Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008862.1 Hibiscus syriacus cultivar Beakdansim tig00112087_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: 59311
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3138 original size:5 final size:5
Alignment explanation
Indices: 3128--3157 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
3118 AACGGTCAAC
3128 GGTCG GGTCG GGTCG CGGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG -GGTCG GGTCG GGTC
3158 AGACCGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.23, G:0.57, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:3148 original size:16 final size:16
Alignment explanation
Indices: 3127--3157 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3117 CAACGGTCAA
3127 CGGTCGGGTCGGGTCG
1 CGGTCGGGTCGGGTCG
3143 CGGTCGGGTCGGGTC
1 CGGTCGGGTCGGGTC
3158 AGACCGGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.55, T:0.19
Consensus pattern (16 bp):
CGGTCGGGTCGGGTCG
Found at i:10382 original size:17 final size:17
Alignment explanation
Indices: 10360--10408 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
10350 AACGGTCAAC
10360 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
10377 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
10394 GCTCAACGGTCGGGT
1 GGTCAACGGTCGGGT
10409 TGGTCGGTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:10448 original size:19 final size:18
Alignment explanation
Indices: 10419--10458 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
10409 TGGTCGGTCG
10419 GGTCAAACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
*
10437 GGTCAGAACCGGTTAAACC
1 GGTCA-AACCGGTCAAACC
10456 GGT
1 GGT
10459 TTCCAGCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:10459 original size:9 final size:9
Alignment explanation
Indices: 10419--10458 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
10409 TGGTCGGTCG
10419 GGTCAAACC
1 GGTCAAACC
10428 GGTCAAACC
1 GGTCAAACC
10437 GGTCAGAACC
1 GGTCA-AACC
*
10447 GGTTAAACC
1 GGTCAAACC
10456 GGT
1 GGT
10459 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:13269 original size:88 final size:89
Alignment explanation
Indices: 13161--13330 Score: 272
Period size: 89 Copynumber: 1.9 Consensus size: 89
13151 AAATCGATAC
* *
13161 GGTTTTTTCATCTAACCAAAAAA-CTAGATTTTAAAAAAATC-GTTCGGATTCTAACCGGTTTGG
1 GGTTTTTTCACCTAACCAAAAAATC-AGATTTTAAAAAAACCGGTTCGGATTCTAACCGGTTTGG
*
13224 ATGGTCGGATGGTGTAACCCGATCT
65 AGGGTCGGATGGTGTAACCCGATCT
* *
13249 GGTTTTTTCACCTAGCCAAAAAATCGGATTTTAAAAAAACCGGTTCGGATTCTAACCGGTTTGGA
1 GGTTTTTTCACCTAACCAAAAAATCAGATTTTAAAAAAACCGGTTCGGATTCTAACCGGTTTGGA
13314 GGGTCGGATGGTGTAAC
66 GGGTCGGATGGTGTAAC
13331 TGGTTTCTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
88 35 0.47
89 40 0.53
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (89 bp):
GGTTTTTTCACCTAACCAAAAAATCAGATTTTAAAAAAACCGGTTCGGATTCTAACCGGTTTGGA
GGGTCGGATGGTGTAACCCGATCT
Found at i:14074 original size:2 final size:2
Alignment explanation
Indices: 14067--14099 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14057 GATGGATGTG
14067 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 A
14100 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14659 original size:25 final size:26
Alignment explanation
Indices: 14613--14668 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
14603 TAATAAGTTA
*
14613 ATATAAAATATTTTCAAGTTAA-TAT
1 ATATAAAATATTATCAAGTTAAGTAT
* * *
14638 ATATAGAATATTATGAATTTAAGTAT
1 ATATAAAATATTATCAAGTTAAGTAT
*
14664 TTATA
1 ATATA
14669 CATTGAGATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (26 bp):
ATATAAAATATTATCAAGTTAAGTAT
Found at i:31184 original size:3 final size:3
Alignment explanation
Indices: 31152--31231 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
31142 GGACTGTTTG
* * * * *
31152 TAA TAT TAA TAAA TAA TATA TAT TAT TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
31199 TAA TAA TAA TAA TTA TAA TAA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31232 AATGAGTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
3 59 0.91
4 6 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:31204 original size:21 final size:21
Alignment explanation
Indices: 31158--31231 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
31148 TTTGTAATAT
31158 TAATAAATAAT-ATATATTAT--
1 TAAT-AATAATAAT-TATTATAA
31178 TAATAATAATAATTATTATAA
1 TAATAATAATAATTATTATAA
*
31199 TAATAATAATAATTATAATAA
1 TAATAATAATAATTATTATAA
*
31220 TACTAATAATAA
1 TAATAATAATAA
31232 AATGAGTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 12 0.24
20 6 0.12
21 31 0.63
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATAATAATAATTATTATAA
Found at i:31227 original size:18 final size:18
Alignment explanation
Indices: 31158--31229 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
31148 TTTGTAATAT
31158 TAATAAATAAT-ATATATTA
1 TAAT-AATAATAATA-ATTA
*
31177 TTAATAATAATAATTATTA
1 -TAATAATAATAATAATTA
31196 TAATAATAATAATAATTA
1 TAATAATAATAATAATTA
*
31214 TAATAATACTAATAAT
1 TAATAATAATAATAAT
31230 AAAATGAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
18 32 0.67
19 10 0.21
20 6 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAATAATTA
Found at i:31792 original size:40 final size:39
Alignment explanation
Indices: 31583--31796 Score: 336
Period size: 40 Copynumber: 5.6 Consensus size: 39
31573 GTTGAACAAA
31583 TTCTTCTCATTATGAA--TCTCTT-C-T-TTCAGATGAG
1 TTCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAG
31617 TTCTTCTCATTATGAAC-T-TCTT-CTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAG
31653 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTC-TCTTCCTTCTTCAGATGAG
31693 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTC-TCTTCCTTCTTCAGATGAG
31733 TTCTTCTCATTATGAACTTTCTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAAC-TTCTCTTCCTTCTTCAGATGAG
31773 TTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAAC-TTCTCT
31797 GGAAAAGCTG
Statistics
Matches: 172, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
34 21 0.12
35 2 0.01
36 27 0.16
37 1 0.01
39 4 0.02
40 114 0.66
41 3 0.02
ACGTcount: A:0.18, C:0.24, G:0.10, T:0.48
Consensus pattern (39 bp):
TTCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAG
Found at i:31884 original size:113 final size:113
Alignment explanation
Indices: 31733--32165 Score: 798
Period size: 113 Copynumber: 3.8 Consensus size: 113
31723 TTCAGATGAG
*
31733 TTCTTCTCATTATGAACTTTC-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAA-TTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
31797 GGAAAAGCTGATCCATCGAA-TGATGGATTTGAGCATAAGGTTGAACAAA
65 GGAAAAGCTGATCCATC-AAGTGATGGATTTGAGCATAAGGTTGAACAAA
31846 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
31911 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAA
* *
31959 TTCTTCTCATTATGAATTTCTTCTTCATCCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
32024 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAA
*
32072 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
32137 GAAAAGCTGATCCATCAAGTGATGGATTT
66 GAAAAGCTGATCCATCAAGTGATGGATTT
32166 AAATCTTTGC
Statistics
Matches: 312, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
112 6 0.02
113 306 0.98
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAA
Found at i:33188 original size:198 final size:197
Alignment explanation
Indices: 32851--33218 Score: 551
Period size: 198 Copynumber: 1.9 Consensus size: 197
32841 ACGATCATGC
* * * *
32851 AATTCATCTTTTAATTCCAATGATTGTTTCTGGGTTTTATATCAAACCAAATCAGAGAATTCAAA
1 AATTCATCTTTAAATTCCAATGATTGGTTCTGGGTTTCATATCAAACCAAATCAGAGAACTCAAA
* * * * *
32916 GAACATTTCCAAAAGATGCTATGAGCACATTTATCTTCCAAATTCAATGATTGATTTTACCAAAT
66 GAACACTTCCAAAAGATGCTATGAGCACATTCATCTTCCAAATTCAATAACTGATTTTACCAAAC
*
32981 CAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
33046 CA
196 CA
* *
33048 AATTCATCTTTCAAATT-TAATGATTGGTTCTGTGGTTTCATATCAAA-CAAGATCAGATAACTC
1 AATTCATCTTT-AAATTCCAATGATTGGTTCTG-GGTTTCATATCAAACCAA-ATCAGAGAACTC
* * * *
33111 AAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTTTACCA
63 AAAGAACACTTCCAAAAGATGCTATGAGCACATTCATCTTCCAAATTCAATAACTGATTTTACCA
33176 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
128 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
33219 GATCACATTC
Statistics
Matches: 152, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
197 27 0.18
198 125 0.82
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (197 bp):
AATTCATCTTTAAATTCCAATGATTGGTTCTGGGTTTCATATCAAACCAAATCAGAGAACTCAAA
GAACACTTCCAAAAGATGCTATGAGCACATTCATCTTCCAAATTCAATAACTGATTTTACCAAAC
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
CA
Found at i:33334 original size:162 final size:162
Alignment explanation
Indices: 33067--33392 Score: 634
Period size: 162 Copynumber: 2.0 Consensus size: 162
33057 TTCAAATTTA
33067 ATGATTGGTTCTGTGGTTTCATATCAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
1 ATGATTGGTTCTGTGGTTTCATATCAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
33132 CTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAA
66 CTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAA
*
33197 GAACACTTCCAGAAGATGCTATGATCACATTC
131 GAACACTTCCAGAAGATGCTATGAGCACATTC
33229 ATGATTGGTTCTGTGGTTTCATATCAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
1 ATGATTGGTTCTGTGGTTTCATATCAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
33294 CTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTTTACCAAACCAGATCATATAACTCAAA
66 CTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAA
33359 GAACACTTCCAGAAGATGCTATGAGCACATTC
131 GAACACTTCCAGAAGATGCTATGAGCACATTC
33391 AT
1 AT
33393 CTTTCAAATT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (162 bp):
ATGATTGGTTCTGTGGTTTCATATCAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
CTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAGCACATTC
Found at i:33401 original size:83 final size:83
Alignment explanation
Indices: 33091--33472 Score: 490
Period size: 83 Copynumber: 4.7 Consensus size: 83
33081 GGTTTCATAT
* * *
33091 CAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
33156 TTCAATAACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
* * *
33174 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATGATT---G
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT-CTTCCAA
* * *
33236 GTTC--T--GTGGTTTCATAT
65 ATTCAATAACTGGTTT--TAC
* * *
33253 CAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
33318 TTCAATAACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
* *
33336 CAAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
* * *
33401 TTCAATGATTAGTTTTAC
66 TTCAATAACTGGTTTTAC
* * * * *
33419 CAAACCAGGTTAGATAAATCAAAGAATACTTCCAGAAGATGCTATGAGTACATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
33473 GCATTTGTTC
Statistics
Matches: 257, Mismatches: 32, Indels: 20
0.83 0.10 0.06
Matches are distributed among these distances:
77 6 0.02
78 2 0.01
79 56 0.22
81 6 0.02
83 179 0.70
84 2 0.01
85 6 0.02
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
TTCAATAACTGGTTTTAC
Found at i:34637 original size:6 final size:6
Alignment explanation
Indices: 34621--34677 Score: 71
Period size: 6 Copynumber: 9.2 Consensus size: 6
34611 TGACACCCCT
*
34621 TTTTTC TTTTTTC TTTTTC TTTTT- TTTTTC TTTTTT TTTCTTC TTCTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC TT-TTTC
34671 TTTTTC T
1 TTTTTC T
34678 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
5 5 0.11
6 24 0.53
7 15 0.33
8 1 0.02
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:34639 original size:13 final size:12
Alignment explanation
Indices: 34620--34677 Score: 73
Period size: 13 Copynumber: 4.7 Consensus size: 12
34610 TTGACACCCC
34620 TTTTTTCTTTTT
1 TTTTTTCTTTTT
34632 TCTTTTTC-TTTT
1 T-TTTTTCTTTTT
34644 TTTTTTCTTTTT
1 TTTTTTCTTTTT
34656 TTTTCTTCTTCTTT
1 TTTT-TTCTT-TTT
*
34670 CTTTTTCT
1 TTTTTTCT
34678 CTTCAAGCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
11 6 0.15
12 14 0.34
13 15 0.37
14 6 0.15
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:34657 original size:27 final size:28
Alignment explanation
Indices: 34627--34680 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
34617 CCCTTTTTTC
* *
34627 TTTTTTCTTTTTCTTT-TTTTTTTCTTT
1 TTTTTTCTTCTTCTTTCTTTTTCTCTTT
34654 TTTTTTCTTCTTCTTTCTTTTTCTCTT
1 TTTTTTCTTCTTCTTTCTTTTTCTCTT
34681 CAAGCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (28 bp):
TTTTTTCTTCTTCTTTCTTTTTCTCTTT
Found at i:34677 original size:10 final size:10
Alignment explanation
Indices: 34630--34677 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
34620 TTTTTTCTTT
34630 TTTCTTTTTC
1 TTTCTTTTTC
34640 -TT-TTTTT-
1 TTTCTTTTTC
*
34647 TTTCTTTTTT
1 TTTCTTTTTC
*
34657 TTTCTTCTTC
1 TTTCTTTTTC
34667 TTTCTTTTTC
1 TTTCTTTTTC
34677 T
1 T
34678 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
8 7 0.22
9 7 0.22
10 18 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:42027 original size:15 final size:15
Alignment explanation
Indices: 42004--42035 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41994 TGAAATGAAT
42004 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
42019 AATGCATGTATGCAA
1 AATGAATGTATGCAA
42034 AA
1 AA
42036 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:47472 original size:3 final size:3
Alignment explanation
Indices: 47443--47522 Score: 70
Period size: 3 Copynumber: 26.0 Consensus size: 3
47433 GGCCTGTTTG
* * * * *
47443 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TTA TTA TTA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
47490 TAA TTA TAA TTA TAA TAA TAC TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47523 AATGAGTAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 57 0.90
4 6 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:49887 original size:3 final size:3
Alignment explanation
Indices: 49879--49955 Score: 145
Period size: 3 Copynumber: 25.3 Consensus size: 3
49869 TATATACCAC
49879 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49927 ATT ATTT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT A
49956 ATCACATCAA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 70 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:50971 original size:31 final size:30
Alignment explanation
Indices: 50932--51004 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
50922 ATATAATAAT
*
50932 TATTTTATAGT-ATTTAGATAAATTTATTAA
1 TATTTTATAATCATTTA-ATAAATTTATTAA
* *
50962 TAATTTTATAATCTTTTAATAAATTTATAAA
1 T-ATTTTATAATCATTTAATAAATTTATTAA
50993 GTATTTTATAAT
1 -TATTTTATAAT
51005 TTTTTAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 31 0.84
32 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TATTTTATAATCATTTAATAAATTTATTAA
Found at i:51010 original size:31 final size:31
Alignment explanation
Indices: 50944--51011 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
50934 TTTTATAGTA
*
50944 TTTAGATAAATTTATTAATAATTTTATAATCT
1 TTTA-ATAAATTTATAAATAATTTTATAATCT
*
50976 TTTAATAAATTTATAAAGT-ATTTTATAATTT
1 TTTAATAAATTTATAAA-TAATTTTATAATCT
51007 TTTAA
1 TTTAA
51012 ACTTTATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATAAATTTATAAATAATTTTATAATCT
Found at i:51765 original size:31 final size:30
Alignment explanation
Indices: 51730--51816 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
51720 TCAATAAAGT
51730 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
51761 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
51792 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
51817 TATTATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:51792 original size:20 final size:20
Alignment explanation
Indices: 51725--51792 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
51715 TTTCGTCAAT
*
51725 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
51743 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
51764 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
51783 ATAA-ATTTAT
1 A-AAGATTTAT
51793 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:53952 original size:11 final size:12
Alignment explanation
Indices: 53936--53976 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
53926 TATTTATCTC
53936 ATTTAATTAAAT
1 ATTTAATTAAAT
*
53948 A-TTAATGAAAT
1 ATTTAATTAAAT
53959 ATTTAATT-AAT
1 ATTTAATTAAAT
53970 -TTTAATT
1 ATTTAATT
53977 TGCGAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 7 0.27
11 13 0.50
12 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
ATTTAATTAAAT
Found at i:55605 original size:40 final size:42
Alignment explanation
Indices: 55545--55627 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 42
55535 TCTGTTAAAT
* **
55545 TAAATAAATAAATACAAATAATT-TTT-TTATATTTATTTAA
1 TAAATAAATAAACACAAATAATTATTTAAGATATTTATTTAA
**
55585 TAAATAAATAAACATGAATAATTATTTAAGATATTTATTTAA
1 TAAATAAATAAACACAAATAATTATTTAAGATATTTATTTAA
55627 T
1 T
55628 TCATTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 20 0.56
41 3 0.08
42 13 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (42 bp):
TAAATAAATAAACACAAATAATTATTTAAGATATTTATTTAA
Found at i:56436 original size:15 final size:15
Alignment explanation
Indices: 56416--56444 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56406 TCGACCACCT
56416 CCATATCCTCCGCCA
1 CCATATCCTCCGCCA
56431 CCATATCCTCCGCC
1 CCATATCCTCCGCC
56445 GTTACGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.55, G:0.07, T:0.21
Consensus pattern (15 bp):
CCATATCCTCCGCCA
Found at i:58429 original size:20 final size:20
Alignment explanation
Indices: 58400--58566 Score: 148
Period size: 20 Copynumber: 8.3 Consensus size: 20
58390 AATCTATAAA
*
58400 TCGCAACACAGAAGTTAAAT
1 TCGCAACACAGAAGTCAAAT
*
58420 TCGTAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
58440 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
58460 TCGCAACACTGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
58480 TCGCAACGCA-AA-TCTGTAAA-
1 TCGCAACACAGAAGTC---AAAT
* * *
58500 TCGCAACGC-GAATTTTTAAA-
1 TCGCAACACAGAA--GTCAAAT
58520 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
58540 TCGCAACACATATGTCAAAT
1 TCGCAACACAGAAGTCAAAT
58560 TCGCAAC
1 TCGCAAC
58567 GCGATAGTTA
Statistics
Matches: 123, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.02
19 8 0.07
20 104 0.85
21 8 0.07
23 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:58447 original size:60 final size:59
Alignment explanation
Indices: 58375--58570 Score: 220
Period size: 60 Copynumber: 3.3 Consensus size: 59
58365 ACCTAGTTTC
* * *
58375 CAAATTCACAACGCGAATCTATAAATCGCAACACAGAAGTTAAATTCGTAACACAGAAGT
1 CAAATTCGCAACGCGAATCTATAAATCGCAACACAGAAGTCAAATTCGCAACACA-AAGT
* * *
58435 CAAATTCGCAACGCGATAGTC-A-AATTCGCAACACTGAAGTCAAATTCGCAACGCAAA-T
1 CAAATTCGCAACGCGA-A-TCTATAAATCGCAACACAGAAGTCAAATTCGCAACACAAAGT
* * *
58493 CTGTAAA-TCGCAACGCGAATTTTTAAATCGCAACACAGAAGTCAAATTCGCAACACATATGT
1 C---AAATTCGCAACGCGAATCTATAAATCGCAACACAGAAGTCAAATTCGCAACACA-AAGT
58555 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
58571 TAGTTAAATT
Statistics
Matches: 114, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
58 3 0.03
59 6 0.05
60 95 0.83
61 6 0.05
62 4 0.04
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (59 bp):
CAAATTCGCAACGCGAATCTATAAATCGCAACACAGAAGTCAAATTCGCAACACAAAGT
Found at i:58618 original size:60 final size:59
Alignment explanation
Indices: 58396--58648 Score: 200
Period size: 60 Copynumber: 4.2 Consensus size: 59
58386 CGCGAATCTA
* * *
58396 TAAA-TCGCAACAC-AGAAGTTAAATTCGTAACACAGAA-GTCAAATTCGCAACGCGATAGT
1 TAAATTCGCAACACTAGAAGTCAAATTCG-CA-AC-GAATTTCAAATTCGCAACGCGATAGT
* **
58455 CAAATTCGCAACACT-GAAGTCAAATTCGCAACGCAAATCTGT-AAA-TCGCAACGCGAATTTT
1 TAAATTCGCAACACTAGAAGTCAAATTCGCAACG--AAT-T-TCAAATTCGCAACGCG-ATAGT
58516 TAAA-TCGCAACAC-AGAAGTCAAATTCGCAAC-ACATATGTCAAATTCGCAACGCGATAGT
1 TAAATTCGCAACACTAGAAGTCAAATTCGCAACGA-AT-T-TCAAATTCGCAACGCGATAGT
* * * * * * **
58575 TAAATTCGTAATACTAAAATTCAAATTCACAACTGAATTTCAAATTCGCAACTCGATTTT
1 TAAATTCGCAACACTAGAAGTCAAATTCGCAAC-GAATTTCAAATTCGCAACGCGATAGT
*
58635 TGAATTCGCAACAC
1 TAAATTCGCAACAC
58649 AAATTTAATT
Statistics
Matches: 157, Mismatches: 21, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
57 2 0.01
58 7 0.04
59 16 0.10
60 103 0.66
61 25 0.16
62 3 0.02
63 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (59 bp):
TAAATTCGCAACACTAGAAGTCAAATTCGCAACGAATTTCAAATTCGCAACGCGATAGT
Found at i:58841 original size:14 final size:15
Alignment explanation
Indices: 58822--58859 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
58812 TCCCCATCTC
58822 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
58836 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
58852 TAATTTTT
1 TAATTTTT
58860 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Done.