Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001117.1 Hibiscus syriacus cultivar Beakdansim tig00002211_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: 73729
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:55 original size:24 final size:25
Alignment explanation
Indices: 10--129 Score: 192
Period size: 24 Copynumber: 4.9 Consensus size: 25
1 GCAACCCTT
10 AGATTAGGGTTTCAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAATC
35 AGATTAGGGTTT-AAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAATC
* *
59 TGATTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAATC
84 A-ATTTAGGGTTTCAAACCCTAAAT-
1 AGA-TTAGGGTTTCAAACCCTAAATC
108 AGATTAGGGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
130 TCCCCTACTC
Statistics
Matches: 88, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
24 44 0.50
25 44 0.50
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (25 bp):
AGATTAGGGTTTCAAACCCTAAATC
Found at i:71 original size:49 final size:49
Alignment explanation
Indices: 9--129 Score: 192
Period size: 49 Copynumber: 2.5 Consensus size: 49
1 GCAACCCT
*
9 TAGATTAGGGTTTCAAACCCTAAATCAGA-TTAGGGTTT-AAACCCTAAA
1 TAGATTAGGGTTTCAAACCCTAAAACA-ATTTAGGGTTTCAAACCCTAAA
*
57 TCTGATTAGGGTTTCAAACCCTAAAACAATTTAGGGTTTCAAACCCTAAA
1 T-AGATTAGGGTTTCAAACCCTAAAACAATTTAGGGTTTCAAACCCTAAA
107 TAGATTAGGGTTTCAAACCCTAA
1 TAGATTAGGGTTTCAAACCCTAA
130 TCCCCTACTC
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
48 2 0.03
49 54 0.81
50 11 0.16
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (49 bp):
TAGATTAGGGTTTCAAACCCTAAAACAATTTAGGGTTTCAAACCCTAAA
Found at i:1759 original size:16 final size:16
Alignment explanation
Indices: 1738--1771 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1728 CTTATAGAAA
1738 TTATTTTATTGTTATT
1 TTATTTTATTGTTATT
*
1754 TTATTTTTTTGTTATT
1 TTATTTTATTGTTATT
1770 TT
1 TT
1772 TTGATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
TTATTTTATTGTTATT
Found at i:4974 original size:18 final size:18
Alignment explanation
Indices: 4936--4987 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
4926 ATTATGTAAA
4936 TATTAAAAAGTATAATAATT
1 TATTAAAAA-T-TAATAATT
* *
4956 TATTTAAAATTAATCATT
1 TATTAAAAATTAATAATT
4974 TATTAAAAATTAAT
1 TATTAAAAATTAAT
4988 TATAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 20 0.69
19 1 0.03
20 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTAAAAATTAATAATT
Found at i:6354 original size:21 final size:22
Alignment explanation
Indices: 6316--6359 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
6306 GTATCTATAG
*
6316 TGGTTGAAGAGAAAATTATATT
1 TGGTTGAAGAGAAAATTAAATT
* *
6338 TGGTTGAA-ATAAGATTAAATT
1 TGGTTGAAGAGAAAATTAAATT
6359 T
1 T
6360 TGATTTTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTGAAGAGAAAATTAAATT
Found at i:7412 original size:18 final size:18
Alignment explanation
Indices: 7389--7438 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
7379 GCGTAGAATT
7389 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
7407 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
7425 TGTCCCGAAAGACC
1 TGTCCCGAAGGACC
7439 GCGTAGAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:8828 original size:10 final size:10
Alignment explanation
Indices: 8813--8867 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
8803 CTTAGTGTTT
8813 TAAGCTTATA
1 TAAGCTTATA
* *
8823 TAAGCTTTCTT
1 TAAGC-TTATA
8834 TAAGCTTATA
1 TAAGCTTATA
* *
8844 TAAGCTTTCTT
1 TAAGC-TTATA
8855 TAAGCTTATA
1 TAAGCTTATA
8865 TAA
1 TAA
8868 CACCCAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (10 bp):
TAAGCTTATA
Found at i:8837 original size:21 final size:21
Alignment explanation
Indices: 8811--8867 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
8801 CTCTTAGTGT
8811 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
8832 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
8853 TTTAAGCTTATATAA
1 TTTAAGCTTATATAA
8868 CACCCAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (21 bp):
TTTAAGCTTATATAAGCTTTC
Found at i:8839 original size:11 final size:11
Alignment explanation
Indices: 8823--8861 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
8813 TAAGCTTATA
8823 TAAGCTTTCTT
1 TAAGCTTTCTT
* *
8834 TAAGC-TTATA
1 TAAGCTTTCTT
8844 TAAGCTTTCTT
1 TAAGCTTTCTT
8855 TAAGCTT
1 TAAGCTT
8862 ATATAACACC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (11 bp):
TAAGCTTTCTT
Found at i:10200 original size:16 final size:16
Alignment explanation
Indices: 10179--10249 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
10169 ATCATTTATG
10179 TATATCATATAACACT
1 TATATCATATAACACT
* *
10195 TATATCATTTCACA-T
1 TATATCATATAACACT
* * * *
10210 AACATCATAT-ATATT
1 TATATCATATAACACT
10225 GTATATCATATAACACT
1 -TATATCATATAACACT
10242 TATATCAT
1 TATATCAT
10250 TTCACATAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 2 0.05
15 9 0.21
16 28 0.67
17 3 0.07
ACGTcount: A:0.41, C:0.17, G:0.01, T:0.41
Consensus pattern (16 bp):
TATATCATATAACACT
Found at i:10211 original size:21 final size:21
Alignment explanation
Indices: 10187--10260 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
10177 TGTATATCAT
10187 ATAACACTTATATCATTTCAC
1 ATAACACTTATATCATTTCAC
* * *
10208 ATAACATCATATATATTGTATATCAT
1 ATAACA-C-T-TATA-T-CATTTCAC
10234 ATAACACTTATATCATTTCAC
1 ATAACACTTATATCATTTCAC
10255 ATAACA
1 ATAACA
10261 TCATGGCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 17 0.40
22 2 0.05
23 5 0.12
24 5 0.12
25 2 0.05
26 11 0.26
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (21 bp):
ATAACACTTATATCATTTCAC
Found at i:10513 original size:22 final size:22
Alignment explanation
Indices: 10487--10550 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
10477 GTTCAGTATT
*
10487 CGTCCCGAAGGACCACTATATA
1 CGTCCCGAAGGACTACTATATA
* **
10509 CGTCCCGTAGGACTACTGGATA
1 CGTCCCGAAGGACTACTATATA
10531 CGTCCCGAAGGACTACTATA
1 CGTCCCGAAGGACTACTATA
10551 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (22 bp):
CGTCCCGAAGGACTACTATATA
Found at i:13216 original size:2 final size:2
Alignment explanation
Indices: 13209--13234 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13199 CAAACTATCC
13209 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
13235 TCTTTCAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14481 original size:2 final size:2
Alignment explanation
Indices: 14474--14503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14464 ATCATCTATC
14474 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
14504 CATAAATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15349 original size:16 final size:16
Alignment explanation
Indices: 15328--15396 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
15318 ATCATTTATG
15328 TATATCATATAACACT
1 TATATCATATAACACT
* *
15344 TATATCATTTCACA-T
1 TATATCATATAACACT
* * *
15359 AACATCATAT---ATT
1 TATATCATATAACACT
15372 GTATATCATATAACACT
1 -TATATCATATAACACT
15389 TATATCAT
1 TATATCAT
15397 TTCACATAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
12 1 0.03
13 1 0.03
14 8 0.20
15 8 0.20
16 20 0.50
17 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.01, T:0.41
Consensus pattern (16 bp):
TATATCATATAACACT
Found at i:15360 original size:21 final size:21
Alignment explanation
Indices: 15336--15407 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
15326 TGTATATCAT
15336 ATAACACTTATATCATTTCAC
1 ATAACACTTATATCATTTCAC
* * * *
15357 ATAACATCATATATTGTATATCAT
1 ATAACA-CTTATA-T-CATTTCAC
15381 ATAACACTTATATCATTTCAC
1 ATAACACTTATATCATTTCAC
15402 ATAACA
1 ATAACA
15408 TCATGACATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 17 0.43
22 6 0.15
23 6 0.15
24 11 0.28
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (21 bp):
ATAACACTTATATCATTTCAC
Found at i:15376 original size:45 final size:44
Alignment explanation
Indices: 15318--15411 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 44
15308 TATTGTACTT
*
15318 ATCATTTATGTATATCATATAACACTTATATCATTTCACATAAC
1 ATCATATATGTATATCATATAACACTTATATCATTTCACATAAC
15362 ATCATATATTGTATATCATATAACACTTATATCATTTCACATAAC
1 ATCATATA-TGTATATCATATAACACTTATATCATTTCACATAAC
15407 ATCAT
1 ATCAT
15412 GACATTTCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 7 0.15
45 41 0.85
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.40
Consensus pattern (44 bp):
ATCATATATGTATATCATATAACACTTATATCATTTCACATAAC
Found at i:15685 original size:22 final size:22
Alignment explanation
Indices: 15634--15715 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
15624 GTTCAGTATT
*
15634 CGTCCCGAATGACTA-T-TAT-
1 CGTCCCGAAGGACTACTATATA
* *
15653 -GTCCTGAAGGACCACTATATA
1 CGTCCCGAAGGACTACTATATA
* **
15674 CGTCCCGTAGGACTACTGGATA
1 CGTCCCGAAGGACTACTATATA
15696 CGTCCCGAAGGACTACTATA
1 CGTCCCGAAGGACTACTATA
15716 CCTCGACTCT
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
18 11 0.23
19 1 0.02
20 3 0.06
22 33 0.69
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (22 bp):
CGTCCCGAAGGACTACTATATA
Found at i:15899 original size:41 final size:41
Alignment explanation
Indices: 15848--15925 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
15838 ACCATGTATT
* *
15848 TCATATCATATCACATGTATCACATATTGCATATTCATATG
1 TCATATCATATAACATATATCACATATTGCATATTCATATG
* * *
15889 TCATTTCATATAACATATATCATATATTGCATTTTCA
1 TCATATCATATAACATATATCACATATTGCATATTCA
15926 CGTAGATCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (41 bp):
TCATATCATATAACATATATCACATATTGCATATTCATATG
Found at i:19198 original size:21 final size:21
Alignment explanation
Indices: 19173--19212 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19163 TAATGAGGTT
*
19173 TTAGTTGATTTAAT-ATTTACA
1 TTAGTT-ATATAATGATTTACA
19194 TTAGTTATATAATGATTTA
1 TTAGTTATATAATGATTTA
19213 TAAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TTAGTTATATAATGATTTACA
Found at i:19950 original size:6 final size:6
Alignment explanation
Indices: 19939--19963 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19929 GTGATGTAGG
19939 TGGGGT TGGGGT TGGGGT TGGGGT T
1 TGGGGT TGGGGT TGGGGT TGGGGT T
19964 TGGATCAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (6 bp):
TGGGGT
Found at i:22030 original size:160 final size:162
Alignment explanation
Indices: 21763--22054 Score: 414
Period size: 160 Copynumber: 1.8 Consensus size: 162
21753 AGATAATCGA
* * *
21763 TTCTTCATTTCTTAAATTGATTTTATAGAATAGATTTGATTAAATGAAGTCCCTTTTTTAACCTT
1 TTCTTCATTTCTTAAATTGATTTTAGAGAATAGATTCGATTAAATGAAATCCCTTTTTTAACCTT
* * *
21828 GGAATTGATAAACTAGACTTTGTAGAGACATTAAAGTTGAATGTGCTTCTATTTAA-TATTAATG
66 GGAACTGATAAACTAGACTTTGTACAGACATTAAAGTTGAATGTGCTTCTATTGAACT-TTAATG
21892 ATGTCAACTAAGGGTTGATTTTTAGGGTTTCAG
130 ATGTCAACTAAGGGTTGATTTTTAGGGTTTCAG
*
21925 TTCTTCATTTCTT-AATTGATTTTAGAGAATAGCTTCGATTAAATGAAAT-CCTTTTTTAA-CTT
1 TTCTTCATTTCTTAAATTGATTTTAGAGAATAGATTCGATTAAATGAAATCCCTTTTTTAACCTT
* ** * *
21987 ATGAACTGATACGCTAGACTTTGTACTGACATTCAAA-TTGAATGTGCTTTTATTGAACTTTAAT
66 -GGAACTGATAAACTAGACTTTGTACAGACATT-AAAGTTGAATGTGCTTCTATTGAACTTTAAT
22051 GATG
129 GATG
22055 ACAAATCGGG
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
159 3 0.03
160 63 0.55
161 36 0.31
162 13 0.11
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (162 bp):
TTCTTCATTTCTTAAATTGATTTTAGAGAATAGATTCGATTAAATGAAATCCCTTTTTTAACCTT
GGAACTGATAAACTAGACTTTGTACAGACATTAAAGTTGAATGTGCTTCTATTGAACTTTAATGA
TGTCAACTAAGGGTTGATTTTTAGGGTTTCAG
Found at i:23965 original size:32 final size:32
Alignment explanation
Indices: 23923--23987 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
23913 TTTTTTCTGA
* *
23923 TGTTTAGTGATTTTCCCAATGAAATGTGTTAT
1 TGTTTAGTGATTTTCCCAAGGAAATGTCTTAT
* *
23955 TGTTTGGTGATTTTCCCGAGGAAATGTCTTAT
1 TGTTTAGTGATTTTCCCAAGGAAATGTCTTAT
23987 T
1 T
23988 CTTGGTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (32 bp):
TGTTTAGTGATTTTCCCAAGGAAATGTCTTAT
Found at i:25576 original size:17 final size:17
Alignment explanation
Indices: 25554--25587 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25544 TGATTATTTA
*
25554 TTTAAATACAAATATAT
1 TTTAAAAACAAATATAT
*
25571 TTTAAAAACTAATATAT
1 TTTAAAAACAAATATAT
25588 ATATATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAAAACAAATATAT
Found at i:25587 original size:2 final size:2
Alignment explanation
Indices: 25582--25609 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25572 TTAAAAACTA
25582 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
25610 TAAAACTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33188 original size:16 final size:17
Alignment explanation
Indices: 33154--33193 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
33144 TTATATAAGC
*
33154 TGATATGTGTTTATATG
1 TGATATGTGATTATATG
*
33171 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
33187 TGATATG
1 TGATATG
33194 CCATATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:35057 original size:7 final size:7
Alignment explanation
Indices: 35045--35075 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
35035 GTCAAAGAAA
35045 GTCAACG
1 GTCAACG
35052 GTCAACG
1 GTCAACG
35059 GTCAACG
1 GTCAACG
35066 GTCAACG
1 GTCAACG
35073 GTC
1 GTC
35076 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:35093 original size:22 final size:22
Alignment explanation
Indices: 35065--35107 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
35055 AACGGTCAAC
35065 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
35087 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
35108 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:35144 original size:29 final size:31
Alignment explanation
Indices: 35110--35184 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
35100 GTCGGGTCAG
35110 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCTGAACCGGTTGAAA
35139 ACCGGTCAAACCGG-TCTGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCTGAACCGGTTGAAA
*
35169 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
35185 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCTGAACCGGTTGAAA
Found at i:35184 original size:9 final size:9
Alignment explanation
Indices: 35110--35184 Score: 69
Period size: 9 Copynumber: 7.8 Consensus size: 9
35100 GTCGGGTCAG
*
35110 ACCGGTCAA
1 ACCGGTTAA
*
35119 ACCGGTTCGA
1 ACCGGTT-AA
35129 ACCGGTTGAA
1 ACCGGTT-AA
*
35139 ACCGGTCAA
1 ACCGGTTAA
*
35148 ACCGGTCTGA
1 ACCGGT-TAA
35158 ACCGGTTGAAA
1 ACCGGTT--AA
35169 ACCGGTTAA
1 ACCGGTTAA
35178 ACCGGTT
1 ACCGGTT
35185 TCCAGCAGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
9 24 0.44
10 22 0.41
11 8 0.15
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:42332 original size:7 final size:7
Alignment explanation
Indices: 42320--42350 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42310 GTCAAAGAAA
42320 GTCAACG
1 GTCAACG
42327 GTCAACG
1 GTCAACG
42334 GTCAACG
1 GTCAACG
42341 GTCAACG
1 GTCAACG
42348 GTC
1 GTC
42351 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:42357 original size:5 final size:5
Alignment explanation
Indices: 42347--42404 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
42337 AACGGTCAAC
* *
42347 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
42396 GGTCG GGTC
1 GGTCG GGTC
42405 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:42368 original size:22 final size:22
Alignment explanation
Indices: 42340--42404 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
42330 AACGGTCAAC
42340 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
42362 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
42384 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
42405 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:42425 original size:19 final size:19
Alignment explanation
Indices: 42403--42500 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
42393 TCGGGTCGGG
42403 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
42422 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
42441 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
42460 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
42480 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
42500 T
1 T
42501 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:42431 original size:10 final size:9
Alignment explanation
Indices: 42401--42499 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
42391 GGTCGGGTCG
*
42401 GGTCAGACC
1 GGTCAAACC
42410 GGTCAAACC
1 GGTCAAACC
*
42419 GGTTCAGACC
1 GG-TCAAACC
42429 GGTCAAACC
1 GGTCAAACC
*
42438 GGTTCGAACC
1 GG-TCAAACC
*
42448 GGTTGAAACC
1 GG-TCAAACC
42458 GGTCAAACC
1 GGTCAAACC
42467 GGTCAGAACC
1 GGTCA-AACC
*
42477 GGTTGAAAACC
1 GG-T-CAAACC
*
42488 GGTTAAACC
1 GGTCAAACC
42497 GGT
1 GGT
42500 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:42458 original size:29 final size:28
Alignment explanation
Indices: 42402--42499 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
42392 GTCGGGTCGG
* * *
42402 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
42430 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
42459 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
42489 GTTAAACCGGT
1 GTCAAACCGGT
42500 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 11 0.18
29 34 0.56
30 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:43499 original size:24 final size:24
Alignment explanation
Indices: 43448--43513 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
43438 CAATCTTATA
*
43448 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTACGGTGCAAATTCTACG
* *
43471 CGGCACTTCGGTGCAAATTCTACG
1 TGGCACTACGGTGCAAATTCTACG
43495 TGGCACTACGGTGCAAATT
1 TGGCACTACGGTGCAAATT
43514 TATACGAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 12 0.32
24 25 0.68
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (24 bp):
TGGCACTACGGTGCAAATTCTACG
Found at i:44229 original size:12 final size:12
Alignment explanation
Indices: 44209--44254 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
44199 TTAACATTCG
44209 GGTATTGTTCAT
1 GGTATTGTTCAT
*
44221 GGTAATGTTCAT
1 GGTATTGTTCAT
*
44233 --TATTGTTCAC
1 GGTATTGTTCAT
44243 GGTATTGTTCAT
1 GGTATTGTTCAT
44255 ACCGTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 8 0.29
12 20 0.71
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.48
Consensus pattern (12 bp):
GGTATTGTTCAT
Found at i:44239 original size:22 final size:22
Alignment explanation
Indices: 44211--44254 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
44201 AACATTCGGG
*
44211 TATTGTTCATGGTAATGTTCAT
1 TATTGTTCACGGTAATGTTCAT
*
44233 TATTGTTCACGGTATTGTTCAT
1 TATTGTTCACGGTAATGTTCAT
44255 ACCGTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.50
Consensus pattern (22 bp):
TATTGTTCACGGTAATGTTCAT
Found at i:44515 original size:19 final size:19
Alignment explanation
Indices: 44491--44530 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
44481 TACTTTATTA
44491 TGTTGGAGGATCCACCTTT
1 TGTTGGAGGATCCACCTTT
*
44510 TGTTGGAGGATGCACCTTT
1 TGTTGGAGGATCCACCTTT
44529 TG
1 TG
44531 GTGTCAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.38
Consensus pattern (19 bp):
TGTTGGAGGATCCACCTTT
Found at i:45395 original size:13 final size:13
Alignment explanation
Indices: 45377--45401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45367 GTCCTTGAGC
45377 TTTTCAACCTTGT
1 TTTTCAACCTTGT
45390 TTTTCAACCTTG
1 TTTTCAACCTTG
45402 CCTTCAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTTCAACCTTGT
Found at i:52186 original size:17 final size:17
Alignment explanation
Indices: 52161--52194 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
52151 CAAAAAATAT
52161 AAAAATATTTT-TTAAA
1 AAAAATATTTTATTAAA
52177 AAAAAGTATTTTATTAAA
1 AAAAA-TATTTTATTAAA
52195 TATAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAAAATATTTTATTAAA
Found at i:54023 original size:21 final size:21
Alignment explanation
Indices: 53997--54042 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
53987 TTAATCAACA
53997 TAAAATTAA-AAGTTTA-AGTAC
1 TAAAATTAATAA-TTTAGA-TAC
54018 TAAAATTAATAATTTAGATAC
1 TAAAATTAATAATTTAGATAC
54039 TAAA
1 TAAA
54043 TACGTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (21 bp):
TAAAATTAATAATTTAGATAC
Found at i:59061 original size:12 final size:13
Alignment explanation
Indices: 59033--59062 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
59023 ATAATATGAT
59033 AAATATTAAATAA
1 AAATATTAAATAA
59046 AAATATTAAA-AA
1 AAATATTAAATAA
59058 AAATA
1 AAATA
59063 AAATAGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATATTAAATAA
Found at i:61311 original size:26 final size:27
Alignment explanation
Indices: 61282--61340 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
61272 TGCAGTCTAG
* *
61282 AAGAAGAG-TGAAGAAAAGTGAAGATA
1 AAGAAGAGAAGAAGAAAAGTGAAGAAA
61308 AAGAA-AGAAGAAGAAAAGTGAAGAAA
1 AAGAAGAGAAGAAGAAAAGTGAAGAAA
61334 AAGAAGA
1 AAGAAGA
61341 TGAGAATGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 26 0.90
27 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (27 bp):
AAGAAGAGAAGAAGAAAAGTGAAGAAA
Found at i:70688 original size:27 final size:27
Alignment explanation
Indices: 70658--70726 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
70648 GTCCCCAACA
* *
70658 GTCGCCATGCATTCC-CCACCCTACAAG
1 GTCGCCATGCACTCCAACA-CCTACAAG
70685 GTCGCCATGCACTCCAACGACCTACAAG
1 GTCGCCATGCACTCCAAC-ACCTACAAG
70713 GTCGCCATGCACTC
1 GTCGCCATGCACTC
70727 AGCGACCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 14 0.37
28 23 0.61
29 1 0.03
ACGTcount: A:0.23, C:0.42, G:0.17, T:0.17
Consensus pattern (27 bp):
GTCGCCATGCACTCCAACACCTACAAG
Found at i:70746 original size:27 final size:28
Alignment explanation
Indices: 70677--70734 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
70667 CATTCCCCAC
70677 CCTACAAGGTCGCCATGCACTCCAACGA
1 CCTACAAGGTCGCCATGCACTCCAACGA
*
70705 CCTACAAGGTCGCCATGCACT-CAGCGA
1 CCTACAAGGTCGCCATGCACTCCAACGA
70732 CCT
1 CCT
70735 TGTAGGTCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.26, C:0.40, G:0.19, T:0.16
Consensus pattern (28 bp):
CCTACAAGGTCGCCATGCACTCCAACGA
Found at i:71080 original size:19 final size:19
Alignment explanation
Indices: 71052--71088 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
71042 TTGCAGCCGA
71052 GAAAGAAAGAAAAAGAAAT
1 GAAAGAAAGAAAAAGAAAT
* *
71071 GAAAGGAAGAAGAAGAAA
1 GAAAGAAAGAAAAAGAAA
71089 GGGAGATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (19 bp):
GAAAGAAAGAAAAAGAAAT
Found at i:71217 original size:22 final size:21
Alignment explanation
Indices: 71192--71232 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
71182 GTTAATTAGT
*
71192 TTGTTAATTTAGGGTTATATGA
1 TTGTTAATTTA-AGTTATATGA
*
71214 TTGTTAGTTTAAGTTATAT
1 TTGTTAATTTAAGTTATAT
71233 TATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTAATTTAAGTTATATGA
Done.