Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005356.1 Hibiscus syriacus cultivar Beakdansim tig00012165_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: 58883
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2380 original size:23 final size:24
Alignment explanation
Indices: 2350--2396 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2340 CGCCTTCCCT
2350 ATTTTTTATTATTTT-ATTAATTA
1 ATTTTTTATTATTTTGATTAATTA
*
2373 ATTTTTTATTATTTTGTTTAATTA
1 ATTTTTTATTATTTTGATTAATTA
2397 TATAAAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTTTTTATTATTTTGATTAATTA
Found at i:2612 original size:19 final size:18
Alignment explanation
Indices: 2585--2620 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2575 AATGAGAAGA
2585 GAGAACGAAAAAGAAATTC
1 GAGAACG-AAAAGAAATTC
*
2604 GAGATCGAAAAGAAATT
1 GAGAACGAAAAGAAATT
2621 GAGGTTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.08, G:0.22, T:0.14
Consensus pattern (18 bp):
GAGAACGAAAAGAAATTC
Found at i:6105 original size:2 final size:2
Alignment explanation
Indices: 6098--6140 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6088 GGTAAAACAA
6098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6140 A
1 A
6141 ATTTATGTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6597 original size:213 final size:215
Alignment explanation
Indices: 6230--6658 Score: 573
Period size: 213 Copynumber: 2.0 Consensus size: 215
6220 TTAGTACTTA
* * *
6230 AAACTTTTAATTTTTTCAAAACCATATGTAACGTTTAATTTTCATTTCATTTTAATACCCACTGT
1 AAACTTTTAATTCTTTCAAAACCATATCTAACGATTAATTTTCATTTCATTTTAATACCCACTGT
* * * *
6295 TAAAAAATTAACACGTTTAGTACCTAAACTATTAGTTGTAGTTTGTTTTAGTACCTAAACTTTTA
66 TAAAAAATTAACACATTTAGTACCTAAACTATCAGTTGTAGTTTGTCTTAGTACCTAAAATTTTA
*
6360 ATTTTTTCAAAATCATACCTAACGTTTAG-T-TTTCATTTTAGT-ACTCGTCGTTAAAAATTTAA
131 ATTTTTTCAAAATCATACCTAACGTTTAGTTATTTCATTTTAGTAACT-GTCGTTAAAAACTTAA
*
6422 TGTGTTTAGTACCTAAACTAC
195 TGCGTTTAGTACCTAAACTAC
* * ***
6443 AAACTTTTAATTCTTTCAAAACCATATCTAAC-ATTAGTTTTCATTTCATTTTAGTACTTTGTCT
1 AAACTTTTAATTCTTTCAAAACCATATCTAACGATTAATTTTCATTTCATTTTAATAC--CCACT
* * * * *
6507 -TTAAAAAATTAACGCATTTAGTGCCTAAATTATCATTTGT-GATTTGTCTTGGTACCTAAAATT
64 GTTAAAAAATTAACACATTTAGTACCTAAACTATCAGTTGTAG-TTTGTCTTAGTACCTAAAATT
*
6570 TTAATTTTTTCAAAATCATACCTAACGTTTAGTTTCATTTCATTTTAGTAACTGTTGTTAAAAAC
128 TTAATTTTTTCAAAATCATACCTAACGTTTAG-TT-ATTTCATTTTAGTAACTGTCGTTAAAAAC
*
6635 TTACTGCGTTTAGTACCTAAACTA
191 TTAATGCGTTTAGTACCTAAACTA
6659 TCAATTTTGG
Statistics
Matches: 187, Mismatches: 21, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
212 23 0.12
213 114 0.61
214 2 0.01
215 1 0.01
217 44 0.24
218 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (215 bp):
AAACTTTTAATTCTTTCAAAACCATATCTAACGATTAATTTTCATTTCATTTTAATACCCACTGT
TAAAAAATTAACACATTTAGTACCTAAACTATCAGTTGTAGTTTGTCTTAGTACCTAAAATTTTA
ATTTTTTCAAAATCATACCTAACGTTTAGTTATTTCATTTTAGTAACTGTCGTTAAAAACTTAAT
GCGTTTAGTACCTAAACTAC
Found at i:6606 original size:121 final size:120
Alignment explanation
Indices: 6443--7352 Score: 994
Period size: 121 Copynumber: 7.6 Consensus size: 120
6433 CCTAAACTAC
* * * * * *
6443 AAACTTTTAATTCTTTCAAAACCATATCTAAC-ATTAGTTTTCATTTCATTTTAGTACTTTGTCT
1 AAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC-TTGTCG
* * * * * * *
6507 TTAAAAAATTAACGCATTTAGTGCCTAAATTATCATTTGTGATTTGTCTTGGTACCT
65 TTAAAAAATTAACGCGTTTAGTACCTAAACTATCATTT-TGGTCTGTTTTAGTACCT
* * *
6564 AAAATTTTAATTTTTTCAAAATCATACCTAACGTTTAG-TTTCATTTCATTTTAGTAAC-TGTTG
1 AAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGT-ACTTGTCG
*
6627 TTAAAAACTT-ACTGCGTTTAGTACCTAAACTATCAATTTTGGTCTGTTTTAGTACCT
65 TTAAAAAATTAAC-GCGTTTAGTACCTAAACTATC-ATTTTGGTCTGTTTTAGTACCT
* * * * *
6684 AAACTTTTAAGTTTTTCAAAACCATATCTAACGTTTAGTTTTCA-TTC-TATTTAGTACCATGTC
1 AAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCAT-TTTAGTA-CTTGTC
*
6747 GTTAAAACATTAACGCGTTTAGTACCTAAACTATCAGTTTTGGTCTGTTTTAGTACCT
64 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* *
6805 AAACTTCCAATTTTTTCAAAATCATACCTAACGTTTAG---T--TTTC--TTTAGTACTCGTCGT
1 AAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCGT
* * * * *
6863 TAAAAATTTAATGTGTTTAGTACCTAAACTATCAGTTTTGGTCAGTTTTAGTATCT
66 TAAAAAATTAACGCGTTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* * *
6919 AAACTTTCAATTTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTC
1 AAACTTTCAA-TTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC-TTGTC
* * * * * *
6984 GTT-AAAAATTAACGCATTTAGTACCTAAACTATCAGTGTGATTTATTTT-GATACCT
64 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATCATTTTGGTCTGTTTTAG-TACCT
* * ** *
7040 AAACTTTCATTTTTTTTCAAAATCATATC-AACGTTTAGTTTTCATTTCATTTTAGTACCCGTCT
1 AAACTTTCA-ATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCG
* * *
7104 TTAAAAATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTCT-ATTTAGTACCT
65 TTAAAAAATTAACGCGTTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* ** *
7160 AAAC-TTCATTTTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCACGCC
1 AAACTTTCA-ATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTA-CTTGTC
* * * *
7224 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAATTGTGATTTGTTTTGGTACCT
64 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATC-ATTTTGGTCTGTTTTAGTACCT
* * * *
7282 GAACATTCATTTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTA-TCCGTCG
1 AAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACT-TGTCG
7346 TTAAAAA
65 TTAAAAA
7353 CTAAATGGGA
Statistics
Matches: 679, Mismatches: 79, Indels: 62
0.83 0.10 0.08
Matches are distributed among these distances:
114 65 0.10
115 32 0.05
117 3 0.00
118 2 0.00
119 32 0.05
120 191 0.28
121 238 0.35
122 105 0.15
123 11 0.02
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (120 bp):
AAACTTTCAATTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCGT
TAAAAAATTAACGCGTTTAGTACCTAAACTATCATTTTGGTCTGTTTTAGTACCT
Found at i:7085 original size:477 final size:475
Alignment explanation
Indices: 6443--7324 Score: 1321
Period size: 477 Copynumber: 1.9 Consensus size: 475
6433 CCTAAACTAC
* *
6443 AAACTTTTAATTCTTTCAAAACCATATCTAACATTAGTTTTCATTTCATTTTAGTACTTTGTCTT
1 AAACTTTCAATTCTTTCAAAACCATATCTAACATTAGTTTTCATTTCATTTTAGTACTTTGTCGT
* * * * * *
6508 TAAAAAATTAACGCATTTAGTGCCTAAATTATCATTTGTGATTTGTCTTGGTACCTAAAATTTTA
66 TAAAAAATTAACGCATTTAGTACCTAAACTATCATGTGTGATTTATCTTGATACCTAAAATTTCA
*
6573 ATTTTTTCAAAATCATACCTAACGTTTAGTTTCATTTCATTTTAGTAACTGT-TGTTAAAAACTT
131 ATTTTTTCAAAATCATACCTAACGTTTAGTTTCATTTCATTTTAGTAACCGTCT-TTAAAAACTT
* *
6637 ACTGCGTTTAGTACCTAAACTATCAATTTTGGTCTGTTTTAGTACCTAAACTT-TTAAGTTTTTC
195 AATGCGTTTAGTACCTAAACTATCAATTTTGGTCT-ATTTAGTACCTAAACTTATT--GTTTTTC
* * * *
6701 AAAACCATATCTAACGTTTAGTTTTCA-TTC-TATTTAGTACCATGTCGTTAAAACATTAACGCG
257 AAAACCATACCTAACGTTTAGTTTTCATTTCAT-TTTAGTACCACGCCGTTAAAAAATTAACGCG
* * *
6764 TTTAGTACCTAAACTATCAGTTTTGGTCTGTTTTAGTACCTAAAC-TTCCAATTTTTTCAAAATC
321 TTTAGTACCTAAACTATCAATTGTGATCTGTTTTAGTACCTAAACATT-CAATTTTTTCAAAATC
6828 ATACCTAACGTTTAGTTTTCTTTAGTACTCGTCGTTAAAAATTTAATGTGTTTAGTACCTAAACT
385 ATACCTAACGTTTAGTTTTCTTTAGTACTCGTCGTTAAAAATTTAATGTGTTTAGTACCTAAACT
6893 ATCAGTTTTGGTCAGTTTTAGTATCT
450 ATCAGTTTTGGTCAGTTTTAGTATCT
*
6919 AAACTTTCAATTTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTC
1 AAACTTTCAA-TTCTTTCAAAACCATATCTAACA-TTAGTTTTCATTTCATTTTAGTACTTTGTC
* *
6984 GTT-AAAAATTAACGCATTTAGTACCTAAACTATCA-GTGTGATTTATTTTGATACCTAAACTTT
64 GTTAAAAAATTAACGCATTTAGTACCTAAACTATCATGTGTGATTTATCTTGATACCTAAAATTT
* * *
7047 CATTTTTTTTCAAAATCATATC-AACGTTTAGTTTTCATTTCATTTTAGTACCCGTCTTTAAAAA
129 CA-ATTTTTTCAAAATCATACCTAACGTTTAG-TTTCATTTCATTTTAGTAACCGTCTTTAAAAA
* * *
7111 TTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTCTATTTAGTACCTAAACTTCATTTTTTTT
192 CTTAATGCGTTTAGTACCTAAACTATCAATTTTGGTCTATTTAGTACCTAAACTT-ATTGTTTTT
*
7176 CAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCACGCCGTTAAAAAATTAACGCG
256 CAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCACGCCGTTAAAAAATTAACGCG
* * * *
7241 TTTAGTACCTAAACTATCAATTGTGATTTGTTTTGGTACCTGAACATTCATTTTTTTCAAAATCA
321 TTTAGTACCTAAACTATCAATTGTGATCTGTTTTAGTACCTAAACATTCAATTTTTTCAAAATCA
7306 TACCTAACGTTTAGTTTTC
386 TACCTAACGTTTAGTTTTC
7325 ATTTCATTTT
Statistics
Matches: 364, Mismatches: 32, Indels: 19
0.88 0.08 0.05
Matches are distributed among these distances:
476 89 0.24
477 237 0.65
478 38 0.10
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (475 bp):
AAACTTTCAATTCTTTCAAAACCATATCTAACATTAGTTTTCATTTCATTTTAGTACTTTGTCGT
TAAAAAATTAACGCATTTAGTACCTAAACTATCATGTGTGATTTATCTTGATACCTAAAATTTCA
ATTTTTTCAAAATCATACCTAACGTTTAGTTTCATTTCATTTTAGTAACCGTCTTTAAAAACTTA
ATGCGTTTAGTACCTAAACTATCAATTTTGGTCTATTTAGTACCTAAACTTATTGTTTTTCAAAA
CCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCACGCCGTTAAAAAATTAACGCGTTTAG
TACCTAAACTATCAATTGTGATCTGTTTTAGTACCTAAACATTCAATTTTTTCAAAATCATACCT
AACGTTTAGTTTTCTTTAGTACTCGTCGTTAAAAATTTAATGTGTTTAGTACCTAAACTATCAGT
TTTGGTCAGTTTTAGTATCT
Found at i:7513 original size:20 final size:21
Alignment explanation
Indices: 7474--7523 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
7464 TTTAAATTCT
7474 TTTTATATTTTATATATT-AA
1 TTTTATATTTTATATATTAAA
*
7494 TTTTATATTTGTATCT-TTAAAA
1 TTTTATATTT-TATATATT-AAA
7516 TTTTATAT
1 TTTTATAT
7524 CTTACCTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 12 0.46
21 4 0.15
22 10 0.38
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATATTTTATATATTAAA
Found at i:19627 original size:18 final size:18
Alignment explanation
Indices: 19604--19639 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19594 TGACACAATC
19604 AAATATTTTTAAAAAATA
1 AAATATTTTTAAAAAATA
*
19622 AAATATTTTTTAAAAATA
1 AAATATTTTTAAAAAATA
19640 TTTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATTTTTAAAAAATA
Found at i:19651 original size:13 final size:13
Alignment explanation
Indices: 19621--19645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19611 TTTAAAAAAT
19621 AAAATATTTTTTA
1 AAAATATTTTTTA
19634 AAAATATTTTTT
1 AAAATATTTTTT
19646 TTAAATCTAG
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AAAATATTTTTTA
Found at i:25595 original size:16 final size:15
Alignment explanation
Indices: 25563--25592 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25553 GTTACAAACA
25563 AAAATACATTGACTT
1 AAAATACATTGACTT
*
25578 AAAATATATTGACTT
1 AAAATACATTGACTT
25593 TAATTTCGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (15 bp):
AAAATACATTGACTT
Found at i:27027 original size:21 final size:21
Alignment explanation
Indices: 27001--27043 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26991 TTTCTGGGTT
* *
27001 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
27022 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
27043 A
1 A
27044 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:27104 original size:66 final size:68
Alignment explanation
Indices: 27023--27173 Score: 198
Period size: 66 Copynumber: 2.2 Consensus size: 68
27013 ACCCATTCAA
* * * *
27023 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATAGGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
27086 GGG
66 GGG
* * * *
27089 GGGGAACCGATACCCCCTCATCGTATAGGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATAGGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
27154 GGG
66 GGG
* *
27157 GAGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
27174 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 25 0.34
67 25 0.34
68 23 0.32
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATAGGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:27510 original size:29 final size:29
Alignment explanation
Indices: 27476--27547 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
27466 CATATTATGA
**
27476 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
27505 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
27534 TACATGACATGAAT
1 TACATGACATGAAT
27548 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:27603 original size:30 final size:31
Alignment explanation
Indices: 27561--27620 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
27551 CAGAAAAGTT
*
27561 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
27592 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
27621 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:27914 original size:22 final size:22
Alignment explanation
Indices: 27840--27906 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
27830 TTATGGACAT
27840 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
27862 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
27884 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
27906 A
1 A
27907 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:33971 original size:21 final size:21
Alignment explanation
Indices: 33945--33987 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33935 TTTCTGGGTT
* *
33945 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
33966 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
33987 A
1 A
33988 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:34048 original size:66 final size:68
Alignment explanation
Indices: 33967--34117 Score: 198
Period size: 66 Copynumber: 2.2 Consensus size: 68
33957 ACCCATTCAA
* * * *
33967 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATAGGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
34030 GGG
66 GGG
* * * *
34033 GGGGAACCGATACCCCCTCATCGTATAGGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATAGGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
34098 GGG
66 GGG
* *
34101 GAGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
34118 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 25 0.34
67 25 0.34
68 23 0.32
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATAGGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:34454 original size:29 final size:29
Alignment explanation
Indices: 34420--34491 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
34410 CATATTATGA
**
34420 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
34449 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
34478 TACATGACATGAAT
1 TACATGACATGAAT
34492 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:34547 original size:30 final size:31
Alignment explanation
Indices: 34505--34564 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
34495 CAGAAAAGTT
*
34505 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
34536 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
34565 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:34858 original size:22 final size:22
Alignment explanation
Indices: 34784--34850 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
34774 TTATGGACAT
34784 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
34806 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
34828 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
34850 A
1 A
34851 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:35267 original size:17 final size:17
Alignment explanation
Indices: 35245--35278 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35235 TGACAGTTGG
35245 CATGTAATTAAAGGGTT
1 CATGTAATTAAAGGGTT
35262 CATGTAATTAAAGGGTT
1 CATGTAATTAAAGGGTT
35279 AAGTTGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
CATGTAATTAAAGGGTT
Found at i:36735 original size:16 final size:15
Alignment explanation
Indices: 36714--36773 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 15
36704 TTAGTTTAAT
36714 TTAATATATAAAATTA
1 TTAATATATAAAA-TA
*
36730 TTAATA-ATTAAATA
1 TTAATATATAAAATA
*
36744 TGTAATATTATAATATA
1 T-TAATA-TATAAAATA
36761 TATATATATATAA
1 T-TA-ATATATAA
36774 CTGGGTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 3 0.08
15 10 0.28
16 6 0.17
17 14 0.39
18 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TTAATATATAAAATA
Found at i:36939 original size:2 final size:2
Alignment explanation
Indices: 36932--36974 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36922 ACCGGCTTGG
36932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36974 A
1 A
36975 AATGGAGCAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37055 original size:13 final size:13
Alignment explanation
Indices: 37037--37062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37027 TTAAAATATT
37037 AATAAAATAAAAA
1 AATAAAATAAAAA
37050 AATAAAATAAAAA
1 AATAAAATAAAAA
37063 TAAAAGTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAAATAAAAA
Found at i:41487 original size:15 final size:15
Alignment explanation
Indices: 41467--41502 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41457 TTAGATGAAA
* *
41467 AAAATTGGGAAGGCT
1 AAAATTGGAAAGACT
41482 AAAATTGGAAAGACT
1 AAAATTGGAAAGACT
41497 AAAATT
1 AAAATT
41503 TGGTGTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (15 bp):
AAAATTGGAAAGACT
Found at i:42526 original size:16 final size:16
Alignment explanation
Indices: 42505--42538 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42495 CAGATTTCCT
*
42505 CTTGCATACGCATCCC
1 CTTGCATACGCATACC
42521 CTTGCATACGCATACC
1 CTTGCATACGCATACC
42537 CT
1 CT
42539 AGAGAGAATT
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:0.21, C:0.41, G:0.12, T:0.26
Consensus pattern (16 bp):
CTTGCATACGCATACC
Found at i:43358 original size:21 final size:21
Alignment explanation
Indices: 43334--43373 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43324 TTTTCAAAGG
43334 CATGCACCGATGCATCAATAT
1 CATGCACCGATGCATCAATAT
*
43355 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
43374 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAT
Found at i:43488 original size:64 final size:65
Alignment explanation
Indices: 43335--43543 Score: 194
Period size: 64 Copynumber: 3.2 Consensus size: 65
43325 TTTCAAAGGC
* * *
43335 ATGCACCGATGCATCAATATCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCAT
1 ATGCACCGATGCA-CAATA-CATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGCAT
*
43399 TCA
63 TTA
** * * *
43402 ATGCACCGATGCACTCTCCATGCATCGATACACTC-TGATTTAATTAAAACATCGAATGCATTTG
1 ATGCACCGATGCACAATACATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTTA
* * * * *
43466 ATGCATCGATGCACAAGACATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCACT
1 ATGCACCGATGCACAATACATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCATT
*
43528 TC
64 TA
*
43530 ATGCATCGATGCAC
1 ATGCACCGATGCAC
43544 TCTTAGTGCA
Statistics
Matches: 119, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
63 1 0.01
64 84 0.71
65 13 0.11
66 8 0.07
67 13 0.11
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (65 bp):
ATGCACCGATGCACAATACATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTTA
Found at i:43543 original size:17 final size:19
Alignment explanation
Indices: 43515--43563 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
43505 ATTTTTCAAA
43515 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
43533 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
43552 CACCGATGCACT
1 CATCGATGCACT
43564 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:49382 original size:24 final size:22
Alignment explanation
Indices: 49354--49433 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
49344 CACTTAACAA
49354 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
49378 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
49398 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
49422 TGCATCGATGCA
1 TGCATCGATGCA
49434 CAAGACCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 13 0.27
24 17 0.35
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:49839 original size:20 final size:21
Alignment explanation
Indices: 49816--49856 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
49806 AAAACTCGCA
49816 AATTTTTCAAA-AAAAAAATT
1 AATTTTTCAAATAAAAAAATT
*
49836 AATTTTTGAAATAAAAAAATT
1 AATTTTTCAAATAAAAAAATT
49857 CGAAATTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTTTTCAAATAAAAAAATT
Found at i:50778 original size:21 final size:21
Alignment explanation
Indices: 50754--50814 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
50744 TTTTCAAAGG
*
50754 CATGCACCGATGCATCAATAC
1 CATGCATCGATGCATCAATAC
50775 CATGCATCGATGCATCAATAC
1 CATGCATCGATGCATCAATAC
50796 CATGCATCGATGCATCAAT
1 CATGCATCGATGCATCAAT
50815 GAATAAATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCATCGATGCATCAATAC
Found at i:50929 original size:64 final size:64
Alignment explanation
Indices: 50776--50935 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
50766 CATCAATACC
* *
50776 ATGCATCGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCATT
1 ATGCATCGATGCA-CAATA-CATGCATCGATACATC-ATGAATAAATTAAAACATCGAATGCATT
50841 CA
63 CA
* ** * * * **
50843 ATGCACCGATGCACTCTCCATGCATCGATACACTC-TGATTTAATTAAAACATCGAATGCATTTG
1 ATGCATCGATGCACAATACATGCATCGATACA-TCATGAATAAATTAAAACATCGAATGCATTCA
*
50907 ATGCATCGATGCACAAGACATGCATCGAT
1 ATGCATCGATGCACAATACATGCATCGAT
50936 GCACCAGGCT
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
64 48 0.62
65 13 0.17
66 4 0.05
67 12 0.16
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAATACATGCATCGATACATCATGAATAAATTAAAACATCGAATGCATTCA
Found at i:52277 original size:24 final size:24
Alignment explanation
Indices: 52250--52319 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
52240 TCTTATAATT
52250 TGCACCAAAGTGCCACGTAGAATA
1 TGCACCAAAGTGCCACGTAGAATA
* * *
52274 TGCACCAAGGTGCCACATAG-ATT
1 TGCACCAAAGTGCCACGTAGAATA
52297 TGTC-CCAAAG-GACCACGTAGAAT
1 TG-CACCAAAGTG-CCACGTAGAAT
52320 TTGTCCCGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 16 0.42
24 21 0.55
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (24 bp):
TGCACCAAAGTGCCACGTAGAATA
Found at i:52360 original size:26 final size:25
Alignment explanation
Indices: 52294--52385 Score: 123
Period size: 24 Copynumber: 3.7 Consensus size: 25
52284 TGCCACATAG
*
52294 ATTTGTCCCAAAGGACCACGTAG-A
1 ATTTGTCCCGAAGGACCACGTAGAA
*
52318 ATTTGTCCCGAATGACCACGTAGAAA
1 ATTTGTCCCGAAGGACCACGTAG-AA
** *
52344 ATTTGTCCTTAAGGACCAAGTAGAA
1 ATTTGTCCCGAAGGACCACGTAGAA
52369 ATTTGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
52386 GCATAGAACC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
24 21 0.36
25 17 0.29
26 20 0.34
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (25 bp):
ATTTGTCCCGAAGGACCACGTAGAA
Found at i:52392 original size:25 final size:25
Alignment explanation
Indices: 52286--52393 Score: 107
Period size: 25 Copynumber: 4.4 Consensus size: 25
52276 CACCAAGGTG
*
52286 CCACATAG--ATTTGTCCCAAAGGA
1 CCACATAGAAATTTGTCCCGAAGGA
* *
52309 CCACGTAG-AATTTGTCCCGAATGA
1 CCACATAGAAATTTGTCCCGAAGGA
* **
52333 CCACGTAGAAAATTTGTCCTTAAGGA
1 CCACATAG-AAATTTGTCCCGAAGGA
52359 CCA-AGTAGAAATTTGTCCCGAAGGA
1 CCACA-TAGAAATTTGTCCCGAAGGA
*
52384 CCGCATAGAA
1 CCACATAGAA
52394 CCCTCGACTC
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
23 7 0.10
24 21 0.30
25 22 0.31
26 20 0.29
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (25 bp):
CCACATAGAAATTTGTCCCGAAGGA
Found at i:52571 original size:16 final size:17
Alignment explanation
Indices: 52544--52580 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
52534 AGAACATTTT
52544 CATATAAAACATATTCA
1 CATATAAAACATATTCA
52561 CATAT-AAACATATTCA
1 CATATAAAACATATTCA
52577 CATA
1 CATA
52581 CCAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (17 bp):
CATATAAAACATATTCA
Done.