Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000965.1 Hibiscus syriacus cultivar Beakdansim tig00001927_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: 122326
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2144 original size:38 final size:38
Alignment explanation
Indices: 2047--2144 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 38
2037 AACCAGTTGC
* * * * *
2047 TGCTGTGGCTGCTGTTGTTGTTGGTTAGTAAACAGCGGA
1 TGCTGAGGCTGCTGCTGCTG-TGGTTACTAAACAACGGA
**
2086 TGCTGAGGCTGCTGGGGCTGTGGTTACTAAACAACGGA
1 TGCTGAGGCTGCTGCTGCTGTGGTTACTAAACAACGGA
**
2124 TGCTGCTGCTGCTGCTGCTGT
1 TGCTGAGGCTGCTGCTGCTGT
2145 TGCTGTTGGT
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
38 33 0.67
39 16 0.33
ACGTcount: A:0.14, C:0.18, G:0.36, T:0.32
Consensus pattern (38 bp):
TGCTGAGGCTGCTGCTGCTGTGGTTACTAAACAACGGA
Found at i:7603 original size:61 final size:61
Alignment explanation
Indices: 7508--7622 Score: 203
Period size: 61 Copynumber: 1.9 Consensus size: 61
7498 GAATACTTGT
* *
7508 TTCGGGCCATGGATGAAAGTACAACATCCAGGTGGAGATGCTATGTTGACCCATCTGGTTA
1 TTCGGGCCATGGATAAAAGTACAACATCCAGGTGGAGATGCTACGTTGACCCATCTGGTTA
*
7569 TTCGGGCCATGGTTAAAAGTACAACATCCAGGTGGAGATGCTACGTTGACCCAT
1 TTCGGGCCATGGATAAAAGTACAACATCCAGGTGGAGATGCTACGTTGACCCAT
7623 TTATTTCTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (61 bp):
TTCGGGCCATGGATAAAAGTACAACATCCAGGTGGAGATGCTACGTTGACCCATCTGGTTA
Found at i:7640 original size:61 final size:61
Alignment explanation
Indices: 7514--7640 Score: 173
Period size: 61 Copynumber: 2.1 Consensus size: 61
7504 TTGTTTCGGG
* * * * *
7514 CCATGGATGAAAGTACAACATCCAGGTGGAGATGCTATGTTGACCCATCTGGTTATTCGGG
1 CCATGGATAAAAGTACAACATCCAGGTGGAGATGCTACGTTGACCCATCTAGTTATTCAGA
* * * *
7575 CCATGGTTAAAAGTACAACATCCAGGTGGAGATGCTACGTTGACCCATTTATTTCTTCAGA
1 CCATGGATAAAAGTACAACATCCAGGTGGAGATGCTACGTTGACCCATCTAGTTATTCAGA
7636 CCATG
1 CCATG
7641 ACTAACGATC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (61 bp):
CCATGGATAAAAGTACAACATCCAGGTGGAGATGCTACGTTGACCCATCTAGTTATTCAGA
Found at i:8638 original size:42 final size:42
Alignment explanation
Indices: 8579--8670 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
8569 CCCCACTTTA
* * * * *
8579 AGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACACCC
1 AGAGCCATAACCTGATCGAGCCGATTATACACCTCCACAACC
*
8621 AGAGCCATAACCTGATCGAGCCGATTATACACCTCCACAACG
1 AGAGCCATAACCTGATCGAGCCGATTATACACCTCCACAACC
8663 AGAGCCAT
1 AGAGCCAT
8671 CAGCTATTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.16
Consensus pattern (42 bp):
AGAGCCATAACCTGATCGAGCCGATTATACACCTCCACAACC
Found at i:8838 original size:21 final size:21
Alignment explanation
Indices: 8790--8842 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
8780 GTTAGGGGAG
**
8790 TTACGTGATGAGGTCAGTGTT
1 TTACGTGATGAGGTCAGTACT
* *
8811 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
8832 TTACGTGATGA
1 TTACGTGATGA
8843 CAATTGTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.34, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:9293 original size:21 final size:21
Alignment explanation
Indices: 9246--9364 Score: 125
Period size: 21 Copynumber: 5.7 Consensus size: 21
9236 GATTCACATG
* *
9246 TCATCATTCAATAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
9267 -CTATCGTTCAAGAGACCCATT
1 TC-ATCGTTCAAGAGGCCCCTC
*
9288 TCATCGTTCAATAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
9309 TCA-CTGTTCAAGAGGCCCCTG
1 TCATC-GTTCAAGAGGCCCCTC
*
9330 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
9351 CCATCGTTCAAGAG
1 TCATCGTTCAAGAG
9365 CCCGATTCAT
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.03
21 76 0.95
22 2 0.03
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:9305 original size:42 final size:42
Alignment explanation
Indices: 9242--9364 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
9232 GCTCGATTCA
*
9242 CATGTCATCATTCAATAGGCCCCTCCTATCGTTCAAGAGACC
1 CATGTCATCGTTCAATAGGCCCCTCCTATCGTTCAAGAGACC
* *
9284 CATTTCATCGTTCAATAGGCCCCT-CTCA-CTGTTCAAGAGGCC
1 CATGTCATCGTTCAATAGGCCCCTCCT-ATC-GTTCAAGAGACC
* * * *
9326 CCTGTCATCGTTCAAGAGGTCCCTCCCATCGTTCAAGAG
1 CATGTCATCGTTCAATAGGCCCCTCCTATCGTTCAAGAG
9365 CCCGATTCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
41 3 0.04
42 64 0.93
43 2 0.03
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (42 bp):
CATGTCATCGTTCAATAGGCCCCTCCTATCGTTCAAGAGACC
Found at i:14295 original size:14 final size:15
Alignment explanation
Indices: 14261--14298 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
14251 GAAATCATTG
14261 AAAAATTATATAGAA
1 AAAAATTATATAGAA
14276 ATAAAATTATATA-AA
1 A-AAAATTATATAGAA
14291 AAAAATTA
1 AAAAATTA
14299 GAGATTGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:14457 original size:18 final size:19
Alignment explanation
Indices: 14436--14482 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
14426 AAAACATTTG
14436 TGTTGCGAAAATAAAA-CA
1 TGTTGCGAAAATAAAATCA
*
14454 TGTTGCGAAATTAAAATTCA
1 TGTTGCGAAAATAAAA-TCA
14474 TGTTGCGAA
1 TGTTGCGAA
14483 TTCGAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (19 bp):
TGTTGCGAAAATAAAATCA
Found at i:14510 original size:21 final size:20
Alignment explanation
Indices: 14479--14547 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
14469 ATTCATGTTG
*
14479 CGAATTCGAAAATCGAGTTA
1 CGAATTTGAAAATCGAGTTA
14499 CGAATTT-AGAAATCGAGTTA
1 CGAATTTGA-AAATCGAGTTA
* * *
14519 CAAATTTGAAATTCAGTGTTA
1 CGAATTTGAAAATC-GAGTTA
14540 CGAATTTG
1 CGAATTTG
14548 GAAACTGTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 27 0.66
21 13 0.32
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (20 bp):
CGAATTTGAAAATCGAGTTA
Found at i:20509 original size:2 final size:2
Alignment explanation
Indices: 20502--20533 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20492 TTAATTATTA
*
20502 AT AT AT AT AT AA 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
20534 TTTAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23039 original size:12 final size:13
Alignment explanation
Indices: 23022--23051 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23012 CGTTTAGATT
23022 TTTTTAAA-AATA
1 TTTTTAAATAATA
23034 TTTTTAAATAATA
1 TTTTTAAATAATA
23047 TTTTT
1 TTTTT
23052 TAGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTAAATAATA
Found at i:23276 original size:24 final size:26
Alignment explanation
Indices: 23232--23282 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
23222 TTTTATTTTT
*
23232 ATAAATTAAATATAAATTA-TTAAAA
1 ATAAATAAAATATAAATTATTTAAAA
23257 ATAAATAAAAT-TAACA-TATTTAAAA
1 ATAAATAAAATATAA-ATTATTTAAAA
23282 A
1 A
23283 ATATTGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
ATAAATAAAATATAAATTATTTAAAA
Found at i:34183 original size:104 final size:103
Alignment explanation
Indices: 33870--34190 Score: 351
Period size: 104 Copynumber: 3.1 Consensus size: 103
33860 CCTCTGAGCG
* * * **
33870 ACCTCCATAGGTCGTCAAGTCCTCCAAACGTTCAAACATTGGTTTCTTAAATTTCCTATAAGTAA
1 ACCTCCACAGGTCGCCAAGTCCTCCAAACGTTCAAACATTGATTTCTTTGATTTCC-ATAAGTAA
* * *
33935 CAGTGATTACCTACATCAGTAATTAGGCTTTTAGTCAAA
65 CAGTGATTACCTACATCAGTAATTAAGATTTTAGTCGAA
* * * * * * *
33974 ACCTCCATAGGTCGCTAAATCCTCCAAACGTTGAAGCATT-AGTTTCCTTGATTTCCCGTAAGTA
1 ACCTCCACAGGTCGCCAAGTCCTCCAAACGTTCAAACATTGA-TTTCTTTGATTT-CCATAAGTA
*
34038 ACAGTGATGACCTACAT-ATGTAATT-AGACTTTTAGTCGAA
64 ACAGTGATTACCTACATCA-GTAATTAAGA-TTTTAGTCGAA
* * * *
34078 ACCTCCACAGGTCGCCAAGTCATTCGAACGTTCAAACATTGATTTCTTTGATTTCTCATAAATAA
1 ACCTCCACAGGTCGCCAAGTCCTCCAAACGTTCAAACATTGATTTCTTTGATTTC-CATAAGTAA
* * * *
34143 CAATGATTACCTACATCGGTAATTAAGATTTTAATGGAA
65 CAGTGATTACCTACATCAGTAATTAAGATTTTAGTCGAA
34182 ACCTCCACA
1 ACCTCCACA
34191 ATTAGACCTT
Statistics
Matches: 179, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
103 3 0.02
104 170 0.95
105 6 0.03
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (103 bp):
ACCTCCACAGGTCGCCAAGTCCTCCAAACGTTCAAACATTGATTTCTTTGATTTCCATAAGTAAC
AGTGATTACCTACATCAGTAATTAAGATTTTAGTCGAA
Found at i:34642 original size:26 final size:27
Alignment explanation
Indices: 34586--34642 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
34576 ATAAATAAAC
34586 TTTA-TGATTTATATATTAAAATATTA
1 TTTATTGATTTATATATTAAAATATTA
*
34612 -ATATTGATTTAT-TA-TAAAATATATA
1 TTTATTGATTTATATATTAAAATAT-TA
34637 TTTATT
1 TTTATT
34643 ATAGATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
24 8 0.31
25 6 0.23
26 12 0.46
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTATTGATTTATATATTAAAATATTA
Found at i:34656 original size:17 final size:18
Alignment explanation
Indices: 34618--34656 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
34608 ATTAATATTG
*
34618 ATTTATTATAAAATATAT
1 ATTTATTATAAAATATAA
*
34636 ATTTATTAT-AGATATAA
1 ATTTATTATAAAATATAA
34653 ATTT
1 ATTT
34657 TATTTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTATTATAAAATATAA
Found at i:34658 original size:18 final size:18
Alignment explanation
Indices: 34618--34660 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
34608 ATTAATATTG
*
34618 ATTTATTATAAAATATAT
1 ATTTATTATAAAATAAAT
*
34636 ATTTATTATAGATATAAAT
1 ATTTATTATA-AAATAAAT
34655 -TTTATT
1 ATTTATT
34661 TGTATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTATTATAAAATAAAT
Found at i:35883 original size:20 final size:22
Alignment explanation
Indices: 35846--35886 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35836 ACCATCCAAA
35846 TCTTCAAAAGAAATTTTAAATT
1 TCTTCAAAAGAAATTTTAAATT
*
35868 TCTTTAAAA-AAA-TTTAAAT
1 TCTTCAAAAGAAATTTTAAAT
35887 AATGCTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (22 bp):
TCTTCAAAAGAAATTTTAAATT
Found at i:37193 original size:2 final size:2
Alignment explanation
Indices: 37180--37215 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
37170 CACCAAGTAA
*
37180 AT AT AC 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
37216 GCAATGATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44950 original size:21 final size:21
Alignment explanation
Indices: 44921--44978 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
44911 CACTGCGAGT
*
44921 TTGACCTTCTTCTTCTT-GTG
1 TTGATCTTCTTCTTCTTGGTG
* *
44941 CTTGATCTTCTTGTGCTTGGTG
1 -TTGATCTTCTTCTTCTTGGTG
44963 TATG-TCTTCTTCTTCT
1 T-TGATCTTCTTCTTCT
44979 CTTCTTGGCG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.05, C:0.22, G:0.17, T:0.55
Consensus pattern (21 bp):
TTGATCTTCTTCTTCTTGGTG
Found at i:44951 original size:15 final size:15
Alignment explanation
Indices: 44931--44959 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44921 TTGACCTTCT
44931 TCTTCTTGTGCTTGA
1 TCTTCTTGTGCTTGA
44946 TCTTCTTGTGCTTG
1 TCTTCTTGTGCTTG
44960 GTGTATGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.21, G:0.21, T:0.55
Consensus pattern (15 bp):
TCTTCTTGTGCTTGA
Found at i:51371 original size:3 final size:3
Alignment explanation
Indices: 51363--51395 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
51353 ACATTTCCTA
51363 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51396 TAATTTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:52350 original size:3 final size:3
Alignment explanation
Indices: 52342--52369 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52332 CTCCACTCCT
52342 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52370 CTAAATCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53864 original size:5 final size:5
Alignment explanation
Indices: 53854--53879 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53844 CTGACCAGTT
53854 GACCC GACCC GACCC GACCC GACCC G
1 GACCC GACCC GACCC GACCC GACCC G
53880 TTGACCCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.58, G:0.23, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:53887 original size:13 final size:13
Alignment explanation
Indices: 53815--53901 Score: 75
Period size: 13 Copynumber: 6.3 Consensus size: 13
53805 AACCCGACCC
53815 GACCCGACCCGTT
1 GACCCGACCCGTT
*
53828 TACCCGACCCGTT
1 GACCCGACCCGTT
* * *
53841 TACCTGACCAGTT
1 GACCCGACCCGTT
**
53854 GACCCGACCCGACCC
1 GACCCGACCCG--TT
53869 GACCCGACCCGTT
1 GACCCGACCCGTT
53882 GACCCGTTGACCCGTT
1 GACCC---GACCCGTT
53898 GACC
1 GACC
53902 GTTGACCCAC
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
13 36 0.61
15 11 0.19
16 12 0.20
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:53905 original size:7 final size:8
Alignment explanation
Indices: 53874--53922 Score: 66
Period size: 8 Copynumber: 6.1 Consensus size: 8
53864 GACCCGACCC
53874 GACCCGTT
1 GACCCGTT
53882 GACCCGTT
1 GACCCGTT
53890 GACCCGTT
1 GACCCGTT
53898 GA-CCGTT
1 GACCCGTT
53905 GACCCACGTT
1 GA-CC-CGTT
53915 GA-CCGTT
1 GACCCGTT
53922 G
1 G
53923 TTGACCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
7 12 0.32
8 19 0.50
9 1 0.03
10 6 0.16
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:58950 original size:5 final size:5
Alignment explanation
Indices: 58940--58965 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
58930 CTGACCAGTT
58940 GACCC GACCC GACCC GACCC GACCC G
1 GACCC GACCC GACCC GACCC GACCC G
58966 TTGACCCGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.58, G:0.23, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:58973 original size:13 final size:13
Alignment explanation
Indices: 58901--58973 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
58891 AACCCGACCC
58901 GACCCGACCCGTT
1 GACCCGACCCGTT
*
58914 TACCCGACCCGTT
1 GACCCGACCCGTT
* * *
58927 TACCTGACCAGTT
1 GACCCGACCCGTT
**
58940 GACCCGACCCGACCC
1 GACCCGACCCG--TT
58955 GACCCGACCCGTT
1 GACCCGACCCGTT
58968 GACCCG
1 GACCCG
58974 TGACCGTTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
13 37 0.77
15 11 0.23
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:58991 original size:14 final size:15
Alignment explanation
Indices: 58960--59006 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
58950 GACCCGACCC
58960 GACCCGTTGACCCG-T
1 GACCCGTTGA-CCGTT
58975 GA-CCGTTGACCGTT
1 GACCCGTTGACCGTT
58989 GACCCACGTTGACCGTT
1 GA-CC-CGTTGACCGTT
59006 G
1 G
59007 TTGACCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.11
14 10 0.36
15 2 0.07
16 1 0.04
17 12 0.43
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:61901 original size:32 final size:31
Alignment explanation
Indices: 61854--61940 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 31
61844 ATCATTCTCG
** *
61854 GGTAGGCCCTGCGGCCCTAAGATGTGTTCTTA
1 GGTAGGCCCCACGGCCCTAAGATGT-ATCTTA
* * *
61886 GGTAGGCCCCACGGCCCGAA-ATCTATCTTG
1 GGTAGGCCCCACGGCCCTAAGATGTATCTTA
*
61916 GGTAGGCTCTCA-GGCCCTAAGATGT
1 GGTAGGC-CCCACGGCCCTAAGATGT
61941 TCCCTTAGGT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
30 18 0.41
31 9 0.20
32 17 0.39
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.24
Consensus pattern (31 bp):
GGTAGGCCCCACGGCCCTAAGATGTATCTTA
Found at i:63926 original size:6 final size:6
Alignment explanation
Indices: 63915--63989 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
63905 CACTTATCTA
63915 TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT
1 TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT
63963 TCCCAT TCCCAT TCCCAT TCCCAT TCC
1 TCCCAT TCCCAT TCCCAT TCCCAT TCC
63990 TATTTTGCTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.16, C:0.51, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCCAT
Found at i:69469 original size:2 final size:2
Alignment explanation
Indices: 69462--69499 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
69452 ATTATGAGTG
69462 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
69500 AAATTATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71952 original size:3 final size:3
Alignment explanation
Indices: 71944--71968 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
71934 GATTGAGAGA
71944 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
71969 GAGCCCTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:72401 original size:28 final size:28
Alignment explanation
Indices: 72369--72426 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
72359 ATTTGTAGCA
72369 TATAAATTATTTAACGATTGATTTTTGT
1 TATAAATTATTTAACGATTGATTTTTGT
72397 TATAAATTATTTAACGATTGATTTTTGT
1 TATAAATTATTTAACGATTGATTTTTGT
72425 TA
1 TA
72427 GGTGCAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (28 bp):
TATAAATTATTTAACGATTGATTTTTGT
Found at i:73848 original size:17 final size:17
Alignment explanation
Indices: 73821--73859 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
73811 AATTTACAAT
73821 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
73837 TAATTATAAATAATATC
1 TAATTATAAATAATATC
73854 TAATTA
1 TAATTA
73860 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:74238 original size:38 final size:38
Alignment explanation
Indices: 74164--74238 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
74154 TTTAATTTGT
* **
74164 CTGAAGACGTCATGCAGTCGTGAAGTTTTTTCATTTAC
1 CTGAAGACGTCATACAGTCGTGAAGTTTCATCATTTAC
* *
74202 CTGAATACGTCATACATTCGTGAAGTCTTCAT-ATTTA
1 CTGAAGACGTCATACAGTCGTGAAGT-TTCATCATTTA
74239 ATTTGAAGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 28 0.90
39 3 0.10
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (38 bp):
CTGAAGACGTCATACAGTCGTGAAGTTTCATCATTTAC
Found at i:75180 original size:19 final size:19
Alignment explanation
Indices: 75141--75181 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
75131 ATAATAATTA
*
75141 AATTTAATAATTATTTAAT
1 AATTTAATAACTATTTAAT
75160 AATTTAATAACTACTTT-AT
1 AATTTAATAACTA-TTTAAT
75179 AAT
1 AAT
75182 ATTATGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTAATAACTATTTAAT
Found at i:75327 original size:21 final size:23
Alignment explanation
Indices: 75284--75328 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
75274 TTTTTTGTAT
* *
75284 TATTATTGAATCAATTGATAATA
1 TATTATTGAATCAATTAAAAATA
75307 TATTATT-AAT-AATTAAAAATA
1 TATTATTGAATCAATTAAAAATA
75328 T
1 T
75329 GTTTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 3 0.15
23 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
TATTATTGAATCAATTAAAAATA
Found at i:75727 original size:60 final size:60
Alignment explanation
Indices: 75663--75788 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
75653 AGTCATGTGG
* ** *
75663 CCATTTTGTAACTTTTAATAGTTGAGTTACTTAACAAAGTAACATTCTATAGTCG-GAGGA
1 CCATTTTGTAACTTTTAATAGTCGAGGGACTTAACAAAATAACATTCTATAGTCGAGA-GA
* *
75723 CCATTTTGTAACTTTTAATAGTCGAGGGACTTAATAAAATAATATTCTATAGTCGAGAGA
1 CCATTTTGTAACTTTTAATAGTCGAGGGACTTAACAAAATAACATTCTATAGTCGAGAGA
75783 CCATTT
1 CCATTT
75789 ACGTACTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 57 0.97
61 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (60 bp):
CCATTTTGTAACTTTTAATAGTCGAGGGACTTAACAAAATAACATTCTATAGTCGAGAGA
Found at i:78454 original size:2 final size:2
Alignment explanation
Indices: 78449--78474 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78439 GTGTATAATC
78449 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
78475 GAGAGAGAGA
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):
TA
Found at i:78479 original size:2 final size:2
Alignment explanation
Indices: 78474--78512 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
78464 ATATATATAT
78474 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
78513 TTGAAAAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:94638 original size:59 final size:59
Alignment explanation
Indices: 94517--94644 Score: 166
Period size: 59 Copynumber: 2.2 Consensus size: 59
94507 GTAGTGCTAA
* * * ** *
94517 CCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCGTTAAGTACAGT
1 CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGT
* ** *
94576 CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATT
1 CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGT
94635 CCCGAATATG
1 CCCGAATATG
94645 CAGCATGCTG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (59 bp):
CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGT
Found at i:100377 original size:24 final size:25
Alignment explanation
Indices: 100345--100392 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
100335 CTATAAGGAT
*
100345 CGTGTCACAAGAGCACAAA-AAACG
1 CGTGCCACAAGAGCACAAAGAAACG
*
100369 CGTGCCACAAGAGCAGAAAGAAAC
1 CGTGCCACAAGAGCACAAAGAAAC
100393 ATATCACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.46, C:0.25, G:0.23, T:0.06
Consensus pattern (25 bp):
CGTGCCACAAGAGCACAAAGAAACG
Found at i:100967 original size:51 final size:52
Alignment explanation
Indices: 100912--101013 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 52
100902 ACAGCACCCC
* * *
100912 AAGCTAGATCTTCAACA-GCACCCTGCTTCAACTAGCTTTCAACACCTCACT
1 AAGCTAGACCTTCAACATGCACCCTGCTCCAACCAGCTTTCAACACCTCACT
* **
100963 AAGCTTGACCTTCAACATTTACCCTGCTCCAACCAGCTTTCAACACCTCAC
1 AAGCTAGACCTTCAACATGCACCCTGCTCCAACCAGCTTTCAACACCTCAC
101014 CAAGTTTCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 15 0.34
52 29 0.66
ACGTcount: A:0.28, C:0.37, G:0.09, T:0.25
Consensus pattern (52 bp):
AAGCTAGACCTTCAACATGCACCCTGCTCCAACCAGCTTTCAACACCTCACT
Found at i:101028 original size:52 final size:52
Alignment explanation
Indices: 100931--101039 Score: 146
Period size: 52 Copynumber: 2.1 Consensus size: 52
100921 CTTCAACAGC
* * * * *
100931 ACCCTGCTTCAACTAGCTTTCAACACCTCACTAAGCTTGACCTTCAACATTT
1 ACCCTGCTCCAACCAGCTTTCAACACCTCACCAAGCTTCACCTTCAACATAT
* **
100983 ACCCTGCTCCAACCAGCTTTCAACACCTCACCAAGTTTCTTCTTCAACATAT
1 ACCCTGCTCCAACCAGCTTTCAACACCTCACCAAGCTTCACCTTCAACATAT
101035 ACCCT
1 ACCCT
101040 ACCAAGATTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.27, C:0.38, G:0.06, T:0.29
Consensus pattern (52 bp):
ACCCTGCTCCAACCAGCTTTCAACACCTCACCAAGCTTCACCTTCAACATAT
Found at i:101052 original size:28 final size:28
Alignment explanation
Indices: 101012--101067 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
101002 TCAACACCTC
*
101012 ACCAAGTTTCTTCTTCAACATATACCCT
1 ACCAAGATTCTTCTTCAACATATACCCT
*
101040 ACCAAGATTCTTCTTCAACATTTACCCT
1 ACCAAGATTCTTCTTCAACATATACCCT
101068 GCTTCAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.04, T:0.36
Consensus pattern (28 bp):
ACCAAGATTCTTCTTCAACATATACCCT
Found at i:106129 original size:2 final size:2
Alignment explanation
Indices: 106124--106161 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
106114 TAACACACAC
106124 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
106162 TTAAAATGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108784 original size:29 final size:31
Alignment explanation
Indices: 108736--108793 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
108726 CTAATCTATG
*
108736 TTCGTTTTTCAGTTTAGTGCTTAACGTTTAT
1 TTCGTTTTTCAGTTTAGTGCATAACGTTTAT
*
108767 TTCG-TTTT-AGTTTGGTGCATAACGTTT
1 TTCGTTTTTCAGTTTAGTGCATAACGTTT
108794 CATTCTGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.68
30 4 0.16
31 4 0.16
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.53
Consensus pattern (31 bp):
TTCGTTTTTCAGTTTAGTGCATAACGTTTAT
Done.