Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002810.1 Hibiscus syriacus cultivar Beakdansim tig00005779_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: 70972
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:3793 original size:15 final size:15
Alignment explanation
Indices: 3773--3802 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3763 TTCTGGCTAT
3773 TTAAGGATGCTGAAC
1 TTAAGGATGCTGAAC
3788 TTAAGGATGCTGAAC
1 TTAAGGATGCTGAAC
3803 GGGCAGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
TTAAGGATGCTGAAC
Found at i:11391 original size:21 final size:22
Alignment explanation
Indices: 11354--11399 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
11344 TCAAAATTTT
*
11354 ATTTTAATATAAAATATTTATA
1 ATTTTAATATAAAATATTCATA
*
11376 ATTTTAATA-CAAATATTCATA
1 ATTTTAATATAAAATATTCATA
11397 ATT
1 ATT
11400 AAAAAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTAATATAAAATATTCATA
Found at i:12311 original size:18 final size:17
Alignment explanation
Indices: 12257--12305 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
12247 TTGGACTCTC
* *
12257 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
12275 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
12293 AGTGCATTCGATG
1 AGTGCA-TCGATG
12306 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:12833 original size:24 final size:25
Alignment explanation
Indices: 12806--12855 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
12796 CCCCTTACTA
12806 TAACAC-TTAAAACTTCTCCCCCTT
1 TAACACTTTAAAACTTCTCCCCCTT
* *
12830 TAACACTTTTACACTTCTCCCCCTT
1 TAACACTTTAAAACTTCTCCCCCTT
12855 T
1 T
12856 TTGTTAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (25 bp):
TAACACTTTAAAACTTCTCCCCCTT
Found at i:19026 original size:149 final size:149
Alignment explanation
Indices: 18582--19041 Score: 856
Period size: 146 Copynumber: 3.1 Consensus size: 149
18572 TATAATTGCA
* *
18582 CCGAAGTACCACGTAGAATTGCACCGTAGTGCCATAT-ATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
18646 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
18711 CACAGAATATATATATATC
131 CACAGAATATATATATATC
*
18730 CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCAC--A-TAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
18792 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
18857 CACAGAATATATATATATC
131 CACAGAATATATATATATC
18876 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
*
18941 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACTTGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
19006 CACAGAATATATATATATC
131 CACAGAATATATATATATC
19025 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
19042 CCCTTTACCC
Statistics
Matches: 303, Mismatches: 5, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
146 144 0.48
147 1 0.00
148 35 0.12
149 123 0.41
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:19601 original size:63 final size:63
Alignment explanation
Indices: 19495--19652 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 63
19485 TAATGGAGGC
* * * *
19495 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGCATTCGATGTTCAT-TTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AAGAA
** **
19558 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
* * *
19621 ATGCATCGATACACTTCATATGCATCGATGCA
1 ATGCATCGATGCACTCCTTATGCATCGATGCA
19653 TCTTCAATAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
63 79 0.95
64 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
Found at i:25771 original size:23 final size:23
Alignment explanation
Indices: 25745--25790 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
25735 CACCACAGCT
*
25745 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
25768 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
25791 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:26163 original size:149 final size:149
Alignment explanation
Indices: 25768--26218 Score: 888
Period size: 149 Copynumber: 3.0 Consensus size: 149
25758 CGAAGTGCCA
25768 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
25833 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
25896 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
25915 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
25980 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
26045 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
26064 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
26129 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
26194 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
26213 CGTAGA
1 CGTAGA
26219 CCCTCTACCC
Statistics
Matches: 302, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
147 124 0.41
148 1 0.00
149 177 0.59
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:26785 original size:63 final size:63
Alignment explanation
Indices: 26674--26831 Score: 192
Period size: 63 Copynumber: 2.5 Consensus size: 63
26664 TAATGGAGGC
* * * *
26674 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGCATTCGATGTTCAT-TTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AAGAA
* ** **
26737 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTTGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
* * *
26800 TTGCATCGATGCACTTCATATGCATCGATGCA
1 ATGCATCGATGCACTCCTTATGCATCGATGCA
26832 TCTTCAACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
63 78 0.95
64 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
Found at i:32498 original size:20 final size:20
Alignment explanation
Indices: 32475--32517 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
32465 AATCCACCAC
* *
32475 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
32495 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
32515 ATG
1 ATG
32518 GGCTCTTAGA
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:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:37432 original size:20 final size:20
Alignment explanation
Indices: 37409--37451 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
37399 AATCCACCAC
*
37409 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
37429 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
37449 ATG
1 ATG
37452 GGCTCTTAGA
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:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:37628 original size:31 final size:31
Alignment explanation
Indices: 37593--37678 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
37583 CTGACACTCT
* *
37593 TGTGCATTATCTGAATGCAATCTGACCATAC
1 TGTGCATTATCTGAATGCAACCTGACCATAA
**
37624 TGTGCATTATCTGAATATAACCTGACCATAA
1 TGTGCATTATCTGAATGCAACCTGACCATAA
* *
37655 TGTGCATTTTCTGAATGCACCCTG
1 TGTGCATTATCTGAATGCAACCTG
37679 GCTAGTGTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (31 bp):
TGTGCATTATCTGAATGCAACCTGACCATAA
Found at i:46516 original size:12 final size:12
Alignment explanation
Indices: 46499--46523 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46489 GTATTTGAAG
46499 AAAAAAAAAACT
1 AAAAAAAAAACT
46511 AAAAAAAAAACT
1 AAAAAAAAAACT
46523 A
1 A
46524 GTACATTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAACT
Found at i:47263 original size:18 final size:17
Alignment explanation
Indices: 47240--47273 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
47230 TAAAAGAATG
47240 GGAAAATAAAATGAAAAA
1 GGAAAATAAAAT-AAAAA
47258 GGAAAATAAAATAAAA
1 GGAAAATAAAATAAAA
47274 TACTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
GGAAAATAAAATAAAAA
Found at i:47378 original size:17 final size:15
Alignment explanation
Indices: 47319--47386 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 15
47309 TGTTAACTTT
*
47319 TAAAAATAA-AATAA
1 TAAAAAAAATAATAA
*
47333 TATAAAAAATAATAA
1 TAAAAAAAATAATAA
* *
47348 TACTAATAACATAATAA
1 TA--AAAAAAATAATAA
47365 TAGAAAAAAGATAA-AA
1 TA-AAAAAA-ATAATAA
47381 TAAAAA
1 TAAAAA
47387 TTGAGGGGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 7 0.17
15 11 0.26
16 8 0.19
17 16 0.38
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (15 bp):
TAAAAAAAATAATAA
Found at i:48498 original size:14 final size:14
Alignment explanation
Indices: 48477--48554 Score: 65
Period size: 14 Copynumber: 5.5 Consensus size: 14
48467 CTAAAACGAG
48477 AAAAATAATAAATA
1 AAAAATAATAAATA
*
48491 ATAAAT-A-AAATAA
1 AAAAATAATAAAT-A
*
48504 AATAAATAAAAAAGTA
1 AA-AAATAATAAA-TA
48520 GAAAAATAATAAAT-
1 -AAAAATAATAAATA
48534 AAAAA-AATATAATA
1 AAAAATAATA-AATA
48548 AAAAATA
1 AAAAATA
48555 TTTTTAAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
12 8 0.15
13 11 0.21
14 14 0.27
15 3 0.06
16 13 0.25
17 3 0.06
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAAATAATAAATA
Found at i:48503 original size:12 final size:12
Alignment explanation
Indices: 48486--48554 Score: 63
Period size: 12 Copynumber: 5.7 Consensus size: 12
48476 GAAAAATAAT
48486 AAATAATAAATA
1 AAATAATAAATA
48498 AAATAAAATAAATA
1 AAAT--AATAAATA
*
48512 AAA-AAGTAGA-A
1 AAATAA-TAAATA
48523 AAATAATAAATA
1 AAATAATAAATA
*
48535 AAAAAATATAATA
1 AAATAATA-AATA
48548 AAA-AATA
1 AAATAATA
48555 TTTTTAAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
11 9 0.19
12 21 0.44
13 7 0.15
14 11 0.23
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (12 bp):
AAATAATAAATA
Found at i:48506 original size:17 final size:16
Alignment explanation
Indices: 48486--48549 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 16
48476 GAAAAATAAT
48486 AAATAATAAATAAAATA
1 AAATAATAAATAAAA-A
*
48503 AAATAAATAAAAAAGTAGAA
1 AAAT-AATAAATAA--A-AA
48523 AAATAATAAATAAAAA
1 AAATAATAAATAAAAA
48539 AATATAATAAA
1 AA-ATAATAAA
48550 AAATATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 4 0.10
17 13 0.32
18 8 0.20
19 8 0.20
20 6 0.15
21 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATAATAAATAAAAA
Found at i:48571 original size:23 final size:25
Alignment explanation
Indices: 48536--48594 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
48526 TAATAAATAA
48536 AAAAATATAATAAAAAATAT-TTTT
1 AAAAATATAATAAAAAATATGTTTT
* * *
48560 AAAACTAT-ATAATATATATGTTTT
1 AAAAATATAATAAAAAATATGTTTT
*
48584 AAAAAAATAAT
1 AAAAATATAAT
48595 TTTCAAAACT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 9 0.32
24 17 0.61
25 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAAATATAATAAAAAATATGTTTT
Found at i:48632 original size:74 final size:73
Alignment explanation
Indices: 48546--48913 Score: 469
Period size: 74 Copynumber: 5.0 Consensus size: 73
48536 AAAAATATAA
* *
48546 TAAAAAAT-ATTTTTAAAACTATATAATATATATGTTTTAAAAAAATAATTTTCAAAACTACATA
1 TAAAAAATAATTTTCAAAACTATATAATATATAT-TTTT-AAAAAATAATTTTCAAAACTATATA
48610 ATATATA-TT
64 ATATATATTT
48619 TAAAAAATAATTTTCAAAACTATATAATATATATTTTT-AAAAATAATTTTCAAAACTATATAAT
1 TAAAAAATAATTTTCAAAACTATATAATATATATTTTTAAAAAATAATTTTCAAAACTATATAAT
48683 ATATATTT
66 ATATATTT
* *
48691 TTAAAAATAATTTTCAAAACTATATAATATATATATTTTTAAAAATAATTTTCAAAACTATATAA
1 TAAAAAATAATTTTCAAAACTATATAATATATAT-TTTTAAAAAATAATTTTCAAAACTATATAA
48756 TATTTATATTT
65 TA--TATATTT
* * *
48767 TTAAAAATAATTTTCAAAACTATATAATACATATATTTTTCAAAAATAATTTTCAAAATTATATA
1 TAAAAAATAATTTTCAAAACTATATAAT--ATATATTTTTAAAAAATAATTTTCAAAACTATATA
48832 GTATATATATTT
64 --ATATATATTT
* ** * ** *
48844 TCAAAAATTGTTTTAAAAACTATATATTATATATATTTTT---AAATTTTTTTAAAAACTATATA
1 TAAAAAATAATTTTCAAAACTATATA--ATATATATTTTTAAAAAATAATTTTCAAAACTATATA
48906 ATATATAT
64 ATATATAT
48914 ATATATATAT
Statistics
Matches: 270, Mismatches: 13, Indels: 25
0.88 0.04 0.08
Matches are distributed among these distances:
71 30 0.11
72 43 0.16
73 16 0.06
74 69 0.26
76 35 0.13
77 66 0.24
78 6 0.02
79 5 0.02
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (73 bp):
TAAAAAATAATTTTCAAAACTATATAATATATATTTTTAAAAAATAATTTTCAAAACTATATAAT
ATATATTT
Found at i:48723 original size:38 final size:38
Alignment explanation
Indices: 48548--48915 Score: 495
Period size: 38 Copynumber: 9.9 Consensus size: 38
48538 AAATATAATA
* * *
48548 AAAAAT-ATTTTTAAAACTATATAATATATATGTTTTAA
1 AAAAATAATTTTCAAAACTATATAATATATATATTTT-T
* *
48586 AAAAATAATTTTCAAAACTACAT-A-ATATATA-TTTA
1 AAAAATAATTTTCAAAACTATATAATATATATATTTTT
48621 AAAAATAATTTTCAAAACTATAT-A-ATATATATTTTT
1 AAAAATAATTTTCAAAACTATATAATATATATATTTTT
48657 AAAAATAATTTTCAAAACTATAT-A-ATATATATTTTT
1 AAAAATAATTTTCAAAACTATATAATATATATATTTTT
48693 AAAAATAATTTTCAAAACTATATAATATATATATTTTT
1 AAAAATAATTTTCAAAACTATATAATATATATATTTTT
*
48731 AAAAATAATTTTCAAAACTATATAATATTTATATTTTT
1 AAAAATAATTTTCAAAACTATATAATATATATATTTTT
*
48769 AAAAATAATTTTCAAAACTATATAATACATATATTTTT
1 AAAAATAATTTTCAAAACTATATAATATATATATTTTT
* * *
48807 CAAAAATAATTTTCAAAATTATATAGTATATATATTTTC
1 -AAAAATAATTTTCAAAACTATATAATATATATATTTTT
** * *
48846 AAAAATTGTTTTAAAAACTATATATTATATATATTTTT
1 AAAAATAATTTTCAAAACTATATAATATATATATTTTT
** *
48884 --AAATTTTTTTAAAAACTATATAATATATATAT
1 AAAAATAATTTTCAAAACTATATAATATATATAT
48916 ATATATATAT
Statistics
Matches: 305, Mismatches: 20, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
35 31 0.10
36 95 0.31
37 7 0.02
38 124 0.41
39 48 0.16
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (38 bp):
AAAAATAATTTTCAAAACTATATAATATATATATTTTT
Found at i:48905 original size:2 final size:2
Alignment explanation
Indices: 48900--48935 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
48890 TTTTAAAAAC
48900 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48936 GTTTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48952 original size:58 final size:57
Alignment explanation
Indices: 48864--48973 Score: 175
Period size: 58 Copynumber: 1.9 Consensus size: 57
48854 TTTTAAAAAC
* * *
48864 TATATATTATATATATTTTTAAATTTTTTTAAAAACTATATAATATATATATATATA
1 TATATATTATATATATTTTTAAAATGTTTTAAAAAATATATAATATATATATATATA
*
48921 TATATATATATATATGTTTTTAAAATGTTTTAAAAAATATATAATATATATAT
1 TATATAT-TATATATATTTTTAAAATGTTTTAAAAAATATATAATATATATAT
48974 GTGTTCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
57 7 0.15
58 41 0.85
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (57 bp):
TATATATTATATATATTTTTAAAATGTTTTAAAAAATATATAATATATATATATATA
Found at i:48970 original size:38 final size:37
Alignment explanation
Indices: 48921--49192 Score: 297
Period size: 38 Copynumber: 7.4 Consensus size: 37
48911 TATATATATA
* *
48921 TATATATATATATATGTTTTTAAAATGTTTTAAAAAA
1 TATATATATATATATGTTTTCAAAATGTTTTAAAAAC
*
48958 TATATAATATATATATGTGTTCAAAATGTTTTAAAAAC
1 TATAT-ATATATATATGTTTTCAAAATGTTTTAAAAAC
*
48996 TATATAT-TATATA--TTTTCAAAATGTGTTAAAAAC
1 TATATATATATATATGTTTTCAAAATGTTTTAAAAAC
*
49030 TATATA-ATATATATGTTTCCAAAATGTTTTAAAAAC
1 TATATATATATATATGTTTTCAAAATGTTTTAAAAAC
* *
49066 TATATATTATATATATGTTTCCAAAATGTTTTAAAGAC
1 TATATA-TATATATATGTTTTCAAAATGTTTTAAAAAC
* ** *
49104 TATATA-ATATATAGGTTTTTGAAATGCTTTCAAAAAC
1 TATATATATATATATGTTTTCAAAATG-TTTTAAAAAC
* * * * **
49141 TATATAT-TATATTTATTTTAAAAATCATTTGCAAAA-
1 TATATATATATATATGTTTTCAAAAT-GTTTTAAAAAC
49177 TATATTATATATATAT
1 TATA-TATATATATAT
49193 ATATATATAT
Statistics
Matches: 201, Mismatches: 23, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
34 31 0.15
36 51 0.25
37 44 0.22
38 75 0.37
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATATATATATATGTTTTCAAAATGTTTTAAAAAC
Found at i:49187 original size:2 final size:2
Alignment explanation
Indices: 49176--49205 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
49166 CATTTGCAAA
49176 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49206 AGAATAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53183 original size:21 final size:21
Alignment explanation
Indices: 53157--53196 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
53147 GATAAATTGT
53157 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
53178 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
53197 AAAACTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:57011 original size:20 final size:20
Alignment explanation
Indices: 56986--57044 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
56976 TTTTGGTACA
56986 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
* *
57006 GAGGGAACCGATTCCCCCCAT
1 GAGGGAATCGA-TACCCCCAT
*
57027 AAGGGAATCGATACCCCC
1 GAGGGAATCGATACCCCC
57045 CTGGGGTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.29, C:0.34, G:0.24, T:0.14
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:59299 original size:21 final size:21
Alignment explanation
Indices: 59273--59322 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
59263 GTTTTAAAGA
59273 GGAGTAGTGTTAAAGTAAGGG
1 GGAGTAGTGTTAAAGTAAGGG
59294 GGAGTAGTGTTAAAGTAAGGG
1 GGAGTAGTGTTAAAGTAAGGG
59315 GGAGTAGT
1 GGAGTAGT
59323 ATTTTCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.44, T:0.24
Consensus pattern (21 bp):
GGAGTAGTGTTAAAGTAAGGG
Found at i:61441 original size:15 final size:15
Alignment explanation
Indices: 61421--61451 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
61411 TGCTCGTTGG
61421 GCTACACTCTGGACC
1 GCTACACTCTGGACC
61436 GCTACACTCTGGACC
1 GCTACACTCTGGACC
61451 G
1 G
61452 ATTGGACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.39, G:0.23, T:0.19
Consensus pattern (15 bp):
GCTACACTCTGGACC
Found at i:61510 original size:9 final size:9
Alignment explanation
Indices: 61493--61534 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
61483 TGAAATAATT
61493 AAATAAATA
1 AAATAAATA
*
61502 AAATGAAT-
1 AAATAAATA
61510 AAATAAAATA
1 AAAT-AAATA
61520 AAAT-AATA
1 AAATAAATA
61528 AAATAAA
1 AAATAAA
61535 AAGAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 12 0.43
9 12 0.43
10 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:61512 original size:17 final size:16
Alignment explanation
Indices: 61485--61534 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 16
61475 TTTGGACCTG
61485 AAATAATTAAATAAATA
1 AAATAA-TAAATAAATA
61502 AAATGAATAAATAAAATA
1 AAAT-AATAAAT-AAATA
61520 AAATAATAAAATAAA
1 AAATAAT-AAATAAA
61535 AAGAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AAATAATAAATAAATA
Found at i:61520 original size:18 final size:17
Alignment explanation
Indices: 61485--61535 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
61475 TTTGGACCTG
61485 AAATAATTAAAT-AAATA
1 AAATAA-TAAATAAAATA
61502 AAATGAATAAATAAAATA
1 AAAT-AATAAATAAAATA
61520 AAATAATAAAATAAAA
1 AAATAAT-AAATAAAA
61536 AGAAAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATAATAAATAAAATA
Found at i:61534 original size:13 final size:14
Alignment explanation
Indices: 61493--61535 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 14
61483 TGAAATAATT
61493 AAATAAATAAAAT-
1 AAATAAATAAAATA
*
61506 GAATAAATAAAATA
1 AAATAAATAAAATA
61520 AAAT-AATAAAATA
1 AAATAAATAAAATA
61533 AAA
1 AAA
61536 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 24 0.89
14 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:61668 original size:20 final size:22
Alignment explanation
Indices: 61639--61691 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
61629 TTCAAAACCC
*
61639 GTTTTAAAAACTATA-TATAT-
1 GTTTTCAAAACTATATTATATA
61659 GTTTTCAAAACTATATTATATA
1 GTTTTCAAAACTATATTATATA
61681 CGTTTTCAAAA
1 -GTTTTCAAAA
61692 ACCGTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.48
21 5 0.17
23 10 0.34
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (22 bp):
GTTTTCAAAACTATATTATATA
Found at i:61718 original size:39 final size:37
Alignment explanation
Indices: 61660--61822 Score: 188
Period size: 37 Copynumber: 4.4 Consensus size: 37
61650 TATATATATG
* *
61660 TTTTCAAAACTATAT-TATATACGTTTTCAAAAACCGT
1 TTTTAAAAACTATATAT-TATATGTTTTCAAAAACCGT
* *
61697 TTTTAAAAACTATATATTATATATTTTCAAAAACCATTT
1 TTTTAAAAACTATATATTATATGTTTTCAAAAACC--GT
61736 TTTTAAAAACTATATATTATATGTTTTC-AAAACCGT
1 TTTTAAAAACTATATATTATATGTTTTCAAAAACCGT
* * **
61772 TTTAAAAAAACTATTTATTATATGTTTTCAAAAA-TAT
1 TTT-TAAAAACTATATATTATATGTTTTCAAAAACCGT
*
61809 TTTCAAAAACTATA
1 TTTTAAAAACTATA
61823 CTATGTATCT
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
36 13 0.12
37 57 0.52
38 11 0.10
39 28 0.26
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAAACCGT
Found at i:61762 original size:76 final size:76
Alignment explanation
Indices: 61660--61805 Score: 215
Period size: 76 Copynumber: 1.9 Consensus size: 76
61650 TATATATATG
* *
61660 TTTTCAAAACTATATTATATACGTTTTCAAAAACCGTTTT-TAAAAACTATATATTATATATTTT
1 TTTTAAAAACTATATTATATACGTTTTC-AAAACCGTTTTAAAAAAACTATATATTATATATTTT
61724 CAAAAACCATTT
65 CAAAAACCATTT
* * *
61736 TTTTAAAAACTATA-TATTATATGTTTTCAAAACCGTTTTAAAAAAACTATTTATTATATGTTTT
1 TTTTAAAAACTATATTA-TATACGTTTTCAAAACCGTTTTAAAAAAACTATATATTATATATTTT
61800 CAAAAA
65 CAAAAA
61806 TATTTTCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
75 13 0.21
76 50 0.79
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (76 bp):
TTTTAAAAACTATATTATATACGTTTTCAAAACCGTTTTAAAAAAACTATATATTATATATTTTC
AAAAACCATTT
Found at i:61838 original size:22 final size:22
Alignment explanation
Indices: 61810--61852 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
61800 CAAAAATATT
61810 TTCAAAAACTATACTA-TGTATC
1 TTCAAAAACTATA-TATTGTATC
*
61832 TTCAAAAGCTATATATTGTAT
1 TTCAAAAACTATATATTGTAT
61853 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (22 bp):
TTCAAAAACTATATATTGTATC
Found at i:63450 original size:24 final size:25
Alignment explanation
Indices: 63422--63547 Score: 99
Period size: 24 Copynumber: 5.3 Consensus size: 25
63412 TATATCAAAA
*
63422 ATCA-AATCATAATTCAAGTATCAT
1 ATCAGAATCATAAGTCAAGTATCAT
* *
63446 ATCAAAATC--CAGTCAAGTATCAT
1 ATCAGAATCATAAGTCAAGTATCAT
*
63469 ATCAGAATC-CAAGTCAAGTATCAT
1 ATCAGAATCATAAGTCAAGTATCAT
* *
63493 ATCATAATCCAT--GTC-AGATATCAG
1 ATCAGAAT-CATAAGTCAAG-TATCAT
*
63517 ATCAGAATTCAT--GTCAAGTATCAG
1 ATCAGAA-TCATAAGTCAAGTATCAT
63541 ATCAGAA
1 ATCAGAA
63548 ATCAAATCGA
Statistics
Matches: 87, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
23 22 0.25
24 57 0.66
25 8 0.09
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (25 bp):
ATCAGAATCATAAGTCAAGTATCAT
Found at i:63534 original size:48 final size:47
Alignment explanation
Indices: 63435--63550 Score: 153
Period size: 48 Copynumber: 2.4 Consensus size: 47
63425 AAATCATAAT
*
63435 TCAAGTATCATATCAAAATCCAGTCAAGTATCATATCAGAATCCAAG
1 TCAAGTATCATATCAAAATCCAGTCAAGTATCAGATCAGAATCCAAG
* * *
63482 TCAAGTATCATATCATAATCCATGTC-AGATATCAGATCAGAATTCATG
1 TCAAGTATCATATCAAAATCCA-GTCAAG-TATCAGATCAGAATCCAAG
*
63530 TCAAGTATCAGATCAGAAATC
1 TCAAGTATCATATCA-AAATC
63551 AAATCGAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
47 23 0.38
48 33 0.55
49 4 0.07
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (47 bp):
TCAAGTATCATATCAAAATCCAGTCAAGTATCAGATCAGAATCCAAG
Found at i:67861 original size:7 final size:7
Alignment explanation
Indices: 67841--67915 Score: 64
Period size: 7 Copynumber: 10.6 Consensus size: 7
67831 TAAAACGAGA
*
67841 AATAAAC
1 AATAAAT
67848 AATAAAT
1 AATAAAT
67855 AATAAAT
1 AATAAAT
*
67862 AA-AATAA
1 AATAA-AT
67869 AATAAAT
1 AATAAAT
67876 AA-AAAGT
1 AATAAA-T
*
67883 AGAAAAAT
1 A-ATAAAT
67891 AATAAAT
1 AATAAAT
*
67898 AAAAAAT
1 AATAAAT
*
67905 AATAAAA
1 AATAAAT
67912 AATA
1 AATA
67916 TTTTTAAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
6 5 0.09
7 43 0.77
8 5 0.09
9 3 0.05
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (7 bp):
AATAAAT
Found at i:67923 original size:23 final size:24
Alignment explanation
Indices: 67897--67952 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 24
67887 AAATAATAAA
67897 TAAAAAATAATAAAAAATAT-TTT
1 TAAAAAATAATAAAAAATATGTTT
* * *
67920 T-AAAACT-ATATAATATATGTTT
1 TAAAAAATAATAAAAAATATGTTT
67942 TAAAAAATAAT
1 TAAAAAATAAT
67953 TTTCAAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 9 0.35
22 9 0.35
23 6 0.23
24 2 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAAAATAATAAAAAATATGTTT
Found at i:67987 original size:34 final size:36
Alignment explanation
Indices: 67907--68007 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
67897 TAAAAAATAA
*
67907 TAAAAAAT-ATTTTTAAAACTATATAATATATGTTT
1 TAAAAAATAATTTTCAAAACTATATAATATATGTTT
67942 TAAAAAATAATTTTCAAAACTATATAATATAT-TTT
1 TAAAAAATAATTTTCAAAACTATATAATATATGTTT
67977 T-AAAAATAATTTTCAAAACTATATAATATAT
1 TAAAAAATAATTTTCAAAACTATATAATATAT
68008 ATATTTTAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
34 30 0.47
35 12 0.19
36 22 0.34
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (36 bp):
TAAAAAATAATTTTCAAAACTATATAATATATGTTT
Found at i:68126 original size:20 final size:19
Alignment explanation
Indices: 68097--68306 Score: 131
Period size: 20 Copynumber: 10.6 Consensus size: 19
68087 AAATGACCAA
68097 CAAATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAATT
* *
68116 CCAATTTCGCAAC-C-AGTTT
1 -CAAATTCGCAACGCGA-ATT
* *
68135 CCAATTTCGCAACACGAATAT
1 -CAAATTCGCAACGCGAAT-T
* ** *
68156 GTAAA-TCGCATTGCGATTTT
1 -CAAATTCGCAACGCGA-ATT
*
68176 CCAAATTCGCAACGCGATAGT
1 -CAAATTCGCAACGCGA-ATT
*
68197 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCG-AATT
* *
68217 CAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGCGA-ATT
*
68237 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCG-AATT
*
68257 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAA-TT
*
68276 CAAATTCGCAACGCAAATT
1 CAAATTCGCAACGCGAATT
* *
68295 TAATTTCGCAAC
1 CAAATTCGCAAC
68307 AGGTTTTAGT
Statistics
Matches: 155, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
18 3 0.02
19 43 0.28
20 91 0.59
21 18 0.12
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (19 bp):
CAAATTCGCAACGCGAATT
Found at i:68206 original size:41 final size:41
Alignment explanation
Indices: 68097--68295 Score: 155
Period size: 40 Copynumber: 5.0 Consensus size: 41
68087 AAATGACCAA
* * *
68097 CAAATTCGCAACGCGA-ATTCCAATTTCGCAAC-C-AGTTTC
1 CAAATTCGCAACGCGATAGT-CAAATTCGCAACGCGAATTTC
* * ** *
68136 CAATTTCGCAACACGAATATGT-AAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCG-ATA-GTCAAATTCGCAACGCGAATTTC
**
68177 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT-
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATTTC
* **
68217 CAAATTCGCAACGTGATAGTCAAATTCGCAACGCGAAAGT-
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATTTC
* * *
68257 CAAATTCGCAAC-TGA-ATTTCAAATTCGCAACGCAAATTT
1 CAAATTCGCAACGCGATA-GTCAAATTCGCAACGCGAATTT
68296 AATTTCGCAA
Statistics
Matches: 133, Mismatches: 19, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
38 1 0.01
39 41 0.31
40 61 0.46
41 29 0.22
42 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (41 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATTTC
Found at i:68229 original size:40 final size:40
Alignment explanation
Indices: 68177--68306 Score: 185
Period size: 40 Copynumber: 3.3 Consensus size: 40
68167 TGCGATTTTC
*
68177 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGTGATAGTCAAATTCGCAACGCGAAAGT
68217 CAAATTCGCAACGTGATAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGTGATAGTCAAATTCGCAACGCGAAAGT
* *
68257 CAAATTCGCAAC-TGA-ATTTCAAATTCGCAACGC-AAATT
1 CAAATTCGCAACGTGATA-GTCAAATTCGCAACGCGAAAGT
* *
68295 TAATTTCGCAAC
1 CAAATTCGCAAC
68307 AGGTTTTAGT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
38 15 0.18
39 18 0.21
40 51 0.61
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (40 bp):
CAAATTCGCAACGTGATAGTCAAATTCGCAACGCGAAAGT
Found at i:68241 original size:60 final size:59
Alignment explanation
Indices: 68177--68288 Score: 179
Period size: 60 Copynumber: 1.9 Consensus size: 59
68167 TGCGATTTTC
*
68177 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAAC-CGAAAGTCAAATTCGCAACGTGATAGT
* **
68237 CAAATTCGCAACGCGAAAGTCAAATTCGCAACTGAATTTCAAATTCGCAACG
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACCGAAAGTCAAATTCGCAACG
68289 CAAATTTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
59 17 0.35
60 31 0.65
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (59 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAACCGAAAGTCAAATTCGCAACGTGATAGT
Found at i:69211 original size:24 final size:24
Alignment explanation
Indices: 69184--69237 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
69174 AGTATCGAAA
69184 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
69208 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
69232 TTTGAT
1 TTTGAT
69238 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:69691 original size:22 final size:22
Alignment explanation
Indices: 69662--69734 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
69652 AGATGGGATA
69662 GACGGATTTCGTCAGAAATGGG
1 GACGGATTTCGTCAGAAATGGG
*
69684 GATGGATTTCGTCAGAAATGGG
1 GACGGATTTCGTCAGAAATGGG
* *
69706 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCAGAAATGGG
69728 GACGGAT
1 GACGGAT
69735 GTCGCCGTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.12, G:0.40, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGGG
Found at i:69879 original size:20 final size:20
Alignment explanation
Indices: 69854--69918 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
69844 GCGTAAAAAC
69854 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
69874 ATTTGACTTAT-GTGTTGCG-
1 ATTTGACTT-TCGCGTTGCGA
*
69893 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
69914 ATTTG
1 ATTTG
69919 GAAAATCGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 2 0.06
19 5 0.14
20 24 0.67
21 5 0.14
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:69927 original size:21 final size:21
Alignment explanation
Indices: 69903--70019 Score: 71
Period size: 21 Copynumber: 5.8 Consensus size: 21
69893 ATTTACAAAT
69903 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
***
69924 TCGCAACGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
** ** * *
69945 TCGCAATGCG-ATTTACATAT
1 TCGCGTTGCGAATTTGGAAAA
* *
69965 TCGCGTTGCGAAATTGGAAAC
1 TCGCGTTGCGAATTTGGAAAA
* * * *
69986 T-GGGTTACGAA-ATGG-AAT
1 TCGCGTTGCGAATTTGGAAAA
70004 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
70020 TTGTCATTTG
Statistics
Matches: 71, Mismatches: 22, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
18 3 0.04
19 11 0.15
20 24 0.34
21 33 0.46
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:70015 original size:19 final size:20
Alignment explanation
Indices: 69963--70015 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
69953 CGATTTACAT
69963 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* * *
69983 A-ACTGGGTTACGAAA-TGGA
1 ATTC-GCGTTGCGAAATTGGA
70002 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
70016 TTTGTTGTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:70149 original size:38 final size:36
Alignment explanation
Indices: 70098--70277 Score: 226
Period size: 38 Copynumber: 5.0 Consensus size: 36
70088 GTTATTTCTC
* *
70098 TTTTAAAAA-ATTTTCAAAACTATATAATACATATA
1 TTTTAAAAATATTTTAAAAACTATATAATATATATA
* *
70133 TTTTCAAAAATAATTTTCAAAACTATATAGTATATATA
1 TTTT-AAAAAT-ATTTTAAAAACTATATAATATATATA
70171 TTTTCAAAAAT-TTTTAAAAACTATAT-ATATATAT-
1 TTTT-AAAAATATTTTAAAAACTATATAATATATATA
*
70205 TTTT-AAAATGTTTTAAAAACTATATAATATATATA
1 TTTTAAAAATATTTTAAAAACTATATAATATATATA
* *
70240 TATTTTAAAATATTTTAAAAAGTATATAATATATATA
1 T-TTTAAAAATATTTTAAAAACTATATAATATATATA
70277 T
1 T
70278 ATATATATAT
Statistics
Matches: 131, Mismatches: 6, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
32 5 0.04
33 15 0.11
34 12 0.09
35 12 0.09
36 22 0.17
37 30 0.23
38 35 0.27
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (36 bp):
TTTTAAAAATATTTTAAAAACTATATAATATATATA
Found at i:70255 original size:71 final size:71
Alignment explanation
Indices: 70098--70275 Score: 218
Period size: 70 Copynumber: 2.5 Consensus size: 71
70088 GTTATTTCTC
* * * *
70098 TTTTAAAAAATTTTCAAAACTATATAATACATATATTTTCAAAAATAATTTTCAAAACTATATAG
1 TTTTTAAAAATTTTAAAAACTATATAAT--ATATATTTTCAAAAATAATTTTAAAAACTATATAA
70163 TATATATA
64 TATATATA
* * *
70171 TTTTCAAAAATTTTTAAAAACTATAT-ATATATATTTT-TAAAAT-GTTTTAAAAACTATATAAT
1 TTTTTAAAAA-TTTTAAAAACTATATAATATATATTTTCAAAAATAATTTTAAAAACTATATAAT
70233 ATATATA
65 ATATATA
*
70240 TATTTTAAAATATTTTAAAAAGTATATAATATATAT
1 T-TTTTAAAA-ATTTTAAAAACTATATAATATATAT
70276 ATATATATAT
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
69 24 0.26
70 26 0.28
71 18 0.19
73 11 0.12
74 14 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (71 bp):
TTTTTAAAAATTTTAAAAACTATATAATATATATTTTCAAAAATAATTTTAAAAACTATATAATA
TATATA
Found at i:70273 original size:2 final size:2
Alignment explanation
Indices: 70262--70295 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
70252 TTTTAAAAAG
70262 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70296 GTTTTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70306 original size:93 final size:92
Alignment explanation
Indices: 70192--70368 Score: 284
Period size: 93 Copynumber: 1.9 Consensus size: 92
70182 TTTTAAAAAC
70192 TATATATATATATTTTTAAAATGTTTTAAAAACTATATAATATATATATATTTT-AAAATATTTT
1 TATATATATATATTTTTAAAATGTTTTAAAAACTATATAATATATATATATTTTCAAAATATTTT
70256 AAAAAGTATATAATATATATATATATA
66 AAAAAGTATATAATATATATATATATA
* * *
70283 TATATATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATATGTTTTCAAAATGTT
1 TATATATATATAT-TTTT-AAAATGTTTTAAAAACTATATAATATATATATATTTTCAAAATATT
* *
70348 TTAAAGATTATATAATATATA
64 TTAAAAAGTATATAATATATA
70369 GGTTTTCTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
91 13 0.17
92 4 0.05
93 35 0.45
94 26 0.33
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (92 bp):
TATATATATATATTTTTAAAATGTTTTAAAAACTATATAATATATATATATTTTCAAAATATTTT
AAAAAGTATATAATATATATATATATA
Found at i:70312 original size:56 final size:54
Alignment explanation
Indices: 70225--70333 Score: 164
Period size: 56 Copynumber: 2.0 Consensus size: 54
70215 TTTTAAAAAC
*
70225 TATATAATATATATATATTTTAAAATATTTTAAAAAGTATATAATATATATATA
1 TATATAATATATATATATTTTAAAATATTTTAAAAACTATATAATATATATATA
* * *
70279 TATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATAT
1 TATATA-ATATATATATATTTT-AAAATATTTTAAAAACTATATAATATATATAT
70334 GTTTTCAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 6 0.12
55 14 0.29
56 29 0.59
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (54 bp):
TATATAATATATATATATTTTAAAATATTTTAAAAACTATATAATATATATATA
Found at i:70331 original size:38 final size:38
Alignment explanation
Indices: 70279--70404 Score: 175
Period size: 38 Copynumber: 3.3 Consensus size: 38
70269 TATATATATA
70279 TATATATATATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATATAT-TATATATATGTTTTCAAAATGTTTTAAAAAC
*
70318 TATATATTATATATATGTTTTCAAAATGTTTTAAAGA-
1 TATATATTATATATATGTTTTCAAAATGTTTTAAAAAC
* * * *
70355 T-TATATAATATATAGGTTTTCTAAATGCTTTCAAAAAC
1 TATATATTATATATATGTTTTCAAAATG-TTTTAAAAAC
70393 TATATATTATAT
1 TATATATTATAT
70405 TTATTTCAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
36 23 0.30
37 8 0.10
38 30 0.39
39 16 0.21
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (38 bp):
TATATATTATATATATGTTTTCAAAATGTTTTAAAAAC
Found at i:70391 original size:131 final size:127
Alignment explanation
Indices: 70156--70404 Score: 317
Period size: 131 Copynumber: 1.9 Consensus size: 127
70146 TTTTCAAAAC
70156 TATATAGTATATATATTTTCAAAAATTTTTAAAAACTATATATATATATTTTTAAAATGTTTTAA
1 TATATAGTATATATATTTTCAAAAATTTTTAAAAACTATATATATATATTTTTAAAATGTTTTAA
* * *
70221 AAACTATATAATATATATATATTTTAAAATATTTTAAAAAGTATATAATATATATATATATA
66 AAACTATATAATATATAGATATTTTAAAATATTTCAAAAACTATATAATATATATATATATA
*
70283 TATATA-TATATATGTTTTC-AAAATGTTTTAAAAACTATATATTATATATATGTTTTCAAAATG
1 TATATAGTATATATATTTTCAAAAAT-TTTTAAAAAC--TATA-TATATATAT-TTTT-AAAATG
* * * * *
70346 TTTTAAAGATTATATAATATATAGGT-TTTCT-AAATGCTTTCAAAAACTATATATTATAT
60 TTTTAAAAACTATATAATATATAGATATTT-TAAAAT-ATTTCAAAAACTATATAATATAT
70405 TTATTTCAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
125 5 0.05
126 22 0.21
127 6 0.06
128 4 0.04
129 9 0.09
130 11 0.10
131 48 0.46
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (127 bp):
TATATAGTATATATATTTTCAAAAATTTTTAAAAACTATATATATATATTTTTAAAATGTTTTAA
AAACTATATAATATATAGATATTTTAAAATATTTCAAAAACTATATAATATATATATATATA
Done.