Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001243.1 Hibiscus syriacus cultivar Beakdansim tig00002444_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: 50844
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1942 original size:31 final size:31
Alignment explanation
Indices: 1889--1986 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
1879 AAATTCATGG
*
1889 GTTAAACTGATA-TTTATCTAAAATTTAAGA
1 GTTAAACTAATATTTTATCTAAAATTTAAGA
* *
1919 GTTAAACTAATATTTTATTTAAAATTTAGGA
1 GTTAAACTAATATTTTATCTAAAATTTAAGA
*
1950 GTTAAATTAATATTTTATCTAAAATTTAATGA
1 GTTAAACTAATATTTTATCTAAAATTTAA-GA
1982 -TTAAA
1 GTTAAA
1987 TTAAAAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
30 11 0.18
31 47 0.78
32 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (31 bp):
GTTAAACTAATATTTTATCTAAAATTTAAGA
Found at i:11128 original size:3 final size:3
Alignment explanation
Indices: 11115--11144 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
11105 CGGAAAAAAG
11115 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA
11145 CATATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:12344 original size:18 final size:19
Alignment explanation
Indices: 12307--12355 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
12297 TAATTTAGGC
*
12307 ATATTATTATATATTTTAAT
1 ATATTATTAT-TATTATAAT
12327 ATATTATTATTA-TATAAT
1 ATATTATTATTATTATAAT
12345 ATATTATTATT
1 ATATTATTATT
12356 GTAATCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 16 0.57
19 2 0.07
20 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTATTATTATTATAAT
Found at i:12351 original size:15 final size:14
Alignment explanation
Indices: 12308--12354 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
12298 AATTTAGGCA
12308 TATTAT-TATATAT
1 TATTATATATATAT
12321 T-TTA-ATATATTAT
1 TATTATATATA-TAT
12334 TATTATATAATATAT
1 TATTATAT-ATATAT
12349 TATTAT
1 TATTAT
12355 TGTAATCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 7 0.24
13 5 0.17
14 3 0.10
15 11 0.38
16 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATATATATAT
Found at i:15515 original size:32 final size:32
Alignment explanation
Indices: 15478--15539 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
15468 TTTCACCAGT
*
15478 ACTAAC-TAATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAACAT-ATTTCTTTTCTTTTGATTGTGTAC
15510 ACTAACATATTTCTTTTCTTTTGATTGTGT
1 ACTAACATATTTCTTTTCTTTTGATTGTGT
15540 CATTTTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (32 bp):
ACTAACATATTTCTTTTCTTTTGATTGTGTAC
Found at i:16121 original size:210 final size:210
Alignment explanation
Indices: 15759--16196 Score: 558
Period size: 210 Copynumber: 2.1 Consensus size: 210
15749 AGTGGTAATC
* * *
15759 CACTGATTCGAGGAGTAATCCAACACTGGAGTATTTTCTACAATCATGTCATCACTAGTCATCCA
1 CACTGATTCGAGGAGTAATCCAACACTGAAGTATTTTCTACAATCATGTCAGCACTAGTCATCAA
* * * * * ** * *
15824 AGAGCGACATAGTGACATCAGTATCGCTGAGGCATTAACGGAGTTGGTTTACAGAGTATTGAGGG
66 AAAGCGACACACTGACATCAGCACCGCTGAGGCATTAACAAAGTTCGTTTACAGAGCATTGAGGG
* * * *
15889 GCATCAGTTTCAAATATGAAGATCCAATATGAAACTA-TGAGCTCGACGATCGTGCAGTATTCGA
131 GCATCAGTTCCAAATATGAAGATCCAAGA-CAAACCAGTGAGCTCGACGATCGTGCAGTATTCGA
15953 GACTAAAATGATGATA
195 GACTAAAATGATGATA
15969 CACTGATTCGAGGAGTAATCCAGA-ACTGAAGT-TTTCTCTACAATCATGTCAGCACTAGTCATC
1 CACTGATTCGAGGAGTAATCCA-ACACTGAAGTATTT-TCTACAATCATGTCAGCACTAGTCATC
** * *
16032 AAAAAGCGATGCACTGACTTCAGCACCGTTGAGGCATTAACAAAGTTCGTTTACAGAGCATTGAG
64 AAAAAGCGACACACTGACATCAGCACCGCTGAGGCATTAACAAAGTTCGTTTACAGAGCATTGAG
* * *
16097 GGGCATCAGTTCCAAATATGAAGATCCGAGACAAACCAGTGAGCTTGACGATTGTGCAGTATTCG
129 GGGCATCAGTTCCAAATATGAAGATCCAAGACAAACCAGTGAGCTCGACGATCGTGCAGTATTCG
* * * *
16162 AGATTGAAATTATGATT
194 AGACTAAAATGATGATA
* * *
16179 CATTCATCCGAGGAGTAA
1 CACTGATTCGAGGAGTAA
16197 CTCAACAGTA
Statistics
Matches: 195, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
209 8 0.04
210 186 0.95
211 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (210 bp):
CACTGATTCGAGGAGTAATCCAACACTGAAGTATTTTCTACAATCATGTCAGCACTAGTCATCAA
AAAGCGACACACTGACATCAGCACCGCTGAGGCATTAACAAAGTTCGTTTACAGAGCATTGAGGG
GCATCAGTTCCAAATATGAAGATCCAAGACAAACCAGTGAGCTCGACGATCGTGCAGTATTCGAG
ACTAAAATGATGATA
Found at i:22031 original size:5 final size:5
Alignment explanation
Indices: 22021--22059 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
22011 TGAAGAAGAA
*
22021 AAAAG AAAAG AAAA- AAGAAA AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
22060 AGGGACGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 2 0.06
5 27 0.87
6 2 0.06
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:22033 original size:12 final size:12
Alignment explanation
Indices: 22016--22060 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
22006 GCACTTGAAG
22016 AAGAAAAAAGAA
1 AAGAAAAAAGAA
22028 AAGAAAAAAGAA
1 AAGAAAAAAGAA
*
22040 AAAAAGAAAAGAA
1 AAGAA-AAAAGAA
22053 AAGAAAAA
1 AAGAAAAA
22061 GGGACGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:22044 original size:15 final size:14
Alignment explanation
Indices: 22013--22061 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
22003 ATTGCACTTG
*
22013 AAGAAGAAAAAAGAA
1 AAGAA-AAAAAAAAA
22028 AAGAAAAAAGAAAAA
1 AAGAAAAAA-AAAAA
22043 AAGAAAAGAAAAGAAA
1 AAGAAAA-AAAA-AAA
22059 AAG
1 AAG
22062 GGACGAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 18 0.60
16 8 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAAA
Found at i:23825 original size:43 final size:44
Alignment explanation
Indices: 23777--23873 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
23767 CCTGATCTCC
* * *
23777 TCATCATGTAGGAG-CTATGTCAATCCTT-GATAACCAAAACTCT
1 TCATCACGTAGGAGTC-ATGTCAACCCTTAGACAACCAAAACTCT
* * * *
23820 TCATCACGTATGAGTCGTGTCAACCCTTAGACGACCAGAACTCT
1 TCATCACGTAGGAGTCATGTCAACCCTTAGACAACCAAAACTCT
23864 TCATCACGTA
1 TCATCACGTA
23874 TGAGAAGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 22 0.49
44 23 0.51
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (44 bp):
TCATCACGTAGGAGTCATGTCAACCCTTAGACAACCAAAACTCT
Found at i:24046 original size:3 final size:3
Alignment explanation
Indices: 24040--24084 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
24030 AAAAAAATAT
24040 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24085 CATGTTTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28992 original size:20 final size:21
Alignment explanation
Indices: 28962--29001 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
28952 AGCCGTTGGG
28962 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
28983 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
29002 CTATATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:31132 original size:14 final size:14
Alignment explanation
Indices: 31113--31141 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31103 CTCTTCTTTC
31113 TTTTTTTCTCTGTT
1 TTTTTTTCTCTGTT
31127 TTTTTTTCTCTGTT
1 TTTTTTTCTCTGTT
31141 T
1 T
31142 CTTTGCTGGT
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:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTCTCTGTT
Found at i:31622 original size:3 final size:3
Alignment explanation
Indices: 31614--31674 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
31604 GGCCTGGTTT
* *
31614 TAA TAA TAA TAT TAA TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
*
31660 TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA
31675 AATCGGGACA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:32154 original size:113 final size:113
Alignment explanation
Indices: 32019--32695 Score: 795
Period size: 113 Copynumber: 6.0 Consensus size: 113
32009 ATAGAGTCCT
* ** * *
32019 GCAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
32084 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAA
* *
32132 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
32197 ATTATGAAC-TTCTCTTGAAAAACTGATCCATCAAATGATGAATTCAA
66 ATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAA
** * * * * * *
32244 ATAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCTTTCATCAGATGAGTTCTTCCC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * ** *
32309 ATTATGAACTCGAC-CTGGCAATGTTGATCCATC-TCTGATGAATTCAA
66 ATTATGAACT-TTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAA
* * * * *
32356 TCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
32421 ATTATGAACTTTTTCTGGGAAAGTTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAA
* * * *
32469 GCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAATTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
32534 ATTATGAACTTTCCCTGGCAAAGCTAATCCATCAATTGATGAATTTAA
66 ATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAA
**
32582 ATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
* * * * *
32647 CTCATTATGAACTCTT-TCTGGCAATGTTAATCCATCAATTGATGGATTT
63 CTCATTATGAACT-TTCTCTGGCAAAGCTGATCCATCAAATGATGAATTT
32696 GAATCTTTGC
Statistics
Matches: 479, Mismatches: 77, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
112 192 0.40
113 231 0.48
114 1 0.00
115 1 0.00
116 52 0.11
117 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAA
Found at i:32424 original size:337 final size:340
Alignment explanation
Indices: 32020--32682 Score: 1026
Period size: 337 Copynumber: 2.0 Consensus size: 340
32010 TAGAGTCCTG
* *
32020 CAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
32085 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
* * *
32150 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAAC-TTCTCTTG
131 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTTCCCTGG
* *
32214 AAAAACTGATCCATCAAATGATGAATTCAAATAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
196 AAAAACTAATCCATCAAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAACT
* *
32279 TATTCTTCTTTCATC-A-GATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTGATCCATC
261 TATTCTTCCTTCATCAATGATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTAATCCATC
32342 TCTGATGAATTCAAT
326 TCTGATGAATTCAAT
* * *
32357 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
32422 TTATGAACTTTTTCTGGGAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
* *
32487 TCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAATTCTTCTCATTATGAACTTTCCCTGG
131 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTTCCCTGG
* * * * *
32552 CAAAGCTAATCCATCAATTGATGAATTTAAATAAAAGGTTGAACAAATTCTTCTCATTATGAACT
196 AAAAACTAATCCATCAAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAACT
* * * ***
32617 TCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTTCTGGCAATGTTAATCCAT
261 TATTCTTCCTTCATCA-ATGATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTAATCCAT
32682 C
325 C
32683 AATTGATGGA
Statistics
Matches: 292, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
337 173 0.59
338 76 0.26
340 1 0.00
341 42 0.14
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (340 bp):
CAAAAAGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTTCCCTGG
AAAAACTAATCCATCAAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAACT
TATTCTTCCTTCATCAATGATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTAATCCATC
TCTGATGAATTCAAT
Found at i:33751 original size:87 final size:83
Alignment explanation
Indices: 33422--33895 Score: 808
Period size: 87 Copynumber: 5.6 Consensus size: 83
33412 GGTTTTATAT
* *
33422 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
33487 TTCAATGATTGA-TTTAC
66 TTCAATGATTGATTTTAC
*
33504 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTATTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
33569 TTCAATGATT-ATTTTAC
66 TTCAATGATTGATTTTAC
*
33586 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAG-A-A--CACTTCCAGAAGATGCTATGAGCACATTATTCTTC
33651 CAAATTCAATGATTGATTTTAC
62 CAAATTCAATGATTGATTTTAC
33673 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
33738 TTCAATGATTGATTTTAC
66 TTCAATGATTGATTTTAC
*
33756 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAG-A-A--CACTTCCAGAAGATGCTATGAGCACATTATTCTTC
33821 CAAATTCAATGATTGATTTTAC
62 CAAATTCAATGATTGATTTTAC
*
33843 CAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
33896 GGCATTTGTT
Statistics
Matches: 373, Mismatches: 9, Indels: 19
0.93 0.02 0.05
Matches are distributed among these distances:
81 1 0.00
82 101 0.27
83 106 0.28
84 2 0.01
85 3 0.01
86 49 0.13
87 111 0.30
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
TTCAATGATTGATTTTAC
Found at i:33827 original size:170 final size:169
Alignment explanation
Indices: 33422--33895 Score: 859
Period size: 170 Copynumber: 2.8 Consensus size: 169
33412 GGTTTTATAT
* * *
33422 CAAACCAAATCAGAGAACTCAAAG-A-A--CACTTCCAGAAGATGCTATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
33483 CAAATTCAATGATTGA-TTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
66 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
33547 ATGAGCACATTATTATTCCAAATTCAATGATTATTTTAC
131 ATGAGCACATTATTATTCCAAATTCAATGATTATTTTAC
33586 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
33651 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
66 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
33716 ATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
131 ATGAGCACATTATTATTCCAAATTCAATGATT-ATTTTAC
33756 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
*
33821 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCT
66 CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
33886 ATGAGCACAT
131 ATGAGCACAT
33896 GGCATTTGTT
Statistics
Matches: 299, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
164 22 0.07
165 1 0.00
166 1 0.00
168 50 0.17
169 79 0.26
170 146 0.49
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26
Consensus pattern (169 bp):
CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
CAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
ATGAGCACATTATTATTCCAAATTCAATGATTATTTTAC
Found at i:35247 original size:10 final size:10
Alignment explanation
Indices: 35234--35266 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
35224 CTTGACCCCC
35234 CTTTTTTCTT
1 CTTTTTTCTT
35244 CTTTTTTC-T
1 CTTTTTTCTT
35253 CTTTTTT-TT
1 CTTTTTTCTT
35262 CTTTT
1 CTTTT
35267 CTTTTTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:35259 original size:11 final size:10
Alignment explanation
Indices: 35235--35274 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
35225 TTGACCCCCC
*
35235 TTTTTTCTTC
1 TTTTTTCTTT
35245 TTTTTTCTCTT
1 TTTTTTCT-TT
35256 TTTTTTCTTT
1 TTTTTTCTTT
35266 TCTTTTTCT
1 T-TTTTTCT
35275 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 11 0.41
11 16 0.59
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:35271 original size:22 final size:21
Alignment explanation
Indices: 35235--35277 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
35225 TTGACCCCCC
35235 TTTTTTCTTCTTTTTTCTCTT
1 TTTTTTCTTCTTTTTTCTCTT
*
35256 TTTTTTCTTTTCTTTTTCTCTT
1 TTTTTTCTTCT-TTTTTCTCTT
35278 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTCTTTTTTCTCTT
Found at i:41297 original size:15 final size:15
Alignment explanation
Indices: 41274--41305 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41264 TGAAATGAAT
41274 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
41289 AATGCATGTATGCAA
1 AATGAATGTATGCAA
41304 AA
1 AA
41306 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:46217 original size:14 final size:14
Alignment explanation
Indices: 46198--46226 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46188 CTCTTCTTTC
46198 TTTTTTTCTCTGTT
1 TTTTTTTCTCTGTT
46212 TTTTTTTCTCTGTT
1 TTTTTTTCTCTGTT
46226 T
1 T
46227 CTTTGGTTTA
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:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTCTCTGTT
Found at i:46703 original size:3 final size:3
Alignment explanation
Indices: 46695--46755 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
46685 GGCCTGGTTG
* *
46695 TAA TAA TAA TAT TAA TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
*
46741 TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA
46756 AACCGGGACA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47108 original size:118 final size:120
Alignment explanation
Indices: 46952--47168 Score: 296
Period size: 118 Copynumber: 1.8 Consensus size: 120
46942 ATGCTTAATC
* *
46952 TATCTCCTTATGTGATAGAATTATGCAAAAGGCTGAACAAACTCTTCTCATTGTGAA-ATTCTTC
1 TATCTCCTTATGTGATAGAATCATGCAAAAGGCTGAACAAACTCTTCTCATTATGAATATTCTTC
47016 -TTCTTCAAATGAGTTCTTCTCATTATGAACTCCTTTTGGAAATGCTGATGATGA
66 TTTCTTCAAATGAGTTCTTCTCATTATGAACTCCTTTTGGAAATGCTGATGATGA
* * * * * * *
47070 TATCTCTTTCTGTGATAGAGTCCTGCAAAAGG-TCGAACAAGCTCTTCTTATTATGAACTTCTTC
1 TATCTCCTTATGTGATAGAATCATGCAAAAGGCT-GAACAAACTCTTCTCATTATGAA--TATTC
*
47134 TTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
63 TTCTTTCTTCAAATGAGTTCTTCTCATTATGAACT
47169 TTCTCTGGAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
117 1 0.01
118 47 0.56
121 6 0.07
122 30 0.36
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (120 bp):
TATCTCCTTATGTGATAGAATCATGCAAAAGGCTGAACAAACTCTTCTCATTATGAATATTCTTC
TTTCTTCAAATGAGTTCTTCTCATTATGAACTCCTTTTGGAAATGCTGATGATGA
Found at i:47419 original size:110 final size:112
Alignment explanation
Indices: 47112--47762 Score: 680
Period size: 110 Copynumber: 5.8 Consensus size: 112
47102 TCGAACAAGC
* *
47112 TCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-CTG
* * * * ** *
47176 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAGGTTGAACAAAT
65 GCAAAGCTGATCCATCAAATGATGAATTTAAATAAAAGTTGAACAAAT
* * *
47224 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAA--CTTCTCTT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-CTG
* * * * *
47287 GAAAAAC-GATCCATCAAATGATGAATTCAAATAAAAATTGAACAAGT
65 GCAAAGCTGATCCATCAAATGATGAATTTAAATAAAAGTTGAACAAAT
* * * * **
47334 TCTTCTCATTATGAACTTATTC-TCTTTCATCAGATGAGTTCTTCCCATTATGAACTCGACCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTGG
* * ** * *
47398 CAATGTTGATCCATC-TCTGATGAA-TTCAATCAAAAGTTGAACAAGT
66 CAAAGCTGATCCATCAAATGATGAATTTAAAT-AAAAGTTGAACAAAT
* * *
47444 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTCTTCTCA-TATGAACTTTTTCT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG--TTCTTCTCATTATGAACTCTTCCT
* * * **
47508 GGAAAAG-TGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAAT
64 GGCAAAGCTGATCCATCAAATGATGAATTTAAATAAAAG-TTGAACAAAT
* * *
47557 TCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAATTC-T-TCATTATGAACT-TTCCCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-CCTG
* *
47619 GCAAAGCTAATCCATCAATTGATG-ATTTAAATAAAAGGTTGAACAAAT
65 GCAAAGCTGATCCATCAAATGATGAATTTAAATAAAA-GTTGAACAAAT
*
47667 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTTC
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTCTTCC
* * * * *
47732 TGGCAATGTTAATCCATCAATTGATGGATTT
63 TGGCAAAGCTGATCCATCAAATGATGAATTT
47763 GAATCTTTGC
Statistics
Matches: 449, Mismatches: 68, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
109 37 0.08
110 163 0.36
111 64 0.14
112 78 0.17
113 63 0.14
114 1 0.00
115 37 0.08
116 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (112 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTGG
CAAAGCTGATCCATCAAATGATGAATTTAAATAAAAGTTGAACAAAT
Found at i:47672 original size:333 final size:336
Alignment explanation
Indices: 47095--47749 Score: 950
Period size: 333 Copynumber: 2.0 Consensus size: 336
47085 TAGAGTCCTG
*
47095 CAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
47160 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAGGTTGAACAAATT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAGATTGAACAAATT
* * *
47225 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTCTCTTGAA
131 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTCCCTGGAA
* *
47290 AAACGATCCATCAAATGATGAATTCAAATAAAAATTGAACAAGTTCTTCTCATTATGAACTTATT
196 AAACAATCCATCAAATGATGAATTCAAATAAAAATTGAACAAATTCTTCTCATTATGAACTTATT
* *
47355 C-TCTTTCATC-A-GATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTGATCCATCTCTG
261 CTTCCTTCATCAATGATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTAATCCATCTCTG
47417 ATGAATTCAAT
326 ATGAATTCAAT
* *
47428 CAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTCTTCT
1 CAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG--TTCTTCT
*
47492 CA-TATGAACTTTTTCTGGAAAAG-TGATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAA
64 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC-AAAGATTGAACAA
* *
47555 ATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAATTC-T-TCATTATGAACTTTCCCT
128 ATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAAC-TTCCCT
* * * * *
47618 GGCAAAGCTAATCCATCAATTGATG-ATTTAAATAAAAGGTTGAACAAATTCTTCTCATTATGAA
192 GGAAAAAC-AATCCATCAAATGATGAATTCAAATAAAA-ATTGAACAAATTCTTCTCATTATGAA
* * * ***
47682 CTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTTCTGGCAATGTTAATCC
255 CTTATTCTTCCTTCATCA-ATGATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTAATCC
47747 ATC
319 ATC
47750 AATTGATGGA
Statistics
Matches: 286, Mismatches: 26, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
331 11 0.04
332 94 0.33
333 122 0.43
334 16 0.06
336 1 0.00
337 42 0.15
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (336 bp):
CAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAGATTGAACAAATT
CTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTCCCTGGAA
AAACAATCCATCAAATGATGAATTCAAATAAAAATTGAACAAATTCTTCTCATTATGAACTTATT
CTTCCTTCATCAATGATGAGTTCTTCCCATTATGAACTCGACCTGGCAATGTTAATCCATCTCTG
ATGAATTCAAT
Found at i:48609 original size:82 final size:83
Alignment explanation
Indices: 48472--48939 Score: 736
Period size: 82 Copynumber: 5.6 Consensus size: 83
48462 GGTTTTATAT
* * *
48472 CAAACCAAATCAGAGAACTCAAAAAACACTTCCAG-AGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
48536 TTCAATGATTGATTTTAC
66 TTCAATGATTGATTTTAC
*
48554 CAAACCAGATCA-ATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTATTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
*
48618 TTCAATGATTTATTTTAC
66 TTCAATGATTGATTTTAC
*
48636 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCATGAGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAG-A-A--CACTTCCAGAAGATGCTATGAGCACATTATTCTTC
48701 CAAATTCAATGATTGATTTTAC
62 CAAATTCAATGATTGATTTTAC
48723 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-TTCTT-C-AA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
48785 TTCAATGATTGA-TTTAC
66 TTCAATGATTGATTTTAC
*
48802 CAAACCAGATCAGATAACTCAAAGAACATTCACTTCCAGAAGATGCCAT-AGCACATTATTCTTC
1 CAAACCAGATCAGATAACTCAAAG-A-A--CACTTCCAGAAGATGCTATGAGCACATTATTCTTC
48866 C-AATTCAATGATTGATTTTAC
62 CAAATTCAATGATTGATTTTAC
*
48887 CAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
48940 GGCATTTGTT
Statistics
Matches: 360, Mismatches: 12, Indels: 28
0.90 0.03 0.07
Matches are distributed among these distances:
79 29 0.08
80 15 0.04
81 39 0.11
82 88 0.24
83 62 0.17
84 17 0.05
85 31 0.09
86 1 0.00
87 78 0.22
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
TTCAATGATTGATTTTAC
Found at i:50288 original size:13 final size:12
Alignment explanation
Indices: 50248--50302 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 12
50238 TGACCCCCCT
50248 TTTTTCTTCTTT-
1 TTTTTCTT-TTTC
* *
50260 TTTCTCTCTTT-
1 TTTTTCTTTTTC
50271 TTTTTCTTTTTC
1 TTTTTCTTTTTC
*
50283 TCTTTTTTTTTTC
1 T-TTTTCTTTTTC
50296 TTTTTCT
1 TTTTTCT
50303 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 12 0.34
12 12 0.34
13 11 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:50305 original size:19 final size:19
Alignment explanation
Indices: 50247--50305 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
50237 TTGACCCCCC
*
50247 TTTTTTCTTCTTTTTTCTCT
1 TTTTTTTTTC-TTTTTCTCT
*
50267 CTTTTTTTTCTTTTTCTCT
1 TTTTTTTTTCTTTTTCTCT
50286 TTTTTTTTTCTTTTTCTCT
1 TTTTTTTTTCTTTTTCTCT
50305 T
1 T
50306 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 28 0.78
20 8 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTCTTTTTCTCT
Done.