Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003226.1 Hibiscus syriacus cultivar Beakdansim tig00006793_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: 123404
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:11904 original size:20 final size:20
Alignment explanation
Indices: 11880--11945 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
11870 ACGTGATTTT
*
11880 CTAATTCGCGATGCTAATTC
1 CTAATTCGCGACGCTAATTC
* *
11900 GTAATTCGCGACACTAATTC
1 CTAATTCGCGACGCTAATTC
*
11920 CAAATTCGCGACGCTAATTC
1 CTAATTCGCGACGCTAATTC
*
11940 CGAATT
1 CTAATT
11946 ACAAAATCGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (20 bp):
CTAATTCGCGACGCTAATTC
Found at i:12021 original size:20 final size:20
Alignment explanation
Indices: 11964--12114 Score: 158
Period size: 20 Copynumber: 7.5 Consensus size: 20
11954 GTGTTGCGAA
11964 TCGCGAATTAGGAATTAGCG
1 TCGCGAATTAGGAATTAGCG
* ** * *
11984 TTGTTAATTCGGATTTAGCG
1 TCGCGAATTAGGAATTAGCG
* *
12004 TCACGGATTAGGAATTAGCG
1 TCGCGAATTAGGAATTAGCG
* * *
12024 TCGCGAATTAGAAAATCGCG
1 TCGCGAATTAGGAATTAGCG
*
12044 TTGCGAATTAGGAATTAGCG
1 TCGCGAATTAGGAATTAGCG
*
12064 TCGCGAATTCGGAATTAGCG
1 TCGCGAATTAGGAATTAGCG
* * * *
12084 TCGCGATTTCGGAATTAACA
1 TCGCGAATTAGGAATTAGCG
12104 TCGCGAATTAG
1 TCGCGAATTAG
12115 AAAATCGCGT
Statistics
Matches: 103, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 103 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (20 bp):
TCGCGAATTAGGAATTAGCG
Found at i:12054 original size:40 final size:40
Alignment explanation
Indices: 12010--12137 Score: 157
Period size: 40 Copynumber: 3.2 Consensus size: 40
12000 AGCGTCACGG
12010 ATTAGGAATTAGCGTCGCGAATTAGAAAATCGCGTTGCGA
1 ATTAGGAATTAGCGTCGCGAATTAGAAAATCGCGTTGCGA
* * * * *
12050 ATTAGGAATTAGCGTCGCGAATTCGGAATTAGCGTCGCGA
1 ATTAGGAATTAGCGTCGCGAATTAGAAAATCGCGTTGCGA
* * * * *
12090 TTTCGGAATTAACATCGCGAATTAGAAAATCGCGTTGCGG
1 ATTAGGAATTAGCGTCGCGAATTAGAAAATCGCGTTGCGA
*
12130 ATTTGGAA
1 ATTAGGAA
12138 AATCGCGTTG
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (40 bp):
ATTAGGAATTAGCGTCGCGAATTAGAAAATCGCGTTGCGA
Found at i:12057 original size:80 final size:80
Alignment explanation
Indices: 11966--12137 Score: 238
Period size: 80 Copynumber: 2.1 Consensus size: 80
11956 GTTGCGAATC
* ** * * *
11966 GCGAATTAGGAATTAGCGTTGTTAATTCGGATTTAGCGTCACGGA-TTAGGAATTAGCGTCGCGA
1 GCGAATTAGGAATTAGCGTCGCGAATTCGGAATTAGCGTCAC-GATTTAGGAATTAACATCGCGA
12030 ATTAGAAAATCGCGTT
65 ATTAGAAAATCGCGTT
* *
12046 GCGAATTAGGAATTAGCGTCGCGAATTCGGAATTAGCGTCGCGATTTCGGAATTAACATCGCGAA
1 GCGAATTAGGAATTAGCGTCGCGAATTCGGAATTAGCGTCACGATTTAGGAATTAACATCGCGAA
12111 TTAGAAAATCGCGTT
66 TTAGAAAATCGCGTT
* *
12126 GCGGATTTGGAA
1 GCGAATTAGGAA
12138 AATCGCGTTG
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 2 0.02
80 79 0.98
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (80 bp):
GCGAATTAGGAATTAGCGTCGCGAATTCGGAATTAGCGTCACGATTTAGGAATTAACATCGCGAA
TTAGAAAATCGCGTT
Found at i:12140 original size:21 final size:21
Alignment explanation
Indices: 12106--12236 Score: 121
Period size: 20 Copynumber: 6.4 Consensus size: 21
12096 AATTAACATC
*
12106 GCGAA-TTAGAAAATCGCGTT
1 GCGAATTTGGAAAATCGCGTT
*
12126 GCGGATTTGGAAAATCGCGTT
1 GCGAATTTGGAAAATCGCGTT
* *
12147 GCGAATTT-TAAAA-CTGAGTT
1 GCGAATTTGGAAAATC-GCGTT
*
12167 GCGAATCTGGAAAATTCGCGTT
1 GCGAATTTGGAAAA-TCGCGTT
* *
12189 GCGAATTTGGAAACT-GTGTT
1 GCGAATTTGGAAAATCGCGTT
* *
12209 GCGAATTT-G-AGATCACGTT
1 GCGAATTTGGAAAATCGCGTT
12228 GCGAATTTG
1 GCGAATTTG
12237 TTGGTTATTT
Statistics
Matches: 89, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
18 2 0.02
19 13 0.15
20 31 0.35
21 26 0.29
22 16 0.18
23 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCGTT
Found at i:12195 original size:42 final size:41
Alignment explanation
Indices: 12106--12236 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 41
12096 AATTAACATC
* * * *
12106 GCGAATTAGAAAA-TCGCGTTGCGGATTTGGAAAATCGCGTT
1 GCGAATTTGAAAACT-GAGTTGCGAATCTGGAAAATCGCGTT
*
12147 GCGAATTTTAAAACTGAGTTGCGAATCTGGAAAATTCGCGTT
1 GCGAATTTGAAAACTGAGTTGCGAATCTGGAAAA-TCGCGTT
* * * * *
12189 GCGAATTTGGAAACTGTGTTGCGAAT-TTG-AGATCACGTT
1 GCGAATTTGAAAACTGAGTTGCGAATCTGGAAAATCGCGTT
12228 GCGAATTTG
1 GCGAATTTG
12237 TTGGTTATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 15 0.19
40 2 0.03
41 29 0.38
42 31 0.40
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (41 bp):
GCGAATTTGAAAACTGAGTTGCGAATCTGGAAAATCGCGTT
Found at i:13372 original size:2 final size:2
Alignment explanation
Indices: 13365--13391 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13355 ATATACTCTA
13365 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 A
13392 AATAGCACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22776 original size:21 final size:21
Alignment explanation
Indices: 22747--22786 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22737 ATAAAATGTA
* *
22747 ATGTGATATCCTACATTAACT
1 ATGTAATATCATACATTAACT
*
22768 ATGTAATATCATGCATTAA
1 ATGTAATATCATACATTAA
22787 ATACAATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (21 bp):
ATGTAATATCATACATTAACT
Found at i:26606 original size:37 final size:36
Alignment explanation
Indices: 26516--26613 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 36
26506 TTGGTCAACT
26516 CGATCCGACCCGAAAATATATATCAACCGCCGAATC
1 CGATCCGACCCGAAAATATATATCAACCGCCGAATC
* * ***
26552 CGATCCGACACGAAAAATTTATATCTTTCGTCCGAATC
1 CGATCCGACCCG-AAAATATATATCAACCG-CCGAATC
26590 CGA-CCTGACCCGAAAATATATATC
1 CGATCC-GACCCGAAAATATATATC
26614 CTCCACCCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
36 11 0.21
37 26 0.50
38 15 0.29
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (36 bp):
CGATCCGACCCGAAAATATATATCAACCGCCGAATC
Found at i:27330 original size:21 final size:21
Alignment explanation
Indices: 27304--27344 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
27294 CTGAAAATGT
27304 TAAAAA-AATTAATATTTTAAG
1 TAAAAATAA-TAATATTTTAAG
27325 TAAAAATAATAATATTTTAA
1 TAAAAATAATAATATTTTAA
27345 TTTTTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:32989 original size:2 final size:2
Alignment explanation
Indices: 32982--33008 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32972 ACATACGTAC
32982 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 A
33009 CACAAATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34243 original size:56 final size:52
Alignment explanation
Indices: 34171--34329 Score: 212
Period size: 51 Copynumber: 3.0 Consensus size: 52
34161 AGGTGTTCCG
* * *
34171 AAATTGAGTATATCTATTAGTTGTTGCCATTAATAAGCATATAAATAAGAGCCCCA
1 AAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAAG-G---CA
* **
34227 AAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCATAAAAAT-AGGGG
1 AAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAAGGCA
34278 AAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAGAGGC
1 AAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATA-AGGC
34330 TTCGAAATCG
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
51 45 0.48
53 3 0.03
54 1 0.01
55 2 0.02
56 42 0.45
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.30
Consensus pattern (52 bp):
AAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAAGGCA
Found at i:34303 original size:51 final size:53
Alignment explanation
Indices: 34168--34349 Score: 233
Period size: 56 Copynumber: 3.4 Consensus size: 53
34158 AATAGGTGTT
* * *
34168 CCGAAATTGAGTATATCTATTAGTTGTTGCCATTAATAAGCATATAAATAAGAG
1 CCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAAT-AGAG
* *
34222 CCCCAAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCATAAAAATAG-G
1 --CCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAGAG
*
34276 -GGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAGAGG
1 CCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAGA-G
*
34329 CTTCGAAATCGAATATATCTA
1 C--CGAAATCGAGTATATCTA
34350 GAAAATAGGG
Statistics
Matches: 111, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
51 47 0.42
53 1 0.01
54 1 0.01
55 2 0.02
56 60 0.54
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (53 bp):
CCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAGAG
Found at i:36092 original size:3 final size:3
Alignment explanation
Indices: 36084--36151 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
36074 ATGAACAGTT
36084 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
36132 GAA GAA GAA G-A GAA G-A GAA G
1 GAA GAA GAA GAA GAA GAA GAA G
36152 TTAGTGGAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 59 0.94
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:44327 original size:12 final size:12
Alignment explanation
Indices: 44310--44334 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44300 AAGAGGACAA
44310 TGACTTCCAAGC
1 TGACTTCCAAGC
44322 TGACTTCCAAGC
1 TGACTTCCAAGC
44334 T
1 T
44335 AGTGTTTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TGACTTCCAAGC
Found at i:47343 original size:332 final size:331
Alignment explanation
Indices: 46705--47368 Score: 901
Period size: 332 Copynumber: 2.0 Consensus size: 331
46695 TTCAAACTAA
* * * * * *
46705 GCACATTGCCTGTTCGATTTCTAGGAATACCACCTATTACTAGAAAGCTCACCATGATGGATTGT
1 GCACATTGCCTGTTCAATATCTAGGAATACCACCTATGACTAGAAAGCTCACCATGAAGAATTGA
* * * *
46770 GAACCTTTGATCCGATGAGTGACCACAAAGATCAATGGACCAGTGGCAAAACACCTATCCCATGC
66 GAAACTTTGATCCAATGAGTGACCAAAAAGATCAATGGACCAGTAGCAAAACACCTATCCCATGC
* *
46835 TAGTAGGATGCAGCTTATTCATCCCAATAATTTGGGGTAATTTACATTCTACATCAGTAAATCAA
131 TA-TAGGACGCAGCTTATTCATCCCAATAATTTGGGGTAATTTACATTCTACATCACTAAATCAA
* * *
46900 TTACATAAAACGATCAGATTCTTTAGCATTAGCCCCAGAAATTCATAGTTAAAGGACCAAAACAT
195 TTACATAAAACAATCACATTCTTTAGCATTAGCCCCAGAAATTCACAGTTAAAGGACCAAAACAT
* * *
46965 TAATAGATAACAAGACAACGCCATGGCAACCACAAAGATGTGTTATTCAAGCTCCAAAGTCTGAA
260 TAAAAGATAACAAGACAACGCCATGGCAACCACAAAGATCTGTTATTCAAGCTCCAAAATCTGAA
47030 CTGCTAG
325 CTGCTAG
* *
47037 GCACATTGCCTGTTCAATATCTAGGAATACCA-CTAATGACTAGAAAGCTCTCTATGAAGAATCT
1 GCACATTGCCTGTTCAATATCTAGGAATACCACCT-ATGACTAGAAAGCTCACCATGAAGAAT-T
* * *
47101 -AGAAACTTTGATCCAATG-GATGA-CAGAAAAGGTCAATGGACCGGTAGTAAAACACCTATCCC
64 GAGAAACTTTGATCCAATGAG-TGACCA-AAAAGATCAATGGACCAGTAGCAAAACACCTAT-CC
* * *
47163 CGTGCT-TAGGACGCATCTTATTCATCCCAAATAATTTGGGTTAATTTACATTCTACATCACTAA
126 CATGCTATAGGACGCAGCTTATTCATCCC-AATAATTTGGGGTAATTTACATTCTACATCACTAA
** ** *
47227 ATCCGTTATGTTAAAACAATCACATTCTTTAGCATTAGCCCTAGAAATTCACAGTTAAAGGACCA
190 ATCAATTA-CATAAAACAATCACATTCTTTAGCATTAGCCCCAGAAATTCACAGTTAAAGGACCA
* *
47292 AAACATTAAAAGATAACAAGACAA-GCCCATGTCAACCGCAAAGA-CTGTTATTCAAGCTCCAAA
254 AAACATTAAAAGATAACAAGACAACG-CCATGGCAACCACAAAGATCTGTTATTCAAGCTCCAAA
47355 ATCTGAACTGCTAG
318 ATCTGAACTGCTAG
47369 CTATTCAGGA
Statistics
Matches: 291, Mismatches: 33, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
331 25 0.09
332 169 0.58
333 97 0.33
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (331 bp):
GCACATTGCCTGTTCAATATCTAGGAATACCACCTATGACTAGAAAGCTCACCATGAAGAATTGA
GAAACTTTGATCCAATGAGTGACCAAAAAGATCAATGGACCAGTAGCAAAACACCTATCCCATGC
TATAGGACGCAGCTTATTCATCCCAATAATTTGGGGTAATTTACATTCTACATCACTAAATCAAT
TACATAAAACAATCACATTCTTTAGCATTAGCCCCAGAAATTCACAGTTAAAGGACCAAAACATT
AAAAGATAACAAGACAACGCCATGGCAACCACAAAGATCTGTTATTCAAGCTCCAAAATCTGAAC
TGCTAG
Found at i:52187 original size:37 final size:36
Alignment explanation
Indices: 52138--52215 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 36
52128 CCCGAGATCT
*
52138 GACCCGACCCGACCCGA-CCAAAACAAGATTCCACCC
1 GACCCGACCCGACCCGACCCAAAA-AAGACTCCACCC
*
52174 GACCCGAACCCGACCCGACCCAATAAAGACTCCACCC
1 GACCCG-ACCCGACCCGACCCAAAAAAGACTCCACCC
52211 GACCC
1 GACCC
52216 AAATATAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 6 0.16
37 27 0.71
38 5 0.13
ACGTcount: A:0.32, C:0.49, G:0.14, T:0.05
Consensus pattern (36 bp):
GACCCGACCCGACCCGACCCAAAAAAGACTCCACCC
Found at i:52194 original size:21 final size:21
Alignment explanation
Indices: 52139--52194 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
52129 CCGAGATCTG
52139 ACCCGACCCGACCCGACCAAA
1 ACCCGACCCGACCCGACCAAA
** * **
52160 ACAAGATTCC-ACCCGACCCGA
1 ACCCGA-CCCGACCCGACCAAA
52181 ACCCGACCCGACCC
1 ACCCGACCCGACCC
52195 AATAAAGACT
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.30, C:0.52, G:0.14, T:0.04
Consensus pattern (21 bp):
ACCCGACCCGACCCGACCAAA
Found at i:65751 original size:10 final size:10
Alignment explanation
Indices: 65736--65771 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
65726 GGTCTTTCCA
65736 TTTTTAATTT
1 TTTTTAATTT
65746 TTTTTAA-TT
1 TTTTTAATTT
65755 TTTTTAATTT
1 TTTTTAATTT
65765 TTTTTAA
1 TTTTTAA
65772 ATTGGGGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTAATTT
Found at i:65756 original size:9 final size:9
Alignment explanation
Indices: 65736--65768 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
65726 GGTCTTTCCA
65736 TTTTTAATTT
1 TTTTTAA-TT
65746 TTTTTAATT
1 TTTTTAATT
65755 TTTTTAATT
1 TTTTTAATT
65764 TTTTT
1 TTTTT
65769 TAAATTGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTAATT
Found at i:71354 original size:14 final size:14
Alignment explanation
Indices: 71335--71373 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
71325 TAATGGGGAG
71335 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
71349 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
71363 GAATCTCTGCA
1 TAATCCCTGCA
71374 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:76919 original size:45 final size:45
Alignment explanation
Indices: 76855--76945 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
76845 TTTCACCTTT
76855 ATACCAAGCACTCCCTGTGTTCAAAACAGATGAATTGAATGAGAA
1 ATACCAAGCACTCCCTGTGTTCAAAACAGATGAATTGAATGAGAA
76900 ATACCAAGCACTCCCTGTGTTCAAAACAGATGAATTGAATGAGAA
1 ATACCAAGCACTCCCTGTGTTCAAAACAGATGAATTGAATGAGAA
76945 A
1 A
76946 AGGCAATCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (45 bp):
ATACCAAGCACTCCCTGTGTTCAAAACAGATGAATTGAATGAGAA
Found at i:80350 original size:26 final size:25
Alignment explanation
Indices: 80314--80367 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
80304 GTAAGTACCC
80314 TAGATTAATAAAA-ATAAATAAATTAT
1 TAGATTAATAAAATAT-AAT-AATTAT
*
80340 TAGATTAATAAATTATAATAATTAT
1 TAGATTAATAAAATATAATAATTAT
80365 TAG
1 TAG
80368 TTAGTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.35
26 15 0.58
27 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
TAGATTAATAAAATATAATAATTAT
Found at i:80585 original size:21 final size:21
Alignment explanation
Indices: 80549--80589 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
80539 TTGAGATCTT
*
80549 GAGTCAAACTCGAGTTCAAATC
1 GAGTCAAACTCAAGTT-AAATC
80571 GAGTC-AACTCAAGTTAAAT
1 GAGTCAAACTCAAGTTAAAT
80590 ATTAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (21 bp):
GAGTCAAACTCAAGTTAAATC
Found at i:83045 original size:17 final size:18
Alignment explanation
Indices: 83023--83057 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
83013 ATTTTTATTA
83023 ATAAAAA-ATAATATTTT
1 ATAAAAATATAATATTTT
*
83040 ATAAAAATATATTATTTT
1 ATAAAAATATAATATTTT
83058 GGTTTAGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAAAATATAATATTTT
Found at i:84856 original size:80 final size:80
Alignment explanation
Indices: 84759--84922 Score: 319
Period size: 80 Copynumber: 2.0 Consensus size: 80
84749 TTAAAAAGAG
84759 AATTTATGTTCGAACTTTGGAGAATGATATTATCAGATATAGGAGTGTTCAAACAGTCAATTTGA
1 AATTTATGTTCGAACTTTGGAGAATGATATTATCAGATATAGGAGTGTTCAAACAGTCAATTTGA
84824 TTATTAACCGAACCA
66 TTATTAACCGAACCA
*
84839 AATTTATGTTCGAACTTTGGAGAATGATATTATCAGATATTGGAGTGTTCAAACAGTCAATTTGA
1 AATTTATGTTCGAACTTTGGAGAATGATATTATCAGATATAGGAGTGTTCAAACAGTCAATTTGA
84904 TTATTAACCGAACCA
66 TTATTAACCGAACCA
84919 AATT
1 AATT
84923 ATTGTTAACT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 83 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (80 bp):
AATTTATGTTCGAACTTTGGAGAATGATATTATCAGATATAGGAGTGTTCAAACAGTCAATTTGA
TTATTAACCGAACCA
Found at i:87076 original size:28 final size:28
Alignment explanation
Indices: 86991--87075 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
86981 GGAATATATA
* *
86991 AATGATCGGATGATTATTTTGTAACTTTT
1 AATGATCGGGTGATCA-TTTGTAACTTTT
*
87020 AATGATCGGGTGATCATTTGCAACTTTT
1 AATGATCGGGTGATCATTTGTAACTTTT
*
87048 AATGGTCGGGTGATCATTTGTATACTTT
1 AATGATCGGGTGATCATTTGTA-ACTTT
87076 ACCCTAAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 31 0.62
29 19 0.38
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.44
Consensus pattern (28 bp):
AATGATCGGGTGATCATTTGTAACTTTT
Found at i:87509 original size:21 final size:21
Alignment explanation
Indices: 87477--87527 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
87467 TTCTCATCGT
* *
87477 TGATCGTT-ACGGTACTGGCG
1 TGATAGTTCACGGTACTGACG
*
87497 TGATAGTTCACGGTGCTGACG
1 TGATAGTTCACGGTACTGACG
87518 TG-TCAGTTCA
1 TGAT-AGTTCA
87528 TATGCCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (21 bp):
TGATAGTTCACGGTACTGACG
Found at i:89294 original size:2 final size:2
Alignment explanation
Indices: 89287--89315 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
89277 AACTTGACAA
89287 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 A
89316 ATTCTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94052 original size:22 final size:22
Alignment explanation
Indices: 93993--94045 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
93983 TATTAAATCT
93993 ATATTTTTATTGAATACAAATA
1 ATATTTTTATTGAATACAAATA
94015 ATATTTTTATTGAATACAAATA
1 ATATTTTTATTGAATACAAATA
94037 ATATTTTTA
1 ATATTTTTA
94046 ATAAATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATTTTTATTGAATACAAATA
Found at i:100567 original size:98 final size:98
Alignment explanation
Indices: 100452--100690 Score: 419
Period size: 98 Copynumber: 2.5 Consensus size: 98
100442 AAACGACTGG
100452 ATTAT-TT-TTTTTAAAATTTTAATAAATTAATATACTTTAAAATATAAAATCACATACTAATAT
1 ATTATCTTATTTTTAAAATTTTAATAAATTAATATACTTTAAAATATAAAATCACATACTAATAT
*
100515 TATCTTATTGCCTTAAACAATGCCATGTCTAAT
66 TATCTTATTGACTTAAACAATGCCATGTCTAAT
* * *
100548 ATTATCTTATTTTTAAAATTTTTATAAATTAATATACTTTAAAATATAATATCATATACTAATAT
1 ATTATCTTATTTTTAAAATTTTAATAAATTAATATACTTTAAAATATAAAATCACATACTAATAT
*
100613 TATCTTGTTGACTTAAACAATGCCATGTCTAAT
66 TATCTTATTGACTTAAACAATGCCATGTCTAAT
100646 ATTATCTTATTTTTAAAATTTTAATAAATTAATATACTTTAAAAT
1 ATTATCTTATTTTTAAAATTTTAATAAATTAATATACTTTAAAAT
100691 TTTATTAAGT
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
96 5 0.04
97 2 0.01
98 128 0.95
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (98 bp):
ATTATCTTATTTTTAAAATTTTAATAAATTAATATACTTTAAAATATAAAATCACATACTAATAT
TATCTTATTGACTTAAACAATGCCATGTCTAAT
Found at i:112662 original size:29 final size:29
Alignment explanation
Indices: 112574--112662 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
112564 GGTAAGTGAC
112574 CATTTTGTAACTTTTAATAGTCAAGGGACT
1 CATTTTGTAACTTTTAATAGTCAAGGGA-T
*** * * *
112604 CAATAAAGCAACTTCCT-ATAATC-AGAGGAT
1 C-ATTTTGTAACTT-TTAATAGTCAAG-GGAT
112634 CATTTTGTAACTTTTAATAGTCAAGGGAT
1 CATTTTGTAACTTTTAATAGTCAAGGGAT
112663 TCAATAAAGA
Statistics
Matches: 42, Mismatches: 12, Indels: 11
0.65 0.18 0.17
Matches are distributed among these distances:
28 1 0.02
29 17 0.40
30 7 0.17
31 16 0.38
32 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (29 bp):
CATTTTGTAACTTTTAATAGTCAAGGGAT
Found at i:112692 original size:60 final size:60
Alignment explanation
Indices: 112571--112707 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
112561 ATAGGTAAGT
*
112571 GACCATTTTGTAACTTTTAATAGTCAAGGGACTCAATAAAGCAACTTCCTATAATCAGAG
1 GACCATTTTGTAACTTTTAATAGTCAAGGGACTCAATAAAGCAACTTCCTACAATCAGAG
* * * * * *
112631 GATCATTTTGTAACTTTTAATAGTCAAGGGATTCAATAAAG-AAGTATCTTACAGTCGGAG
1 GACCATTTTGTAACTTTTAATAGTCAAGGGACTCAATAAAGCAACT-TCCTACAATCAGAG
112691 GACCA-TTTGTATACTTT
1 GACCATTTTGTA-ACTTT
112708 ACCCTAAACT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 9 0.13
60 58 0.87
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCAAGGGACTCAATAAAGCAACTTCCTACAATCAGAG
Found at i:114169 original size:21 final size:21
Alignment explanation
Indices: 114139--114203 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
114129 ATCAACCATT
*
114139 GTGGAATGCCACGTCAGCACC
1 GTGGATTGCCACGTCAGCACC
** * *
114160 GTGGATTGCCATATCATCACT
1 GTGGATTGCCACGTCAGCACC
* *
114181 GTGAATTACCACGTCAGCACC
1 GTGGATTGCCACGTCAGCACC
114202 GT
1 GT
114204 AACGATCAAC
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (21 bp):
GTGGATTGCCACGTCAGCACC
Found at i:116860 original size:35 final size:35
Alignment explanation
Indices: 116814--116889 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
116804 AAAACAGTCC
* *
116814 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
116849 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
116884 TCAATT
1 TCAATT
116890 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:117428 original size:128 final size:128
Alignment explanation
Indices: 117285--117530 Score: 420
Period size: 128 Copynumber: 1.9 Consensus size: 128
117275 TTATTATATA
* **
117285 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
117350 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATGCT
117413 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
117478 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
117531 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
128 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (128 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATGCT
Found at i:117889 original size:28 final size:27
Alignment explanation
Indices: 117858--117920 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
117848 AGTTGATACA
*
117858 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
117886 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
117914 ATATTTT
1 ATATTTT
117921 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:118019 original size:16 final size:18
Alignment explanation
Indices: 117998--118031 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
117988 ATTTCTTATT
117998 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
118014 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
118032 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:120139 original size:282 final size:282
Alignment explanation
Indices: 119335--120503 Score: 1309
Period size: 282 Copynumber: 4.1 Consensus size: 282
119325 CAAATTATGC
* * * * * * *
119335 TAGTTTATGTTCTAGTCATTGGGTAACTTCTCATAGTTGATGTTAGTCGAGCTTATGGATCGATA
1 TAGTTTATGTTCTAGTCATTAGGTAATTTCTCGTCGTTGAAGTTAATCGAGCTCATGGATCGATA
* ** * * *
119400 AGTGTGT-TCAAATTTGGCAATGATATTGAATGATTAGTCAAGACAGCGACCGAGTTTTCAAACT
66 AGTGTGTGT-AAATTTGGCAATGAAATCAAATGATTGGTCAAGACAGTGATCGAGTTTTCAAACT
*
119464 TGTAGTTTAACATTGTTAGCTGTCATAGCCTCAGAGGTTGTGAATGGTGATGGAGGGGTCTTATA
130 TGTAGTTTAACATTGTTA---GT--T-G--TCATAGGTTGTGAATGGTGATGGAGGGG-------
* * ** *
119529 CTCTTATATAATTAGTGTAAACATGTA-CAGTGGTCATATAATCGGGAGAACTTATACTGATTTT
180 -TCTTATATAATTAGTGTAAACATGTATGA-TGGTCATATAATCGGGAGAAATCGTAGTGATTTT
* *
119593 ACCGATTTTCATCTTCCACA-TGTTGCTAGTAT-A--A---
243 ACCAATTTCCATCTTCCACATTG-TGCTAGTATAATGATGT
*
119627 T-G---ATGTTCGAGTCATTAGGTAATTTCTCGTCGTTGAAGTTAATCGAGCTCATGGATC-AGT
1 TAGTTTATGTTCTAGTCATTAGGTAATTTCTCGTCGTTGAAGTTAATCGAGCTCATGGATCGA-T
* *
119687 AA--GTGTGTAAATTTGGCGATGAAATCAAATGATTGGTCAAGATAGTGATCGAGTTTTCAAACT
65 AAGTGTGTGTAAATTTGGCAATGAAATCAAATGATTGGTCAAGACAGTGATCGAGTTTTCAAACT
* * * *
119750 TGTAG-TTAACATTGTTCGTTGTCATAGGTTGTGAATGGTGACGGAGGGGCCTTTTATAATTAGT
130 TGTAGTTTAACATTGTTAGTTGTCATAGGTTGTGAATGGTGATGGAGGGGTCTTATATAATTAGT
* * * ** *
119814 GTAAACATGTATGACGGTCATATAATCGGGAGAACTTGTAGTGATTTTACTGATTTTCATCTTCC
195 GTAAACATGTATGATGGTCATATAATCGGGAGAAATCGTAGTGATTTTACCAATTTCCATCTTCC
*
119879 ACATTGTGCTAGTATAATGCTGT
260 ACATTGTGCTAGTATAATGATGT
* *
119902 TAGTTTATGTTTTAGTCATTAGGTAATTTCTCGTCGTTGAAGTTAATTGAGCTCATGGATCGATA
1 TAGTTTATGTTCTAGTCATTAGGTAATTTCTCGTCGTTGAAGTTAATCGAGCTCATGGATCGATA
* * * *
119967 AGTGCGAGTAAATTTGGCAATGAAATCAAATGATTGGTCTAGACAGTGATTGAGTTTTCAAACTT
66 AGTGTGTGTAAATTTGGCAATGAAATCAAATGATTGGTCAAGACAGTGATCGAGTTTTCAAACTT
* * *
120032 GTAGTTGAACATTGTTAGTTGTCATAGGTTGGGAATGGTGATGGAGGGGTCTTATATAGTTAGTG
131 GTAGTTTAACATTGTTAGTTGTCATAGGTTGTGAATGGTGATGGAGGGGTCTTATATAATTAGTG
*
120097 TAAACATGTATGATGGTCATATAATCGGGAGAAATCGTAGTGATTTCACCAATTTCCATCTTCCA
196 TAAACATGTATGATGGTCATATAATCGGGAGAAATCGTAGTGATTTTACCAATTTCCATCTTCCA
* *
120162 AATTATGCTAGTATAATGATATGT
261 CATTGTGCTAGTATAATG--ATGT
* * ** * *
120186 TAGTTTAAGTTATAGTCATTAGGTAACCTCTCGTCGCTGAAGTTAGTCGAGCTCATGGATCGATA
1 TAGTTTATGTTCTAGTCATTAGGTAATTTCTCGTCGTTGAAGTTAATCGAGCTCATGGATCGATA
* ** * * * *
120251 AGTGTGTGTAAATTTGGCGATGAAATTGAATTATTGGTAAAGACAGTGATTGAG-TTTCAAGCTT
66 AGTGTGTGTAAATTTGGCAATGAAATCAAATGATTGGTCAAGACAGTGATCGAGTTTTCAAACTT
* * *
120315 GTAGTTTAACATTGTTAATTGTCATAGGCT-CGAATGGTGATGGAGGGGTCTTATATAATTAGTG
131 GTAGTTTAACATTGTTAGTTGTCATAGGTTGTGAATGGTGATGGAGGGGTCTTATATAATTAGTG
* * * * * *
120379 TAAACATATATGATAGCCATATAATCGGGA-AAACTCGTAGCGATTTTTCCAATTTCCGTCTTCC
196 TAAACATGTATGATGGTCATATAATCGGGAGAAA-TCGTAGTGATTTTACCAATTTCCATCTTCC
* * * *
120443 ACATTTTTCTAGTATAGTGATAT
260 ACATTGTGCTAGTATAATGATGT
* *
120466 TAGTTTATGTT-TAGTCATTAAGTAATTTTTCGTCGTTG
1 TAGTTTATGTTCTAGTCATTAGGTAATTTCTCGTCGTTG
120504 TGGTTAGTTT
Statistics
Matches: 764, Mismatches: 92, Indels: 55
0.84 0.10 0.06
Matches are distributed among these distances:
269 83 0.11
270 4 0.01
275 1 0.00
276 1 0.00
277 26 0.03
279 78 0.10
280 15 0.02
281 63 0.08
282 229 0.30
283 36 0.05
284 107 0.14
285 11 0.01
286 56 0.07
287 2 0.00
288 50 0.07
291 1 0.00
292 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (282 bp):
TAGTTTATGTTCTAGTCATTAGGTAATTTCTCGTCGTTGAAGTTAATCGAGCTCATGGATCGATA
AGTGTGTGTAAATTTGGCAATGAAATCAAATGATTGGTCAAGACAGTGATCGAGTTTTCAAACTT
GTAGTTTAACATTGTTAGTTGTCATAGGTTGTGAATGGTGATGGAGGGGTCTTATATAATTAGTG
TAAACATGTATGATGGTCATATAATCGGGAGAAATCGTAGTGATTTTACCAATTTCCATCTTCCA
CATTGTGCTAGTATAATGATGT
Done.