTCATCTGTACTCGTTGAGCGTGACATCATCATCCTT
455 AACGGTACTCATCTGTACTCGTTGAGCGTGACATCATCATCCTT
14726 TATATATATATATATAT-TAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTTA
1 TATATATATATATATATATAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTTA
14790 ACTCTTGATAATAAATATACTATTAAGACCACTCAATAGATTATCTTATCTATATATTTATATTA
66 ACTCTTGATAATAAATATACTATTAAGACCACTCAATAGATTATCTTATCTATATATTTATATTA
14855 TGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAGAAAAAAATAAAATCTTTTGAATGAAAAA
131 TGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAGAAAAAAATAAAATCTTTTGAATGAAAAA
*
14920 TGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTTAATTAAAAATCAAA
196 TGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTAAATTAAAAATCAAA
14985 ATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAATTTTTATCGATTGA
261 ATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAATTTTTATCGATTGA
*
15050 TCGATAATTATTTGTTAAATAAAATTTTATGATAATTTACTAATATTAAATATTTTCTTTTATCT
326 TCGATAATTATTTGTTAAATAAAATTTTATAATAATTTACTAATATTAAATATTTTCTTTTATCT
*
15115 ATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAGTTTTTTT
391 ATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAATTTTTTT
15179 CACATGCAAA
Statistics
Matches: 444, Mismatches: 7, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
496 338 0.76
497 106 0.24
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (498 bp):
TATATATATATATATATATAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTTA
ACTCTTGATAATAAATATACTATTAAGACCACTCAATAGATTATCTTATCTATATATTTATATTA
TGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAGAAAAAAATAAAATCTTTTGAATGAAAAA
TGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTAAATTAAAAATCAAA
ATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAATTTTTATCGATTGA
TCGATAATTATTTGTTAAATAAAATTTTATAATAATTTACTAATATTAAATATTTTCTTTTATCT
ATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAATTTTTTTA
ACGGTACTCATCTGTACTCGTTGAGCGTGACATCATCATCCTT
Found at i:15382 original size:20 final size:20
Alignment explanation
Indices: 15351--15415 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
15341 TTCCAAATTT
*
15351 GCAACACGAATATGTAAATC
1 GCAACGCGAATATGTAAATC
* *
15371 GTAACGCGAATATGTAAATT
1 GCAACGCGAATATGTAAATC
*
15391 GCAACGCGAATTTGTAAATC
1 GCAACGCGAATATGTAAATC
15411 GCAAC
1 GCAAC
15416 ACATAAGTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (20 bp):
GCAACGCGAATATGTAAATC
Found at i:15432 original size:20 final size:20
Alignment explanation
Indices: 15409--15451 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
15399 AATTTGTAAA
15409 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
15429 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
15449 TCG
1 TCG
15452 TAAAGCACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.21
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:15435 original size:40 final size:40
Alignment explanation
Indices: 15344--15437 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 40
15334 ACACAGTTTC
* * *
15344 CAAATTTGCAACACGAATATGTAAATCGTAACGCGAATATGT
1 CAAA-TTGCAACACGAATATGTAAATCGCAACAC-AATAAGT
* *
15386 -AAATTGCAACGCGAATTTGTAAATCGCAACAC-ATAAGT
1 CAAATTGCAACACGAATATGTAAATCGCAACACAATAAGT
15424 CAAATTCGCAACAC
1 CAAATT-GCAACAC
15438 ATAAGTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
38 5 0.11
39 5 0.11
40 31 0.70
41 3 0.07
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.23
Consensus pattern (40 bp):
CAAATTGCAACACGAATATGTAAATCGCAACACAATAAGT
Found at i:15987 original size:20 final size:20
Alignment explanation
Indices: 15964--16006 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
15954 AAACTTAAAT
15964 TCGTAACACGAAAATGAAAA
1 TCGTAACACGAAAATGAAAA
*
15984 TCGTAACGCGAAAATGAAAA
1 TCGTAACACGAAAATGAAAA
16004 TCG
1 TCG
16007 CAACGCGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (20 bp):
TCGTAACACGAAAATGAAAA
Found at i:16011 original size:20 final size:20
Alignment explanation
Indices: 15972--16014 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
15962 ATTCGTAACA
*
15972 CGAAAATGAAAATCGTAACG
1 CGAAAATGAAAATCGCAACG
15992 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACG
16012 CGA
1 CGA
16015 TTTTAGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.12
Consensus pattern (20 bp):
CGAAAATGAAAATCGCAACG
Found at i:16070 original size:20 final size:20
Alignment explanation
Indices: 16011--16073 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
16001 AAATCGCAAC
*
16011 GCGATTTT-AGTTTCGTGTT
1 GCGATTTTCATTTTCGTGTT
**
16030 GCGATTTTCATTTTCACGTT
1 GCGATTTTCATTTTCGTGTT
*
16050 GCGATTTTCATTTTTGTGTT
1 GCGATTTTCATTTTCGTGTT
16070 GCGA
1 GCGA
16074 ATTTAAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.13, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GCGATTTTCATTTTCGTGTT
Found at i:18007 original size:4 final size:4
Alignment explanation
Indices: 17998--18043 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
17988 TTTTTCGGCA
* * * *
17998 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
18044 TTAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:18209 original size:21 final size:22
Alignment explanation
Indices: 18181--18257 Score: 106
Period size: 21 Copynumber: 3.6 Consensus size: 22
18171 GATTCACCTG
18181 TCATCGTTCAAGAGGCCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
*
18203 T-ATCGTTCAAGAGGCTCCT-C
1 TCATCGTTCAAGAGGCCCCTCC
18223 TCATCGTTCAAGAGGCCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
* *
18245 -CACCGTTTAAGAG
1 TCATCGTTCAAGAG
18258 CCCGATTCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.04
21 45 0.92
22 2 0.04
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (22 bp):
TCATCGTTCAAGAGGCCCCTCC
Found at i:19155 original size:21 final size:21
Alignment explanation
Indices: 19129--19171 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
19119 CAAGAAGCCA
19129 AATAAGTTAAAAGTTACAATG
1 AATAAGTTAAAAGTTACAATG
19150 AATAAGTTAAAAGTTACAATG
1 AATAAGTTAAAAGTTACAATG
19171 A
1 A
19172 TGAGAGACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (21 bp):
AATAAGTTAAAAGTTACAATG
Found at i:19790 original size:20 final size:20
Alignment explanation
Indices: 19765--19803 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19755 GCACACTTTC
19765 GCAACGCGAAAATCAAATTT
1 GCAACGCGAAAATCAAATTT
*
19785 GCAACGCGAAAGTCAAATT
1 GCAACGCGAAAATCAAATT
19804 CGCGTTGCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
GCAACGCGAAAATCAAATTT
Found at i:19845 original size:20 final size:20
Alignment explanation
Indices: 19817--19860 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
19807 GTTGCGGTTA
*
19817 TTGCGAAAGTCAAATTCGAG
1 TTGCAAAAGTCAAATTCGAG
*
19837 TTGCAAAAGTCAAATTCGCG
1 TTGCAAAAGTCAAATTCGAG
19857 TTGC
1 TTGC
19861 GATTGTTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (20 bp):
TTGCAAAAGTCAAATTCGAG
Found at i:19889 original size:49 final size:49
Alignment explanation
Indices: 19793--19889 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
19783 TTGCAACGCG
* * *
19793 AAAGTCAAATTCGCGTTGCGGTTATTGCGAAAGTCAAATTCGAGTTGCA
1 AAAGTCAAATTCGCGTTGCGATTATTACGAAAGTCAAATTCCAGTTGCA
*
19842 AAAGTCAAATTCGCGTTGCGATTGTTACGAAAGTCAAA-TCCACGTTGC
1 AAAGTCAAATTCGCGTTGCGATTATTACGAAAGTCAAATTCCA-GTTGC
19890 GATTGTTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 3 0.07
49 40 0.93
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (49 bp):
AAAGTCAAATTCGCGTTGCGATTATTACGAAAGTCAAATTCCAGTTGCA
Found at i:22427 original size:24 final size:24
Alignment explanation
Indices: 22393--22446 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
22383 CTGAAACATC
22393 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
22417 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
22441 ATCAAA
1 ATCAAA
22447 TTTCGAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:22593 original size:12 final size:12
Alignment explanation
Indices: 22572--22605 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22562 GGTTGTGGGT
*
22572 TTTGAGATTGTG
1 TTTGATATTGTG
22584 TTTGATATTGTG
1 TTTGATATTGTG
*
22596 TTTGGTATTG
1 TTTGATATTG
22606 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:23433 original size:40 final size:40
Alignment explanation
Indices: 23370--23447 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
23360 TGCGAAATTT
* *
23370 AAATTCGTGTTGCAAATTCGAAAAT-TCAGTTGCGAAAACA
1 AAATTCGGGTTGCAAATTAGAAAATCT-AGTTGCGAAAACA
* * *
23410 AAATTCGGGTTGCGATTTAGAAAATCTTGTTGCGAAAA
1 AAATTCGGGTTGCAAATTAGAAAATCTAGTTGCGAAAA
23448 GGAAATTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (40 bp):
AAATTCGGGTTGCAAATTAGAAAATCTAGTTGCGAAAACA
Found at i:23493 original size:20 final size:20
Alignment explanation
Indices: 23465--23524 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
23455 TGTTTTACGA
23465 AAAAGAAATTCGCGTTGCGAG
1 AAAA-AAATTCGCGTTGCGAG
23486 AAAAAAATTCGCGTTGCGAG
1 AAAAAAATTCGCGTTGCGAG
*
23506 AAAAAAATTCGCATTGCGA
1 AAAAAAATTCGCGTTGCGA
23525 TTGCAAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 34 0.89
21 4 0.11
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAAAAATTCGCGTTGCGAG
Found at i:24337 original size:15 final size:15
Alignment explanation
Indices: 24313--24348 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
24303 GTATCATTAA
*
24313 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
24328 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
24343 ATTAAA
1 ATTAAA
24349 CGTATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:24655 original size:9 final size:9
Alignment explanation
Indices: 24641--24673 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
24631 GGTCCTAACT
24641 TTTAATTAA
1 TTTAATTAA
24650 TTTAATTAA
1 TTTAATTAA
*
24659 TTTAATAAA
1 TTTAATTAA
24668 TTTAAT
1 TTTAAT
24674 CCTCAATCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TTTAATTAA
Found at i:26109 original size:23 final size:23
Alignment explanation
Indices: 26083--26133 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
26073 ATATATGTTA
* *
26083 TTTTAATTAAATTATATTTATAT
1 TTTTAACTAAATTATAATTATAT
*
26106 TTTTAACTAATTTATAATTATAT
1 TTTTAACTAAATTATAATTATAT
*
26129 GTTTA
1 TTTTA
26134 GTACTTTGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTAACTAAATTATAATTATAT
Found at i:36009 original size:21 final size:21
Alignment explanation
Indices: 35983--36077 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
35973 GATTTACATA
35983 TTCGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
36004 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
36025 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
36046 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
36065 TTTGCGTTACGAT
1 TTCGCGTTGCGAT
36078 TTATTACAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 16 0.25
21 47 0.75
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:36053 original size:19 final size:19
Alignment explanation
Indices: 36029--36098 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
36019 TCGAAGTTCG
36029 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
36048 CGTTGCGATAGTCCAAGTTT
1 CGTTGCGATTTTCCAA-ATT
* *
36068 GCGTTACGATTTATTACAAATT
1 -CGTTGCGA-TT-TTCCAAATT
36090 CGTTGCGAT
1 CGTTGCGAT
36099 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
19 14 0.37
20 3 0.08
21 14 0.37
22 3 0.08
23 4 0.11
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:36100 original size:42 final size:40
Alignment explanation
Indices: 36008--36105 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 40
35998 TCCAAGTTCG
* * *
36008 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTACGATTTTACAAATT
*
36048 CGTTGCGATAGTCCAAGTTTGCGTTACGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTACGA-TT-TTACAAATT
36090 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
36106 AATCGCAACG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 26 0.50
41 2 0.04
42 24 0.46
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCGCGTTACGATTTTACAAATT
Found at i:36105 original size:61 final size:60
Alignment explanation
Indices: 35987--36106 Score: 136
Period size: 61 Copynumber: 2.0 Consensus size: 60
35977 TACATATTCG
* * **
35987 CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTACGATAGTCGAAATTC-CGTTGCGATAGTCCAAATT
* *
36048 CGTTGCGATAGTCCAAGTTTGCGTTACGATTTATTAC-AAATT-CGTTGCGATAGTCCAAA
1 CGTTGCGATAGTCCAAGTTCGCGTTACGA--TAGT-CGAAATTCCGTTGCGATAGTCCAAA
36107 ATCGCAACGA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
61 42 0.84
63 7 0.14
64 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (60 bp):
CGTTGCGATAGTCCAAGTTCGCGTTACGATAGTCGAAATTCCGTTGCGATAGTCCAAATT
Found at i:37251 original size:21 final size:21
Alignment explanation
Indices: 37225--37369 Score: 229
Period size: 21 Copynumber: 6.9 Consensus size: 21
37215 TGCGATTTTG
37225 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
37246 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
* *
37267 GACTACCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
37288 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
*
37309 GACT-TCCGCAACGAACTTGGA
1 GACTAT-CGCAACGAATTTGGA
* *
37330 GACTATCACAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
37351 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
37370 TAATAAATCG
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
20 1 0.01
21 112 0.98
22 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGAATTTGGA
Found at i:37397 original size:42 final size:40
Alignment explanation
Indices: 37341--37443 Score: 143
Period size: 40 Copynumber: 2.5 Consensus size: 40
37331 ACTATCACAA
*
37341 CGAACTTGGAGACTATCGCAACGAATTTGTAATAAATCGTAACG
1 CGAACTT-G-GACTATCGCAACGAATTTG-AA-AAATCGCAACG
*
37385 CGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACG
1 CGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACG
*
37425 CGAACTTCGACTATCGCAA
1 CGAACTTGGACTATCGCAA
37444 TGCGAATATG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
40 28 0.50
41 1 0.02
42 19 0.34
43 1 0.02
44 7 0.12
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (40 bp):
CGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACG
Found at i:37397 original size:63 final size:63
Alignment explanation
Indices: 37225--37413 Score: 206
Period size: 63 Copynumber: 3.0 Consensus size: 63
37215 TGCGATTTTG
* * * * *
37225 GACTATCGCAACGAATTTGGAGACTAT-CGCAACGAATTTGGAGACTACCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGAAGA-AATCCGCAACGAACTTGGAGACTATCACAACGAACTTGGA
* **
37288 GACTATCGCAACGAATTTGGAGACTTCCGCAACGAACTTGGAGACTATCACAACGAACTTGGA
1 GACTATCGCAACGAATTTGAAGAAATCCGCAACGAACTTGGAGACTATCACAACGAACTTGGA
* * * *
37351 GACTATCGCAACGAATTTGTAATAAAT-CGTAACGCGAACTT-G-GACTATCGCAACGAATTTGG
1 GACTATCGCAACGAATTTG-AAGAAATCCGCAA--CGAACTTGGAGACTATCACAACGAACTTGG
37413 A
63 A
37414 AAATCGCAAC
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
62 1 0.01
63 98 0.89
64 4 0.04
65 7 0.06
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (63 bp):
GACTATCGCAACGAATTTGAAGAAATCCGCAACGAACTTGGAGACTATCACAACGAACTTGGA
Found at i:37400 original size:21 final size:21
Alignment explanation
Indices: 37376--37449 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
37366 TTTGTAATAA
*
37376 ATCGTAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
37397 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
37416 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
37437 ATCGCAATGCGAA
1 ATCGCAACGCGAA
37450 TATGTAAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
19 16 0.38
21 26 0.62
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:42890 original size:22 final size:22
Alignment explanation
Indices: 42865--42926 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
42855 AAACTCTGTC
*
42865 AAAGATCGGTGATGAAGCCATT
1 AAAGAACGGTGATGAAGCCATT
*
42887 AAAGAACGGTGATGAATCCATT
1 AAAGAACGGTGATGAAGCCATT
* **
42909 GAAGAACTATGATGAAGC
1 AAAGAACGGTGATGAAGC
42927 TGTTACTTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (22 bp):
AAAGAACGGTGATGAAGCCATT
Found at i:48147 original size:36 final size:36
Alignment explanation
Indices: 48100--48171 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
48090 TAGAAAAAGG
*
48100 GAGGGAATAGATGAAATATTGGGATTTGGTTAGACT
1 GAGGGAATAGATGAAAGATTGGGATTTGGTTAGACT
48136 GAGGGAATAGATGAAAGATTGGGATTTGGTTAGACT
1 GAGGGAATAGATGAAAGATTGGGATTTGGTTAGACT
48172 AACTTTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.29
Consensus pattern (36 bp):
GAGGGAATAGATGAAAGATTGGGATTTGGTTAGACT
Found at i:48645 original size:18 final size:18
Alignment explanation
Indices: 48622--48667 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
48612 CGAATTTATT
48622 AATGCTATGATGATGTGA
1 AATGCTATGATGATGTGA
48640 AATGCTATGATGATGTGA
1 AATGCTATGATGATGTGA
48658 AATGCTATGA
1 AATGCTATGA
48668 GCAGCCACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33
Consensus pattern (18 bp):
AATGCTATGATGATGTGA
Found at i:59960 original size:12 final size:13
Alignment explanation
Indices: 59934--59966 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
59924 GAATCCTACA
*
59934 TTTTTTCTTAGAT
1 TTTTTTTTTAGAT
59947 TTTTTTTTTA-AT
1 TTTTTTTTTAGAT
59959 TTTTTTTT
1 TTTTTTTT
59967 CACGCTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTAGAT
Found at i:64887 original size:47 final size:47
Alignment explanation
Indices: 64818--64925 Score: 189
Period size: 47 Copynumber: 2.3 Consensus size: 47
64808 CTATCGGATA
*
64818 TCTCGGCGTCTTCTATATATGTTAGTTCAAACGATGTTCATGGGAGC
1 TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
* *
64865 TCTCGGCGTCTTCTATATATGTTCGTTCAAAAGATGTTCATGGGAGT
1 TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
64912 TCTCGGCGTCTTCT
1 TCTCGGCGTCTTCT
64926 TCAGCCTTGG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (47 bp):
TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
Found at i:64943 original size:32 final size:32
Alignment explanation
Indices: 64907--64992 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
64897 GATGTTCATG
*
64907 GGAGTTCTCGGCGTCTTCTTCAGCCTTGGGGT
1 GGAGTTCTCGGCGTCTTCTTCAACCTTGGGGT
*
64939 GGAGTTCTTGGCGTCTTCTTCAACCTTGGGGT
1 GGAGTTCTCGGCGTCTTCTTCAACCTTGGGGT
* *
64971 GGAGTTTTCGACGTCTTCTTCA
1 GGAGTTCTCGGCGTCTTCTTCA
64993 TCAGCATCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.09, C:0.23, G:0.30, T:0.37
Consensus pattern (32 bp):
GGAGTTCTCGGCGTCTTCTTCAACCTTGGGGT
Found at i:69803 original size:13 final size:13
Alignment explanation
Indices: 69785--69810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69775 GTAATGTAAT
69785 AACATATAATCAC
1 AACATATAATCAC
69798 AACATATAATCAC
1 AACATATAATCAC
69811 TAAACCTTAA
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:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
AACATATAATCAC
Found at i:69917 original size:26 final size:28
Alignment explanation
Indices: 69883--69938 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
69873 TTGACTACGA
69883 TGATGA-TCCTCTCACTCTCTTTGCTTC
1 TGATGACTCCTCTCACTCTCTTTGCTTC
69910 TGAT-ATCCTTCCTCTCACTCTCTTTGCTT
1 TGATGA--C-TCCTCTCACTCTCTTTGCTT
69939 GTGTTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 1 0.04
27 4 0.16
30 20 0.80
ACGTcount: A:0.11, C:0.34, G:0.09, T:0.46
Consensus pattern (28 bp):
TGATGACTCCTCTCACTCTCTTTGCTTC
Found at i:70117 original size:30 final size:32
Alignment explanation
Indices: 70046--70126 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 32
70036 ATCCCCTCCC
*
70046 ATGTGAAGAAAACGCCGAGCATTCCACCCCAA
1 ATGTGAAGAAAACGCCGAGCAATCCACCCCAA
* *
70078 ATTGTGAAGAAAACGTCGAGTAATCCA-CCCAA
1 A-TGTGAAGAAAACGCCGAGCAATCCACCCCAA
*
70110 A-GTGAAGAAGACGCCGA
1 ATGTGAAGAAAACGCCGA
70127 TACATCCTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
30 14 0.33
32 7 0.16
33 22 0.51
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.14
Consensus pattern (32 bp):
ATGTGAAGAAAACGCCGAGCAATCCACCCCAA
Found at i:70192 original size:20 final size:20
Alignment explanation
Indices: 70167--70205 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
70157 CTATTATCAA
*
70167 CTCACCCCGTGAATTCCCTG
1 CTCACCACGTGAATTCCCTG
70187 CTCACCACGTGAATTCCCT
1 CTCACCACGTGAATTCCCT
70206 TTTGCGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.44, G:0.13, T:0.26
Consensus pattern (20 bp):
CTCACCACGTGAATTCCCTG
Found at i:78625 original size:23 final size:22
Alignment explanation
Indices: 78598--78640 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
78588 TATAAAAAAT
78598 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
78621 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
78641 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:79224 original size:4 final size:4
Alignment explanation
Indices: 79217--79401 Score: 370
Period size: 4 Copynumber: 46.2 Consensus size: 4
79207 AACAAGATAG
79217 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
79265 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
79313 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
79361 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
79402 AGAGAAAAAA
Statistics
Matches: 181, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 181 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:80801 original size:2 final size:2
Alignment explanation
Indices: 80790--80826 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
80780 ATATTATACT
80790 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80827 ATGTCTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:81293 original size:16 final size:16
Alignment explanation
Indices: 81272--81304 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
81262 GATATTTTTC
81272 TTAAAGTAGTCTAAAA
1 TTAAAGTAGTCTAAAA
81288 TTAAAGTAGTCTAAAA
1 TTAAAGTAGTCTAAAA
81304 T
1 T
81305 AAATAATGAA
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:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (16 bp):
TTAAAGTAGTCTAAAA
Found at i:87440 original size:13 final size:14
Alignment explanation
Indices: 87412--87445 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
87402 TGATATAGGT
87412 AAATACGGTAAAAA
1 AAATACGGTAAAAA
*
87426 AAATTCGGTAAAAA
1 AAATACGGTAAAAA
87440 ATAATA
1 A-AATA
87446 TTTTAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 14 0.82
15 3 0.18
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (14 bp):
AAATACGGTAAAAA
Found at i:88963 original size:18 final size:18
Alignment explanation
Indices: 88906--88965 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 18
88896 ATTTTTTAAA
*
88906 TTTAAATTTAAT-ATATT
1 TTTATATTTAATAATATT
*
88923 TTTATTATTTATTTTCAATTATT
1 TTTA-TATTTA--AT-AA-TATT
88946 TTTATATTTAATAATATT
1 TTTATATTTAATAATATT
88964 TT
1 TT
88966 AAAATGTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
17 4 0.12
18 11 0.32
19 2 0.06
20 2 0.06
22 7 0.21
23 8 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATATTTAATAATATT
Found at i:89387 original size:14 final size:14
Alignment explanation
Indices: 89368--89396 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
89358 ATTAAATAAA
89368 AATAAAAAAAATTT
1 AATAAAAAAAATTT
89382 AATAAAAAAAATTT
1 AATAAAAAAAATTT
89396 A
1 A
89397 GATTGAACCG
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAAAAAAAATTT
Found at i:90881 original size:3 final size:3
Alignment explanation
Indices: 90873--90912 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
90863 CACAAATACA
*
90873 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
90913 TGAGGTGATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:97030 original size:12 final size:11
Alignment explanation
Indices: 96999--97033 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
96989 AAATGTATAA
*
96999 TTTTATTATAT
1 TTTTATTATTT
97010 TTTTATTATTT
1 TTTTATTATTT
97021 TTTATATTATTT
1 TTT-TATTATTT
97033 T
1 T
97034 ATAAATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTATTT
Found at i:106647 original size:21 final size:21
Alignment explanation
Indices: 106621--106897 Score: 105
Period size: 21 Copynumber: 12.6 Consensus size: 21
106611 GATTTACATA
106621 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
106642 TTCGCATTGTGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* **
106663 TTCGCGTTGCGATTTTCCAAATTCG
1 TTCGCATTGCGATAGTCC-AA---G
** * * * *
106688 ACTATCGCAACGCGA-ACTTCGAC
1 --T-TCGCATTGCGATAGTCCAAG
* *
106711 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
106732 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
106753 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* ** *
106774 TTCGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCCAAG
* * * * * *
106795 TTCGACTATCGCAACGTAAACTTCGAC
1 TTCG-C-ATTG---CG-ATAGTCCAAG
* * *
106822 TATCGCATTGTGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
106843 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
106864 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
106885 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
106898 TTTCCAAATT
Statistics
Matches: 188, Mismatches: 47, Indels: 42
0.68 0.17 0.15
Matches are distributed among these distances:
20 25 0.13
21 127 0.68
22 6 0.03
23 3 0.02
25 1 0.01
26 6 0.03
27 9 0.05
28 11 0.06
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:106775 original size:111 final size:111
Alignment explanation
Indices: 106581--106987 Score: 715
Period size: 111 Copynumber: 3.7 Consensus size: 111
106571 GTTTCCATAT
106581 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
*
106646 CATTGTGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
106692 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
106757 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
** *
106803 TCGCAACGTAAACTTCGACTATCGCATTGTGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
*
106868 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTAGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
* * * *
106914 TCACAACGTGAACTTCAACTATCGCATTGTGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
**
106979 TGTTGCGAT
66 CATTGCGAT
106988 TTTCCAAATT
Statistics
Matches: 286, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 286 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (111 bp):
TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
Found at i:106904 original size:42 final size:42
Alignment explanation
Indices: 106843--107052 Score: 144
Period size: 42 Copynumber: 4.9 Consensus size: 42
106833 GATTTACATA
* ** *
106843 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTTCCAAATTCGCATTGCGATAGTCGAAG
* ** * * *
106885 TTCGCGTTGCGATTTTCCAAATTAGACTATCACAACGTGAACTTC-AAC
1 TTCGCGTTGCGATTTTCCAAATTCG-C-ATTGCGA--T--A-GTCGAAG
* * * * *
106933 TATCGCATTGTGA-TTTACATATTCGCATTGCGATAGTCCAAG
1 T-TCGCGTTGCGATTTTCCAAATTCGCATTGCGATAGTCGAAG
*
106975 TTCGTGTTGCGATTTTCCAAATTCG--TTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTTCCAAATTCGCATTGCGATAGTCGAAG
107015 TTCGCGTTGCGATTTATTCCAAATTCG--TTGCGATAGTC
1 TTCGCGTTGCGA-TT-TTCCAAATTCGCATTGCGATAGTC
107053 CAAAATCGCA
Statistics
Matches: 129, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
40 25 0.19
41 12 0.09
42 56 0.43
43 1 0.01
44 5 0.04
46 5 0.04
47 1 0.01
48 13 0.10
49 11 0.09
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (42 bp):
TTCGCGTTGCGATTTTCCAAATTCGCATTGCGATAGTCGAAG
Found at i:106984 original size:21 final size:19
Alignment explanation
Indices: 106960--107056 Score: 86
Period size: 21 Copynumber: 4.8 Consensus size: 19
106950 CATATTCGCA
*
106960 TTGCGATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAATTC--G
**
106981 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAATTCG
* *
107000 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
*
107021 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCG
107042 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
107057 ATCGCAACGA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
19 22 0.36
21 31 0.51
23 8 0.13
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:107004 original size:40 final size:42
Alignment explanation
Indices: 106960--107055 Score: 160
Period size: 40 Copynumber: 2.3 Consensus size: 42
106950 CATATTCGCA
*
106960 TTGCGATAGTCCAAGTTCGTGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
107000 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
107042 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
107056 AATCGCAACG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 25 0.49
41 2 0.04
42 24 0.47
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:111043 original size:20 final size:20
Alignment explanation
Indices: 111018--111055 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
111008 CTTGGTTCAC
111018 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
111038 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
111056 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:111170 original size:20 final size:20
Alignment explanation
Indices: 111145--111202 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
111135 TTTGGTTCAC
111145 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
111165 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
111185 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
111203 GGAATATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.10, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:111394 original size:37 final size:36
Alignment explanation
Indices: 111352--111425 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
111342 GTTGGAAAAT
*
111352 ATTTATAT-ATTTTATTTAAAAAAAATAAATTCATAAA
1 ATTTATATAATTTT-TTTAAAAAAAATAAAAT-ATAAA
* * *
111389 ATTTATTTAATTTTTTTACAAAAATTAAAATATAAA
1 ATTTATATAATTTTTTTAAAAAAAATAAAATATAAA
111425 A
1 A
111426 AGATTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 21 0.66
38 5 0.16
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTTATATAATTTTTTTAAAAAAAATAAAATATAAA
Found at i:112033 original size:27 final size:27
Alignment explanation
Indices: 111995--112047 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
111985 AACCCAATCA
*
111995 AGAAATTGTTGGAAGCTCTCCTAATTT
1 AGAAATTGTTGGAAGCTCCCCTAATTT
*
112022 AGAATTTGTTGGAAGCTCCCCTAATT
1 AGAAATTGTTGGAAGCTCCCCTAATT
112048 CTTCCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (27 bp):
AGAAATTGTTGGAAGCTCCCCTAATTT
Found at i:114472 original size:31 final size:29
Alignment explanation
Indices: 114434--114556 Score: 122
Period size: 31 Copynumber: 4.0 Consensus size: 29
114424 AAATATAGAG
*
114434 GTTAAATTATTATTTTATCTAAAGTTTAAGA
1 GTTAAATTAATATTTTATCTAAA-TTTAA-A
*
114465 GTTAAATTAATGTTTTATCTGAAATTTAAAA
1 GTTAAATTAATATTTTATCT-AAATTT-AAA
* *
114496 ATTAAATTGAT-TTTTATCTAATATTTAAA
1 GTTAAATTAATATTTTATCTAA-ATTTAAA
* *
114525 GGTTAGATTAATATTTTATCCAAAATTTAAA
1 -GTTAAATTAATATTTTAT-CTAAATTTAAA
114556 G
1 G
114557 AATAAATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.06
30 21 0.27
31 44 0.56
32 8 0.10
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (29 bp):
GTTAAATTAATATTTTATCTAAATTTAAA
Found at i:114523 original size:61 final size:61
Alignment explanation
Indices: 114446--114564 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 61
114436 TAAATTATTA
* **
114446 TTTTATCTAAAGTTT-AAGAGTTAAATTAATGTTTTATCTGAAATTTAAA-AATTAAATTGAT
1 TTTTATCTAAAGTTTAAAG-GTTAAATTAATATTTTATCCAAAATTTAAAGAA-TAAATTGAT
*
114507 TTTTATCTAATA-TTTAAAGGTTAGATTAATATTTTATCCAAAATTTAAAGAATAAATT
1 TTTTATCTAA-AGTTTAAAGGTTAAATTAATATTTTATCCAAAATTTAAAGAATAAATT
114565 TAAAATTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
61 45 0.88
62 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (61 bp):
TTTTATCTAAAGTTTAAAGGTTAAATTAATATTTTATCCAAAATTTAAAGAATAAATTGAT
Found at i:119597 original size:15 final size:16
Alignment explanation
Indices: 119577--119614 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
119567 CAATTTGATT
119577 AAAATAATAAA-TTAA
1 AAAATAATAAATTTAA
119592 AAAAT-ATAAATTTAA
1 AAAATAATAAATTTAA
*
119607 AATATAAT
1 AAAATAAT
119615 TCGTTATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 5 0.25
15 13 0.65
16 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATAATAAATTTAA
Found at i:119613 original size:13 final size:13
Alignment explanation
Indices: 119575--119613 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
119565 AGCAATTTGA
119575 TTAAAATAATAAAT
1 TTAAAAT-ATAAAT
*
119589 TAAAAAATATAAAT
1 T-TAAAATATAAAT
119603 TTAAAATATAA
1 TTAAAATATAA
119614 TTCGTTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 8 0.36
15 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAAATATAAAT
Found at i:129984 original size:17 final size:18
Alignment explanation
Indices: 129953--129986 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
129943 AAAGTAGTAA
*
129953 TTAAAAATTACATTATTT
1 TTAAAAATTAAATTATTT
129971 TTAAAAA-TAAATTATT
1 TTAAAAATTAAATTATT
129987 ATTATTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAAATTAAATTATTT
Done.