Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001311.1 Hibiscus syriacus cultivar Beakdansim tig00002556_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: 100895
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:12705 original size:20 final size:21
Alignment explanation
Indices: 12663--12705 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
12653 TGAAAATCTG
*
12663 TTTTATTTTGAATACTGAGAAA
1 TTTTATTTTG-ATACTCAGAAA
*
12685 TTTTATTTTG-TACTCATAAA
1 TTTTATTTTGATACTCAGAAA
12705 T
1 T
12706 GATTTTATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTTATTTTGATACTCAGAAA
Found at i:16598 original size:18 final size:18
Alignment explanation
Indices: 16572--16610 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
16562 ACGAACTTAT
*
16572 AAAATTTTAAGTAGTAAA
1 AAAAGTTTAAGTAGTAAA
16590 AAAAGTTTAAGTAGTAAA
1 AAAAGTTTAAGTAGTAAA
16608 AAA
1 AAA
16611 TTTATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (18 bp):
AAAAGTTTAAGTAGTAAA
Found at i:16608 original size:17 final size:17
Alignment explanation
Indices: 16572--16614 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
16562 ACGAACTTAT
*
16572 AAAATTTTAAGTAGTAA
1 AAAAATTTAAGTAGTAA
16589 AAAAAGTTTAAGTAGT-A
1 AAAAA-TTTAAGTAGTAA
16606 AAAAATTTA
1 AAAAATTTA
16615 TAAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 10 0.42
18 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (17 bp):
AAAAATTTAAGTAGTAA
Found at i:19168 original size:6 final size:6
Alignment explanation
Indices: 19157--19192 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
19147 TAATCTAATC
19157 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA T-AAAA T
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA T
19193 TATAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (6 bp):
TCAAAA
Found at i:20365 original size:2 final size:2
Alignment explanation
Indices: 20358--20394 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20348 TGTTGTTGCT
20358 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20395 TATCATCTCG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23661 original size:2 final size:2
Alignment explanation
Indices: 23654--23696 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
23644 TTAATAAATT
23654 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23696 T
1 T
23697 CGATACTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37389 original size:23 final size:23
Alignment explanation
Indices: 37343--37389 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
37333 AATCTTCCTG
**
37343 TATGACACGTTTTCCTCTGTCTT
1 TATGACACGTTTTCCTCTACCTT
*
37366 TATGACATGTTTTCCTCTACCTT
1 TATGACACGTTTTCCTCTACCTT
37389 T
1 T
37390 TAACACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.49
Consensus pattern (23 bp):
TATGACACGTTTTCCTCTACCTT
Found at i:38302 original size:29 final size:29
Alignment explanation
Indices: 38259--38368 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
38249 TTTTATATGT
38259 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
38287 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
38316 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
38345 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
38369 ATATCACATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:38960 original size:21 final size:21
Alignment explanation
Indices: 38934--38977 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
38924 TTTAACCTTG
38934 ATGCATCGATGCACTATGAAT
1 ATGCATCGATGCACTATGAAT
38955 ATGCATCGATGCACTATGAAT
1 ATGCATCGATGCACTATGAAT
38976 AT
1 AT
38978 CCTTCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGCATCGATGCACTATGAAT
Found at i:45215 original size:29 final size:29
Alignment explanation
Indices: 45163--45277 Score: 160
Period size: 29 Copynumber: 4.0 Consensus size: 29
45153 TTATATTTTA
*
45163 TATGTTCATGTA-CTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
*
45191 TATGATCATGTAGTTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
* * *
45220 TGTGATCATGTAGCTCTTATCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
*
45249 TGTGATCATGTAGCTCATGTCATGTTCTC
1 TATGATCATGTAGCTCATGTCAT-TTCTC
45278 ATATCACATA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 11 0.14
29 61 0.79
30 5 0.06
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (29 bp):
TATGATCATGTAGCTCATGTCATTTCTCT
Found at i:45728 original size:64 final size:63
Alignment explanation
Indices: 45654--45810 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 63
45644 TAATAAAGGT
* * **
45654 ATGCAACGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
45717 G
63 G
* * * * *
45718 ATGCATCGATGCA-TGCCTTATGCATCGATTCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
45781 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
45811 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 3 0.04
64 64 0.84
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:47151 original size:24 final size:26
Alignment explanation
Indices: 47093--47149 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
47083 CAAGATTTTG
47093 ATAAAAA-TATAATATATATATAAATA
1 ATAAAAATTA-AATATATATATAAATA
*
47119 ATAAAAATTAAATATATA-ATAATTA
1 ATAAAAATTAAATATATATATAAATA
47144 TATAAA
1 -ATAAA
47150 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 6 0.21
26 20 0.71
27 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAAAAATTAAATATATATATAAATA
Found at i:48066 original size:22 final size:22
Alignment explanation
Indices: 48041--48090 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
48031 TTTTCTTCAT
48041 TTGAAAACACTCGTATTCTAAC
1 TTGAAAACACTCGTATTCTAAC
48063 TTGAAAACACTCGTATTCTAAC
1 TTGAAAACACTCGTATTCTAAC
48085 TT-AAAA
1 TTGAAAA
48091 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (22 bp):
TTGAAAACACTCGTATTCTAAC
Found at i:48878 original size:36 final size:36
Alignment explanation
Indices: 48831--48933 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
48821 TTGGAGCTGG
48831 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
48867 ACATTGATACACGAATGTACCAAAGTTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
48903 ACATTGATACACAAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
48934 ATACTCAACT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:51724 original size:22 final size:22
Alignment explanation
Indices: 51689--51740 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
51679 CATAATTATT
*
51689 TAAAAA-ATTAAATAAAAATAC
1 TAAAAATATTAAATAAAAAAAC
*
51710 TAAAAATATTTAATAAAAAAAC
1 TAAAAATATTAAATAAAAAAAC
51732 TAAAAATAT
1 TAAAAATAT
51741 CCCCACAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAAATATTAAATAAAAAAAC
Found at i:54482 original size:12 final size:13
Alignment explanation
Indices: 54448--54485 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
54438 GATTTTTATT
*
54448 GAATAAACAAATA
1 GAATAAATAAATA
54461 GAATAAATAAATA
1 GAATAAATAAATA
*
54474 -AATATATAAATA
1 GAATAAATAAATA
54486 TATTTATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
GAATAAATAAATA
Found at i:55854 original size:3 final size:3
Alignment explanation
Indices: 55825--55871 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
55815 TTGGGTTTTG
* *
55825 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
55872 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:56548 original size:113 final size:113
Alignment explanation
Indices: 56346--57019 Score: 1208
Period size: 113 Copynumber: 6.0 Consensus size: 113
56336 GAATTATGCG
* ** * *
56346 AAAGGTTGAATAAGCTCTTCTCATTGTGAACTTT-TTCTT-CTCCTTCAGATGAGTTCTTCTCAT
1 AAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
56409 TATGAACTTTTTCTGGAAAAGTTGATCCATCAGATGATGGATTTGAGCA
65 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
56458 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
56523 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
56571 AAAGGTTGAACAAATTATTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
56636 ATGAACTTTTTCTGGAAAAACTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
56684 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
56749 AAGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATAGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
56797 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
56862 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
56910 AAATGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
56975 ATGAACTTTTTCTGGAAAAGCTGATCCATCGGATGATGGATTTGA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
57020 ATCTTTGCTA
Statistics
Matches: 542, Mismatches: 18, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
111 3 0.01
112 31 0.06
113 508 0.94
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
Found at i:57445 original size:22 final size:22
Alignment explanation
Indices: 57420--57475 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
57410 GATAAAGCTT
* *
57420 TCATCTTTGAAAAGAGAATTTG
1 TCATCTTTGAAAAGAGAATCTA
* *
57442 TCATCTTTTAAAAAGGGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
57465 TCATCTTTGAA
1 TCATCTTTGAA
57476 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:58910 original size:76 final size:76
Alignment explanation
Indices: 58769--58939 Score: 218
Period size: 76 Copynumber: 2.3 Consensus size: 76
58759 GATGTGGGCC
* * * * *
58769 TTCAGCATGTCCCAACA-ATTGCTGATACGAACGTTCAAAATACATCAACATTCTTCATTCCGAT
1 TTCAGCATGCCCCAACATTTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATTCCGAT
58833 TGAAAAAGGCT
66 TGAAAAAGGCT
* * * * * *
58844 TTCAGCATGCCCCAGCATTTTGCTGATATAAACATTCAAGATACATCAATATTCCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATTCCGAT
* *
58909 TGAAAAGGGTT
66 TGAAAAAGGCT
58920 TTCAGCATGCCCCAACATTT
1 TTCAGCATGCCCCAACATTT
58940 GCTTCTTGTT
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
75 15 0.19
76 66 0.81
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (76 bp):
TTCAGCATGCCCCAACATTTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATTCCGAT
TGAAAAAGGCT
Found at i:60358 original size:115 final size:114
Alignment explanation
Indices: 60044--60384 Score: 578
Period size: 114 Copynumber: 3.0 Consensus size: 114
60034 GATCATGCAG
* * * * *
60044 TTCATCTTTC-AATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATT-CAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
60108 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
60158 TTCATCTTTCAAA-TCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTC-AATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
60222 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
60272 TTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
60337 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
60385 CATGACACTT
Statistics
Matches: 216, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
113 1 0.00
114 124 0.57
115 91 0.42
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATTCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:62952 original size:2 final size:2
Alignment explanation
Indices: 62945--62977 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
62935 ACAACAAATG
62945 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
62978 AAGGATAAAT
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:65965 original size:14 final size:15
Alignment explanation
Indices: 65931--65969 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
65921 TTGTGCAATA
*
65931 CAAATGCAAAGATGC
1 CAAATGTAAAGATGC
*
65946 CAAATGTAAATATG-
1 CAAATGTAAAGATGC
65960 CAAATGTAAA
1 CAAATGTAAA
65970 AATGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (15 bp):
CAAATGTAAAGATGC
Found at i:65978 original size:14 final size:14
Alignment explanation
Indices: 65931--65978 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
65921 TTGTGCAATA
* *
65931 CAAATGCAAAGATG
1 CAAATGTAAAAATG
*
65945 CCAAATGTAAATATG
1 -CAAATGTAAAAATG
65960 CAAATGTAAAAATG
1 CAAATGTAAAAATG
*
65974 TAAAT
1 CAAAT
65979 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (14 bp):
CAAATGTAAAAATG
Found at i:68453 original size:14 final size:15
Alignment explanation
Indices: 68423--68455 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
68413 AATAGAATAA
68423 ATAAATAAATATTAT
1 ATAAATAAATATTAT
*
68438 ATAAATATAT-TTAT
1 ATAAATAAATATTAT
68452 ATAA
1 ATAA
68456 CTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATAAATATTAT
Found at i:69814 original size:3 final size:3
Alignment explanation
Indices: 69785--69849 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
69775 TTGGGTTTTG
* * * * *
69785 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
69832 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
69850 ATTTTAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:69860 original size:24 final size:24
Alignment explanation
Indices: 69809--69861 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
69799 AATATATATT
* *
69809 AATAATAATAATAATTATTATTAT
1 AATAATAATAATAATAATTATTAA
69833 AATAATAATAATAATAAATT-TTAA
1 AATAATAATAATAAT-AATTATTAA
69857 AATAA
1 AATAA
69862 AAAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAATAATAATAATAATTATTAA
Found at i:70987 original size:30 final size:30
Alignment explanation
Indices: 70953--71017 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
70943 TTTATGAGTT
70953 AAATTGACATTTATATAATTTTTAGGGGTC
1 AAATTGACATTTATATAATTTTTAGGGGTC
* * *
70983 AAATTGATATTTATCTAATTTTTTGGGGTC
1 AAATTGACATTTATATAATTTTTAGGGGTC
71013 AAATT
1 AAATT
71018 AATATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (30 bp):
AAATTGACATTTATATAATTTTTAGGGGTC
Found at i:71023 original size:30 final size:30
Alignment explanation
Indices: 70961--71024 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
70951 TTAAATTGAC
*
70961 ATTTATATAATTTTTAGGGGTCAAATTGAT
1 ATTTATATAATTTTTAGGGGTCAAATTAAT
* *
70991 ATTTATCTAATTTTTTGGGGTCAAATTAAT
1 ATTTATATAATTTTTAGGGGTCAAATTAAT
71021 ATTT
1 ATTT
71025 TTATCTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (30 bp):
ATTTATATAATTTTTAGGGGTCAAATTAAT
Found at i:71046 original size:32 final size:31
Alignment explanation
Indices: 71010--71082 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
71000 ATTTTTTGGG
* *
71010 GTCAAATTAATATTTTTATCTAAAATTTATAA
1 GTCAAATTAATA-TTTTATCTAAAATTCAAAA
* *
71042 GTCAAATCAATATTTTATCTAAAGTTCAAAA
1 GTCAAATTAATATTTTATCTAAAATTCAAAA
*
71073 ATCAAATTAA
1 GTCAAATTAA
71083 AAAATATCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.40
Consensus pattern (31 bp):
GTCAAATTAATATTTTATCTAAAATTCAAAA
Found at i:80405 original size:19 final size:19
Alignment explanation
Indices: 80381--80424 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
80371 TGCACCTTTT
80381 CCTTCCCTTCAAATTCA-AC
1 CCTTCCCTTCAAATT-ATAC
80400 CCTTCCCTTCAAATTATAC
1 CCTTCCCTTCAAATTATAC
80419 CCTTCC
1 CCTTCC
80425 AATAGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.23, C:0.43, G:0.00, T:0.34
Consensus pattern (19 bp):
CCTTCCCTTCAAATTATAC
Found at i:85581 original size:17 final size:17
Alignment explanation
Indices: 85559--85592 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
85549 ATAATGATAA
85559 ATTAATAAAAAAATATT
1 ATTAATAAAAAAATATT
* *
85576 ATTAATTAAATAATATT
1 ATTAATAAAAAAATATT
85593 TTATATAATA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATAAAAAAATATT
Found at i:85609 original size:14 final size:13
Alignment explanation
Indices: 85585--85623 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
85575 TATTAATTAA
85585 ATAATA-TTTTAT
1 ATAATATTTTTAT
*
85597 ATAATATTATTTAG
1 ATAATATT-TTTAT
85611 ATAATATTTTTAT
1 ATAATATTTTTAT
85624 CACGTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
ATAATATTTTTAT
Found at i:87182 original size:2 final size:2
Alignment explanation
Indices: 87175--87208 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
87165 TTCTAAGACC
87175 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
87209 TTGAGTCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92500 original size:27 final size:27
Alignment explanation
Indices: 92470--92523 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
92460 CTATTGGCCT
* *
92470 GTCAT-TGCTTTCAATCACTGGCTCGAC
1 GTCATATG-TTTCAAGCACTGACTCGAC
92497 GTCATAATGTTTCAAGCACTGACTCGA
1 GTCAT-ATGTTTCAAGCACTGACTCGA
92524 TGATATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 16 0.70
29 2 0.09
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (27 bp):
GTCATATGTTTCAAGCACTGACTCGAC
Done.