Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006341.1 Hibiscus syriacus cultivar Beakdansim tig00015156_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: 61147
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2335 original size:3 final size:3
Alignment explanation
Indices: 2327--2391 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
2317 TTTACTTAAT
* * * *
2327 TTA TTA TTA TTA -AA ATA TTA TTA TTAA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
2372 -TA TATA TTA -TA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA
2392 AATAATTACA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
2 5 0.10
3 40 0.80
4 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2360 original size:16 final size:16
Alignment explanation
Indices: 2328--2381 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
2318 TTACTTAATT
2328 TATTATTATT-A-AAA
1 TATTATTATTAATAAA
2342 TATTATTATTAATAAA
1 TATTATTATTAATAAA
* *
2358 TATTATTATTATTATA
1 TATTATTATTAATAAA
2374 TA-TATTAT
1 TATTATTAT
2382 ATTATTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 10 0.28
15 7 0.19
16 19 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTATTATTAATAAA
Found at i:2385 original size:36 final size:33
Alignment explanation
Indices: 2327--2395 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 33
2317 TTTACTTAAT
2327 TTATTATTATTAAAATATTATTATTAATAAATA
1 TTATTATTATTAAAATATTATTATTAATAAATA
* *
2360 TTATTATTATTATATATATTATATTATTATTAAATA
1 TTATTATTATTA-AAATA-T-TATTATTAATAAATA
2396 ATTACAAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 12 0.39
34 4 0.13
35 1 0.03
36 14 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TTATTATTATTAAAATATTATTATTAATAAATA
Found at i:9878 original size:17 final size:15
Alignment explanation
Indices: 9856--9964 Score: 87
Period size: 17 Copynumber: 6.7 Consensus size: 15
9846 CTCATCCAGC
9856 AAAGAAAGAAGAAGGAA
1 AAAGAAA-AA-AAGGAA
*
9873 AAAGAAAAAAGAGAAA
1 AAAGAAAAAA-AGGAA
*
9889 GAAAGAAAAAAAAGAAA
1 -AAAG-AAAAAAAGGAA
9906 AAAGAAAAAAAGAGAAA
1 AAAGAAAAAAAG-G-AA
*
9923 AAACGAAAAAAAACGAA
1 AAA-G-AAAAAAAGGAA
9940 AAA-AAAGAAAA-GAA
1 AAAGAAA-AAAAGGAA
9954 AAAGAAAAAAA
1 AAAGAAAAAAA
9965 ATGAAAAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
14 13 0.16
15 16 0.20
16 10 0.12
17 26 0.32
18 8 0.10
19 7 0.09
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGGAA
Found at i:9888 original size:26 final size:26
Alignment explanation
Indices: 9858--9950 Score: 95
Period size: 26 Copynumber: 3.6 Consensus size: 26
9848 CATCCAGCAA
*
9858 AGAAAGAAGAAGGAAAAAGAAAAAAG
1 AGAAAGAAGAAGAAAAAAGAAAAAAG
9884 AGAAAGAAAGAA-AAAAAAGAAAAAAG
1 AGAAAG-AAGAAGAAAAAAGAAAAAAG
* *
9910 A-AAAAAAG-AGAAAAAACGAAAAAAA
1 AGAAAGAAGAAGAAAAAA-GAAAAAAG
*
9935 ACGAAA-AAAAAGAAAA
1 A-GAAAGAAGAAGAAAA
9951 GAAAAAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.02
24 9 0.16
25 11 0.19
26 22 0.39
27 14 0.25
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (26 bp):
AGAAAGAAGAAGAAAAAAGAAAAAAG
Found at i:9915 original size:34 final size:34
Alignment explanation
Indices: 9856--9965 Score: 129
Period size: 34 Copynumber: 3.3 Consensus size: 34
9846 CTCATCCAGC
* *
9856 AAAGAAAGAAGAAGGAAAAAG-AAAAAAGAGAAAG
1 AAAGAAA-AAAAAGAAAAAAGAAAAAAAGAGAAAG
9890 AAAGAAAAAAAAGAAAAAAGAAAAAAAGAGAAA-
1 AAAGAAAAAAAAGAAAAAAGAAAAAAAGAGAAAG
* *
9923 AAACGAAAAAAAACGAAAAAA-AAGAAAAGAAAAAG
1 AAA-GAAAAAAAA-GAAAAAAGAAAAAAAGAGAAAG
9958 AAA-AAAAA
1 AAAGAAAAA
9966 TGAAAAAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
33 19 0.28
34 39 0.57
35 10 0.15
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (34 bp):
AAAGAAAAAAAAGAAAAAAGAAAAAAAGAGAAAG
Found at i:9930 original size:8 final size:8
Alignment explanation
Indices: 9871--9974 Score: 90
Period size: 8 Copynumber: 12.6 Consensus size: 8
9861 AAGAAGAAGG
9871 AAAAAGAA
1 AAAAAGAA
9879 AAAAGAGAA
1 AAAA-AGAA
*
9888 AGAAAGAA
1 AAAAAGAA
9896 AAAAA-AGA
1 AAAAAGA-A
9904 AAAAAGAA
1 AAAAAGAA
9912 AAAAAGAGA
1 AAAAAGA-A
9921 AAAAACGAA
1 AAAAA-GAA
9930 AAAAA-ACGA
1 AAAAAGA--A
9939 AAAAA-AA
1 AAAAAGAA
*
9946 GAAAAGAA
1 AAAAAGAA
9954 AAAGAA-AA
1 AAA-AAGAA
*
9962 AAAATGAA
1 AAAAAGAA
9970 AAAAA
1 AAAAA
9975 AGGGGAGAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
7 8 0.10
8 41 0.51
9 29 0.36
10 2 0.03
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.01
Consensus pattern (8 bp):
AAAAAGAA
Found at i:9971 original size:6 final size:5
Alignment explanation
Indices: 9879--9976 Score: 68
Period size: 4 Copynumber: 20.0 Consensus size: 5
9869 GGAAAAAGAA
*
9879 AAAAG AGAAAG -AAAG AAAA- AAAAG AAAA- AAGAAA AAAAG AGAAA-
1 AAAAG A-AAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG A-AAAG
*
9923 AAACG AAAA- AAAACG AAAA- AAAAG AAAAG AAAAAG AAAA- AAAATG
1 AAAAG AAAAG AAAA-G AAAAG AAAAG AAAAG -AAAAG AAAAG AAAA-G
9968 AAAA- AAAAG
1 AAAAG AAAAG
9977 GGGAGAAATT
Statistics
Matches: 76, Mismatches: 3, Indels: 28
0.71 0.03 0.26
Matches are distributed among these distances:
4 28 0.37
5 26 0.34
6 22 0.29
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:9974 original size:10 final size:9
Alignment explanation
Indices: 9871--9976 Score: 112
Period size: 10 Copynumber: 11.7 Consensus size: 9
9861 AAGAAGAAGG
9871 AAAAAGAAA
1 AAAAAGAAA
*
9880 AAAGAG-AA
1 AAAAAGAAA
*
9888 AGAAAGAAA
1 AAAAAGAAA
9897 AAAAAG--A
1 AAAAAGAAA
9904 AAAAAG-AA
1 AAAAAGAAA
9912 AAAAAGAGAA
1 AAAAAGA-AA
*
9922 AAAACGAAA
1 AAAAAGAAA
9931 AAAAACGAAA
1 AAAAA-GAAA
9941 AAAAAGAAAA
1 AAAAAG-AAA
9951 GAAAAAGAAA
1 -AAAAAGAAA
9961 AAAAATGAAA
1 AAAAA-GAAA
9971 AAAAAG
1 AAAAAG
9977 GGGAGAAATT
Statistics
Matches: 83, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
7 7 0.08
8 13 0.16
9 25 0.30
10 32 0.39
11 6 0.07
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.01
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:14563 original size:22 final size:22
Alignment explanation
Indices: 14534--14588 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
14524 ATCTACACTC
14534 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
14556 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
14578 TTCAAAGATGA
1 TTCAAAGATGA
14589 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:15482 original size:76 final size:76
Alignment explanation
Indices: 15240--16402 Score: 2140
Period size: 76 Copynumber: 15.4 Consensus size: 76
15230 CTATTTCCCA
15240 CATCTGTAAGTCCTACAGTGCATGATG-TTCC-AAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
15302 AGCCTTAGGGT
66 AGCCTTAGGGT
*
15313 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTCGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
15377 AGCCTTAGGGT
66 AGCCTTAGGGT
15388 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
15453 AGCCTTAGGGT
66 AGCCTTAGGGT
*
15464 CATATGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
15529 AGCCTTAGGGT
66 AGCCTTAGGGT
*
15540 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
15605 AGCCTTAGGGC
66 AGCCTTAGGGT
15616 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
15681 AACCTTAGGGT
66 AGCCTTAGGGT
15692 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
15757 AGCCTTAGGGT
66 AGCCTTAGGGT
*
15768 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTCGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
15833 AGCCTTAGGGT
66 AGCCTTAGGGT
*
15844 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTCGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
15909 AGCCTTAGGGT
66 AGCCTTAGGGT
*
15920 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTC-GGAGCTTTTCGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
15983 AGCCTTAGGGT
66 AGCCTTAGGGT
15994 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
16059 AGCCTTAGGGT
66 AGCCTTAGGGT
*
16070 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
16135 AGCCTTAGGGC
66 AGCCTTAGGGT
16146 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
16211 AACCTTAGGGT
66 AGCCTTAGGGT
16222 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
16287 AGCCTTAGGGT
66 AGCCTTAGGGT
*
16298 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
16363 AACCTTCGGGT
66 AGCCTTAGGGT
* *
16374 CATCTGTAAGCCCTTCAGTGCATGATGTT
1 CATCTGTAAGTCCTACAGTGCATGATGTT
16403 GTTAAGACCT
Statistics
Matches: 1061, Mismatches: 23, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
73 27 0.03
74 73 0.07
75 98 0.09
76 863 0.81
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:21125 original size:16 final size:15
Alignment explanation
Indices: 21104--21141 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
21094 CATTAAATTT
*
21104 TTAAAATTATTTTGAA
1 TTAAAATTAATTT-AA
21120 TTAAAATTAATTTAA
1 TTAAAATTAATTTAA
21135 -TAAAATT
1 TTAAAATT
21142 TGGTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 2 0.10
16 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAAAATTAATTTAA
Found at i:21506 original size:12 final size:12
Alignment explanation
Indices: 21489--21529 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
21479 ACCAAAAACT
21489 CATCTTCTTCTC
1 CATCTTCTTCTC
21501 CATCTT-TTCT-
1 CATCTTCTTCTC
21511 CAT-TTCTTCTCC
1 CATCTTCTTCT-C
21523 CATCTTC
1 CATCTTC
21530 AAGTTGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.08
10 7 0.28
11 4 0.16
12 9 0.36
13 3 0.12
ACGTcount: A:0.10, C:0.39, G:0.00, T:0.51
Consensus pattern (12 bp):
CATCTTCTTCTC
Found at i:21518 original size:21 final size:23
Alignment explanation
Indices: 21487--21528 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
21477 CCACCAAAAA
21487 CTCATCTTCTTCT-CCATCTTTT
1 CTCATCTTCTTCTCCCATCTTTT
21509 CTCAT-TTCTTCTCCCATCTT
1 CTCATCTTCTTCTCCCATCTT
21529 CAAGTTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.10, C:0.38, G:0.00, T:0.52
Consensus pattern (23 bp):
CTCATCTTCTTCTCCCATCTTTT
Found at i:22181 original size:20 final size:20
Alignment explanation
Indices: 22156--22193 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22146 AGTTTCTAGG
*
22156 CAAGAGTATCGATACTTTAT
1 CAAGAGTATCGAAACTTTAT
22176 CAAGAGTATCGAAACTTT
1 CAAGAGTATCGAAACTTT
22194 GGGTCATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
CAAGAGTATCGAAACTTTAT
Found at i:25591 original size:16 final size:16
Alignment explanation
Indices: 25572--25624 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
25562 CCATAACCCC
25572 TATCACACATATATCA
1 TATCACACATATATCA
** * *
25588 TATCATGCACACATCA
1 TATCACACATATATCA
25604 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
25622 TAT
1 TAT
25625 ATCACCTAGC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:25820 original size:23 final size:23
Alignment explanation
Indices: 25794--25862 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
25784 CACCACAGCT
*
25794 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
25817 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTGCCA
**
25840 CGTAGAATTGCACCTTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
25863 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:26049 original size:103 final size:103
Alignment explanation
Indices: 25878--26198 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
25868 TAATGTCCAT
* * * * *
25878 AAGGACTACATATCATTCCTTAAGAATCGTATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
25943 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
25981 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
26046 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
26084 AAGAACCACATATCATTCCTTAAGAATCATATGCATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
26149 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
26187 AAGGACCACATA
1 AAGGACCACATA
26199 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:26737 original size:15 final size:15
Alignment explanation
Indices: 26717--26746 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26707 ATAAACTTAC
*
26717 TCATATTTTCATATA
1 TCATATTTTAATATA
26732 TCATATTTTAATATA
1 TCATATTTTAATATA
26747 ATTTGTATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (15 bp):
TCATATTTTAATATA
Found at i:27702 original size:21 final size:21
Alignment explanation
Indices: 27672--27716 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
27662 TTTTATTCGT
*
27672 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
27693 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
27714 TTG
1 TTG
27717 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:32184 original size:21 final size:21
Alignment explanation
Indices: 32160--32210 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
32150 GGCAAGAGTA
32160 TCGAAACTTTGGGTCATAGTT
1 TCGAAACTTTGGGTCATAGTT
32181 TCGAAACTTTGGGTCATAGTT
1 TCGAAACTTTGGGTCATAGTT
32202 TCGAAACTT
1 TCGAAACTT
32211 CCATAATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (21 bp):
TCGAAACTTTGGGTCATAGTT
Found at i:33719 original size:23 final size:24
Alignment explanation
Indices: 33663--33721 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
33653 CCATAAGAAA
*
33663 CGTATCACAAGAGTAGAGAAAAAAG
1 CGTATCACAAGAGCAGAG-AAAAAG
**
33688 CGTGCCACAAGAGCAGAG-AAAAG
1 CGTATCACAAGAGCAGAGAAAAAG
*
33711 CTTATCACAAG
1 CGTATCACAAG
33722 GACAAAGCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
23 13 0.46
25 15 0.54
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.12
Consensus pattern (24 bp):
CGTATCACAAGAGCAGAGAAAAAG
Found at i:34007 original size:47 final size:46
Alignment explanation
Indices: 33956--34097 Score: 109
Period size: 47 Copynumber: 3.2 Consensus size: 46
33946 CTTTATATAA
33956 TTATTTTAAATTTATAACTCATTTATTATCAAATACATGTATGCACT
1 TTATTTTAAATTTATAACTCATTTATTATCAAATACATGTATGCA-T
* *** * * ** *
34003 TTATTATGTCTTTAT---T--TTT-TAATTAAATA-ATCTGTATATAA
1 TTATTTTAAATTTATAACTCATTTATTATCAAATACA--TGTATGCAT
*
34044 TTATTTTAAAATTATAACTCATTTATTATCAAATACATGTATGCATT
1 TTATTTTAAATTTATAACTCATTTATTATCAAATACATGTATGCA-T
34091 TTATTTT
1 TTATTTT
34098 TTAATGTTAT
Statistics
Matches: 66, Mismatches: 19, Indels: 20
0.63 0.18 0.19
Matches are distributed among these distances:
40 1 0.02
41 18 0.27
42 9 0.14
44 2 0.03
46 9 0.14
47 26 0.39
48 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.51
Consensus pattern (46 bp):
TTATTTTAAATTTATAACTCATTTATTATCAAATACATGTATGCAT
Found at i:34077 original size:88 final size:88
Alignment explanation
Indices: 33929--34095 Score: 298
Period size: 88 Copynumber: 1.9 Consensus size: 88
33919 TTATAATAAT
* *
33929 TTTTTTAATTAAATAACCTTTATATAATTATTTTAAATTTATAACTCATTTATTATCAAATACAT
1 TTTTTTAATTAAATAACCTGTATATAATTATTTTAAAATTATAACTCATTTATTATCAAATACAT
33994 GTATGCACTTTATTATGTCTTTA
66 GTATGCACTTTATTATGTCTTTA
*
34017 TTTTTTAATTAAATAATCTGTATATAATTATTTTAAAATTATAACTCATTTATTATCAAATACAT
1 TTTTTTAATTAAATAACCTGTATATAATTATTTTAAAATTATAACTCATTTATTATCAAATACAT
*
34082 GTATGCATTTTATT
66 GTATGCACTTTATT
34096 TTTTAATGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.51
Consensus pattern (88 bp):
TTTTTTAATTAAATAACCTGTATATAATTATTTTAAAATTATAACTCATTTATTATCAAATACAT
GTATGCACTTTATTATGTCTTTA
Found at i:41132 original size:98 final size:96
Alignment explanation
Indices: 40924--41176 Score: 327
Period size: 98 Copynumber: 2.7 Consensus size: 96
40914 CATAAGCGAT
* * *
40924 GAATCGAGCGAGAATGACAATGTTGATGACGTTGATCCAACTCAGTATGCGATGGATGAGCCATG
1 GAATCGAGCAAGAATGACAATGTTGATGACATTGATCCAACTCAGTATGCGATGGATGAGCCAAG
* * *
40989 TATTGGTGTTGTTCCAACTCTGTATGTGATG
66 CATTGGTGCTGTTCCAACTCCGTATGTGATG
* * * * *
41020 GAATTGAGCAAGAATGACAATGTTGATGATATTGATCCAACTCCGTATGTGATGGATTTGAGCGA
1 GAATCGAGCAAGAATGACAATGTTGATGACATTGATCCAACTCAGTATGCGATGGA--TGAGCCA
41085 AGCATTGGTGCTGTTCCAACTCCGTATGTGATG
64 AGCATTGGTGCTGTTCCAACTCCGTATGTGATG
* *
41118 GAATCGAGAAAGAATGACACTG-TGATG-C--TGATCCAACT-ATGTATGCGATGGATGAGCCA
1 GAATCGAGCAAGAATGACAATGTTGATGACATTGATCCAACTCA-GTATGCGATGGATGAGCCA
41177 GAAGGAACAA
Statistics
Matches: 136, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
92 6 0.04
94 21 0.15
96 50 0.37
97 5 0.04
98 54 0.40
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (96 bp):
GAATCGAGCAAGAATGACAATGTTGATGACATTGATCCAACTCAGTATGCGATGGATGAGCCAAG
CATTGGTGCTGTTCCAACTCCGTATGTGATG
Found at i:41336 original size:91 final size:91
Alignment explanation
Indices: 41181--41565 Score: 558
Period size: 91 Copynumber: 4.2 Consensus size: 91
41171 GAGCCAGAAG
* *
41181 GAACAAATTCTTCTCATTATTAACTTTTTCTCCTTCGTTGGACGAGTTCTTCTCATTATGAACTC
1 GAACAAATTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGACGAGTTCTTCTCATTATGAACTC
* **
41246 TTCGTTGGAAATGCTGAGCTAAGGTT
66 TCCACTGGAAATGCTGAGCTAAGGTT
* *
41272 GAACAAATTCTTCTCATTATGAATTTTTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAATTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGACGAGTTCTTCTCATTATGAACTC
*
41337 TCCACTGGAAATGCTGAGCTAAGATT
66 TCCACTGGAAATGCTGAGCTAAGGTT
* * * *
41363 GAACAATTTCTTCTCATTATGAAC-TTTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAATTC
1 GAACAAATTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGACGAGTTCTTCTCATTATGAACTC
* *
41427 TCCACTGGAAAT-CTTGAACCAAGGTT
66 TCCACTGGAAATGC-TGAGCTAAGGTT
* * *
41453 GAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGACGAGTTCTTCTCATTATGAACTC
1 GAACAAATTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGACGAGTTCTTCTCATTATGAACTC
** *
41518 TCCGTTGGAAATGCTGAGCTGAGGTT
66 TCCACTGGAAATGCTGAGCTAAGGTT
*
41544 GAACAAGTTCTTCTCATTATGA
1 GAACAAATTCTTCTCATTATGA
41566 GTTAAGGTAT
Statistics
Matches: 265, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
89 1 0.00
90 82 0.31
91 181 0.68
92 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (91 bp):
GAACAAATTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGACGAGTTCTTCTCATTATGAACTC
TCCACTGGAAATGCTGAGCTAAGGTT
Found at i:41493 original size:181 final size:182
Alignment explanation
Indices: 41181--41565 Score: 560
Period size: 181 Copynumber: 2.1 Consensus size: 182
41171 GAGCCAGAAG
*
41181 GAACAAATTCTTCTCATTATTAACTTTTTCTCCTTCGTTGGACGAGTTCTTCTCATTATGAACTC
1 GAACAAATTCTTCTCATTATGAACTTTTTCTCCTTCGTTGGACGAGTTCTTCTCATTATGAACTC
* ** * * * *
41246 TTCGTTGGAAATGCTGAGCTAAGGTTGAACAAATTCTTCTCATTATGAATTTTTTCTCCCTCGTT
66 TCCACTGGAAATGCTGAACCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCGTT
*
41311 GGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGCTGAGCTAAGATT
131 GGACGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGCTGAGCTAAGATT
* * *
41363 GAACAATTTCTTCTCATTATGAAC-TTTTCTTCC-TCGTTGGATGAGTTCTTCTCATTATGAATT
1 GAACAAATTCTTCTCATTATGAACTTTTTC-TCCTTCGTTGGACGAGTTCTTCTCATTATGAACT
* *
41426 CTCCACTGGAAAT-CTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCG
65 CTCCACTGGAAATGC-TGAACCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCG
** * *
41490 TTGGACGAGTTCTTCTCATTATGAACTCTCCGTTGGAAATGCTGAGCTGAGGTT
129 TTGGACGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGCTGAGCTAAGATT
*
41544 GAACAAGTTCTTCTCATTATGA
1 GAACAAATTCTTCTCATTATGA
41566 GTTAAGGTAT
Statistics
Matches: 182, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
180 1 0.01
181 156 0.86
182 25 0.14
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (182 bp):
GAACAAATTCTTCTCATTATGAACTTTTTCTCCTTCGTTGGACGAGTTCTTCTCATTATGAACTC
TCCACTGGAAATGCTGAACCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCGTT
GGACGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGCTGAGCTAAGATT
Found at i:41997 original size:2 final size:2
Alignment explanation
Indices: 41990--42026 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41980 TTGTGATAAA
41990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42027 GGCATAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42431 original size:21 final size:20
Alignment explanation
Indices: 42407--42450 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
42397 CGGTAAAAAA
*
42407 TTACCTAAAATATTATTATTT
1 TTACCTAAAATATCATT-TTT
42428 TTACCTAAAATATCATTTTT
1 TTACCTAAAATATCATTTTT
42448 TTA
1 TTA
42451 GTATTTCCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.52
Consensus pattern (20 bp):
TTACCTAAAATATCATTTTT
Found at i:42958 original size:19 final size:20
Alignment explanation
Indices: 42936--42978 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
42926 AAAGTTAACC
42936 ACAAATAAATTAAT-TAA-TA
1 ACAAATAAA-TAATCTAATTA
*
42955 ACAATTAAATAATCTAATTA
1 ACAAATAAATAATCTAATTA
42975 ACAA
1 ACAA
42979 TACTAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 11 0.52
20 6 0.29
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (20 bp):
ACAAATAAATAATCTAATTA
Found at i:47061 original size:24 final size:24
Alignment explanation
Indices: 47029--47077 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
47019 TTTTTTATTG
47029 ACATAATCATAAAGTCATGGTCAA
1 ACATAATCATAAAGTCATGGTCAA
47053 ACATAATCATAAAGTCATGGTCAA
1 ACATAATCATAAAGTCATGGTCAA
47077 A
1 A
47078 GTAGAATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (24 bp):
ACATAATCATAAAGTCATGGTCAA
Found at i:48155 original size:2 final size:2
Alignment explanation
Indices: 48148--48193 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
48138 TGTTAAGTGG
48148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48190 AT AT
1 AT AT
48194 CTACCCATTA
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):
AT
Found at i:51865 original size:18 final size:18
Alignment explanation
Indices: 51842--51876 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51832 TTCCATCCGG
*
51842 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
51860 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
51877 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:56678 original size:24 final size:23
Alignment explanation
Indices: 56613--56710 Score: 89
Period size: 22 Copynumber: 4.4 Consensus size: 23
56603 CATTGAAGTG
*
56613 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
* * *
56636 -C-C-TTGTAA-TATCCCAAAGGA
1 CCACATAG-AATTGTCCCGAAGGA
*
56656 CCACGTAGAATTTGTCCCGAAGGA
1 CCACATAGAA-TTGTCCCGAAGGA
56680 CCACATAGAATTGT-CCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
*
56702 CCGCATAGA
1 CCACATAGA
56711 GAACCTTCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
20 12 0.20
21 4 0.07
22 20 0.33
23 6 0.10
24 19 0.31
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (23 bp):
CCACATAGAATTGTCCCGAAGGA
Found at i:56713 original size:24 final size:24
Alignment explanation
Indices: 56646--56710 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
56636 CCTTGTAATA
* *
56646 TCCCAAAGGACCACGTAGAATTTG
1 TCCCGAAGGACCACATAGAATTTG
56670 TCCCGAAGGACCACATAGAA-TTG
1 TCCCGAAGGACCACATAGAATTTG
*
56693 T-CCGAAGGACCGCATAGA
1 TCCCGAAGGACCACATAGA
56711 GAACCTTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 16 0.42
23 4 0.11
24 18 0.47
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (24 bp):
TCCCGAAGGACCACATAGAATTTG
Found at i:57150 original size:2 final size:2
Alignment explanation
Indices: 57143--57196 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
57133 CTTTCACATA
57143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57185 AT AT AT AT AT AT
1 AT AT AT AT AT AT
57197 TCATAACATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58934 original size:22 final size:22
Alignment explanation
Indices: 58906--58947 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
58896 CATAACTGCA
58906 TCCATAAGGACTTACCCTAGGG
1 TCCATAAGGACTTACCCTAGGG
*
58928 TCCATAAGGTCTTACCCTAG
1 TCCATAAGGACTTACCCTAG
58948 CTGAAACGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (22 bp):
TCCATAAGGACTTACCCTAGGG
Done.