Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008479.1 Hibiscus syriacus cultivar Beakdansim tig00111310_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: 457438
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:385813 original size:17 final size:17
Alignment explanation
Indices: 385793--385838 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
385783 GTTATGTATT
385793 TTCGTATTTTATCGTTA
1 TTCGTATTTTATCGTTA
*
385810 TTCGTATTTCATCGTTA
1 TTCGTATTTTATCGTTA
*
385827 TTCATATTTTAT
1 TTCGTATTTTAT
385839 TTACCGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.59
Consensus pattern (17 bp):
TTCGTATTTTATCGTTA
Found at i:386985 original size:20 final size:21
Alignment explanation
Indices: 386944--386985 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
386934 ATTCTCTCTT
*
386944 ATTTTATTAATTGTATTTTTA
1 ATTTTATTAATTGTATTATTA
386965 ATTTT-TTAATT-TACTTATTA
1 ATTTTATTAATTGTA-TTATTA
386985 A
1 A
386986 ACTTTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 12 0.63
21 5 0.26
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTATTAATTGTATTATTA
Found at i:387075 original size:16 final size:17
Alignment explanation
Indices: 387056--387089 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
387046 GATAATTTTT
*
387056 ATTTAATATAAA-AATA
1 ATTTAAAATAAATAATA
387072 ATTTAAAATAAATAATA
1 ATTTAAAATAAATAATA
387089 A
1 A
387090 AAAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATAAATAATA
Found at i:387100 original size:17 final size:17
Alignment explanation
Indices: 387080--387112 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
387070 TAATTTAAAA
387080 TAAATAATAAAAAATAT
1 TAAATAATAAAAAATAT
387097 TAAATAATAAAAAATA
1 TAAATAATAAAAAATA
387113 GTACATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATAATAAAAAATAT
Found at i:392929 original size:22 final size:22
Alignment explanation
Indices: 392888--392929 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
392878 ATAAATATTA
* *
392888 AAAATTCTAACAATAGTAAACT
1 AAAATTCTAACAAAAATAAACT
*
392910 AAAATTCTAAGAAAAATAAA
1 AAAATTCTAACAAAAATAAA
392930 TTCCTAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAATTCTAACAAAAATAAACT
Found at i:397882 original size:29 final size:29
Alignment explanation
Indices: 397848--397907 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
397838 CCTAAATTAA
397848 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
397877 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
397906 TT
1 TT
397908 GGTTGAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:402507 original size:29 final size:29
Alignment explanation
Indices: 402473--402532 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
402463 CCTAAATTAA
402473 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
402502 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
402531 TT
1 TT
402533 GGTGAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:410495 original size:30 final size:31
Alignment explanation
Indices: 410461--410523 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
410451 AAAAAACATT
*
410461 TTTTTAAAA-TATATAGAAATTCA-TAATTTA
1 TTTTTAAAATTATA-AAAAATTCATTAATTTA
*
410491 TTTTTAAAATTATAAAAAATTTATTAATTTA
1 TTTTTAAAATTATAAAAAATTCATTAATTTA
410522 TT
1 TT
410524 CATTCATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (31 bp):
TTTTTAAAATTATAAAAAATTCATTAATTTA
Found at i:410770 original size:13 final size:15
Alignment explanation
Indices: 410740--410769 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
410730 CCTGAAATTT
410740 AATATGTTTTTTAAA
1 AATATGTTTTTTAAA
410755 AATA-GTTTTTTAAA
1 AATATGTTTTTTAAA
410769 A
1 A
410770 TTTTTACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
AATATGTTTTTTAAA
Found at i:421372 original size:38 final size:38
Alignment explanation
Indices: 421321--421394 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
421311 TGAACAGAAT
*
421321 TTCTTACGTTTAAAATTTGAAATTTAGAGGCATTTGGC
1 TTCTTACGTTTAAAATTTGAAATTTAGAGACATTTGGC
* * *
421359 TTCTTACGTTTAAATTTTGGAGTTTAGAGACATTTG
1 TTCTTACGTTTAAAATTTGAAATTTAGAGACATTTG
421395 TCCGGTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (38 bp):
TTCTTACGTTTAAAATTTGAAATTTAGAGACATTTGGC
Found at i:422094 original size:11 final size:11
Alignment explanation
Indices: 422069--422107 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
422059 AAACTATAAC
422069 AAAAGTACAAA-
1 AAAA-TACAAAT
422080 AAAATACAAAT
1 AAAATACAAAT
422091 AAAATACAAAT
1 AAAATACAAAT
422102 AAAATA
1 AAAATA
422108 ATATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.22
11 21 0.78
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAATACAAAT
Found at i:424202 original size:30 final size:30
Alignment explanation
Indices: 424144--424202 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
424134 AATCAATATC
**
424144 CAAGTGACCAAAACTAATAAAATGATAATG
1 CAAGTGACCAAAACTAATAAAACAATAATG
424174 CAAG-GACCAAAACTTAATAAAACAATAAT
1 CAAGTGACCAAAAC-TAATAAAACAATAAT
424203 TTAAAATACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (30 bp):
CAAGTGACCAAAACTAATAAAACAATAATG
Found at i:424958 original size:15 final size:15
Alignment explanation
Indices: 424938--424969 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
424928 CAATCAAAAA
424938 ATGAATTAACGTCGC
1 ATGAATTAACGTCGC
*
424953 ATGAATTAACGTTGC
1 ATGAATTAACGTCGC
424968 AT
1 AT
424970 CGCATGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (15 bp):
ATGAATTAACGTCGC
Found at i:424974 original size:20 final size:20
Alignment explanation
Indices: 424949--424989 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
424939 TGAATTAACG
424949 TCGCATGAATTAACGTTGCA
1 TCGCATGAATTAACGTTGCA
424969 TCGCATGAATTAACGTTGCA
1 TCGCATGAATTAACGTTGCA
424989 T
1 T
424990 GGGACATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (20 bp):
TCGCATGAATTAACGTTGCA
Found at i:425048 original size:25 final size:26
Alignment explanation
Indices: 425019--425069 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
425009 AAATAGGTCT
*
425019 CCATGCCCTCCGGGCGA-CAAGGAGG
1 CCATGCACTCCGGGCGATCAAGGAGG
425044 CCATGCACTCCGGGCGATCAAGGAGG
1 CCATGCACTCCGGGCGATCAAGGAGG
425070 TCGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.22, C:0.33, G:0.35, T:0.10
Consensus pattern (26 bp):
CCATGCACTCCGGGCGATCAAGGAGG
Found at i:425508 original size:15 final size:15
Alignment explanation
Indices: 425488--425516 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
425478 GTTTGTTAGT
425488 TTAGGGTTAGGGTAG
1 TTAGGGTTAGGGTAG
425503 TTAGGGTTAGGGTA
1 TTAGGGTTAGGGTA
425517 AAAAATTACT
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:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (15 bp):
TTAGGGTTAGGGTAG
Found at i:433207 original size:23 final size:23
Alignment explanation
Indices: 433172--433230 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
433162 ATCAAGCACA
*
433172 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
433195 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
433218 ATAATAAAATAGG
1 ATAATATAATAGG
433231 CATTTAACCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:433462 original size:20 final size:20
Alignment explanation
Indices: 433416--433462 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
433406 ATTGGTAGCG
433416 CTTTACCGGTTTTATCATTT
1 CTTTACCGGTTTTATCATTT
** *
433436 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTATCAT-TT
433457 -TTTACC
1 CTTTACC
433463 TATTATATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTATCATTT
Found at i:433707 original size:182 final size:180
Alignment explanation
Indices: 433390--434038 Score: 793
Period size: 182 Copynumber: 3.6 Consensus size: 180
433380 ATTAAAGTAC
* * * * *
433390 CGACACTTTCAACATAAT-TGGTAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTTTGTCAT
1 CGACACTTTCAATAT-ATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCAT
* * * * * * *
433454 ATTTTTACCTATTATATTGTTATTGATCGATACATTTTCATAAAGTATCGACACTTTTTAGACGT
65 ATTTTTACATGTTATATTGCTATGGATCGATACATTTT-ATAAAGTATCGACACTTTATAGGCGC
*
433519 TATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
129 TATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATTAATTTAT
* ** *
433572 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACATGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCATA
* *
433637 TTCTTACATGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTATAGGCACT
66 TTTTTACATGTTATATTGCTATGGATCGATACATTT-TATAAAGTATCGACACTTTATAGGCGCT
**
433702 ATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAACGTAT
130 ATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATTAATTTAT
* * * * *
433754 CGACACTTTCAATATATCTGATAG-TTCTTTACCGGTTTTATCATTCCGTGACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCGT-TTTACCGGTTTTATCATTTCGAGACCGGTTTTATCAT
* * * * *
433818 ACTTATACATGTTATATTGTTATAGATCGATACGTTTTTATAAAGTATCGACACTTTATAGGCGC
65 ATTTTTACATGTTATATTGCTATGGATCGATAC-ATTTTATAAAGTATCGACACTTTATAGGCGC
* *
433883 TATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTAT-TTAAATCTAAT
129 TATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATT-AAT-TTAT
* * * * * * * *
433937 CGATACTTTCGATATATCCAGTAGCGGTTTACCGGTTTTATCATAAT-GAAACTGATTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCAT-TTCGAGACCGGTTTTATCAT
*
434001 ATTTTTACATGTTATATTGCTATGGAGCGATACATTTT
65 ATTTTTACATGTTATATTGCTATGGATCGATACATTTT
434039 TCATTTGTAT
Statistics
Matches: 401, Mismatches: 56, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
181 7 0.02
182 310 0.77
183 84 0.21
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (180 bp):
CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCATA
TTTTTACATGTTATATTGCTATGGATCGATACATTTTATAAAGTATCGACACTTTATAGGCGCTA
TAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTATATTAATTTAT
Found at i:436656 original size:14 final size:15
Alignment explanation
Indices: 436622--436656 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
436612 ATTCAACCAT
436622 ACAAAAATTCTAAAG
1 ACAAAAATTCTAAAG
436637 ACAAAAATTCTAAAG
1 ACAAAAATTCTAAAG
436652 A-AAAA
1 ACAAAA
436657 TATAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (15 bp):
ACAAAAATTCTAAAG
Found at i:436777 original size:31 final size:30
Alignment explanation
Indices: 436741--436818 Score: 92
Period size: 28 Copynumber: 2.7 Consensus size: 30
436731 CCAACTGAAA
436741 TTAAATGAATATAATAATTTTTCCTAAGAAT
1 TTAAAT-AATATAATAATTTTTCCTAAGAAT
*
436772 TTAAAT--TAAAATAATTTTTCCTAAGAAT
1 TTAAATAATATAATAATTTTTCCTAAGAAT
* *
436800 TCAAAT--TAAAATAATTTTT
1 TTAAATAATATAATAATTTTT
436819 ATTCAACCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 39 0.87
31 6 0.13
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (30 bp):
TTAAATAATATAATAATTTTTCCTAAGAAT
Found at i:436786 original size:28 final size:28
Alignment explanation
Indices: 436753--436818 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
436743 AAATGAATAT
*
436753 AATAATTTTTCCTAAGAATTTAAATTAA
1 AATAATTTTTCCTAAGAATTCAAATTAA
436781 AATAATTTTTCCTAAGAATTCAAATTAA
1 AATAATTTTTCCTAAGAATTCAAATTAA
436809 AATAATTTTT
1 AATAATTTTT
436819 ATTCAACCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (28 bp):
AATAATTTTTCCTAAGAATTCAAATTAA
Found at i:439088 original size:105 final size:105
Alignment explanation
Indices: 438952--439199 Score: 451
Period size: 105 Copynumber: 2.4 Consensus size: 105
438942 TTTGTCGGAT
*
438952 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGAATTTGAAA
*
439017 GGAACATGTTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
439057 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGAATTTGAAA
*
439122 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAG
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
439162 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGAT
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGAT
439200 CGGTTTATCC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 138 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGAATTTGAAA
GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:440378 original size:51 final size:53
Alignment explanation
Indices: 440183--440430 Score: 187
Period size: 52 Copynumber: 4.6 Consensus size: 53
440173 TTTTTAGTTG
* * * * **
440183 TCAAGGAACCCCTAAGAATTAGGCTTAGTTTCCTTTTAAAAACTCATTGAAAATCATCA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTT-C-TTT-CAAATTCATTTCAAA--A-CA
* * ** ** ** * *
440242 TCAAGAAACCCCTGAAAATCAAACTTAGTTTC-TAAAAACACATTTGAAAATA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCATTTCAAAACA
* * *
440294 TCAAGAAATCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTT-AAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCATTTCAAAACA
* * * *
440346 TTAAGAAACCCCT-AAAATTAGGTTTAGCTTCTTTCAAGTTCATTTCAAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCATTTCAAAACA
* * *
440398 TCGAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCT
440431 AAAAGTCTTC
Statistics
Matches: 152, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
51 27 0.18
52 60 0.39
53 26 0.17
55 12 0.08
56 1 0.01
58 1 0.01
59 25 0.16
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (53 bp):
TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCATTTCAAAACA
Found at i:440757 original size:37 final size:36
Alignment explanation
Indices: 440651--440765 Score: 115
Period size: 36 Copynumber: 3.2 Consensus size: 36
440641 GAAAAAAATG
* * * * * *
440651 TCTCAAGCGAGACAAAGTCTGTTTTAGGGGAAACTA
1 TCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTA
* ** *
440687 TCTCAAGGGAGACAAAATTTGTTTCAATAGAAACTG
1 TCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTA
440723 TCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACCTA
1 TCTCAAGGGAGAAAAAA-TTTGTTTCAAGGGAAA-CTA
440761 T-TCAA
1 TCTCAA
440766 AGATTTTGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
36 44 0.68
37 18 0.28
38 3 0.05
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (36 bp):
TCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTA
Found at i:440934 original size:37 final size:37
Alignment explanation
Indices: 440893--441086 Score: 154
Period size: 37 Copynumber: 5.4 Consensus size: 37
440883 CGAGACGATG
*
440893 TTTGTTTTGAGAGAAAAATATCTCAAGTGAAACAAAA
1 TTTGTTTTGAGAGAAAAATGTCTCAAGTGAAACAAAA
* * *
440930 TTTGTTTTAAGAGAAAAATGTCTCAAGCGAGACAAAA
1 TTTGTTTTGAGAGAAAAATGTCTCAAGTGAAACAAAA
* * *** *
440967 TTTGTTTTTA-AGAAAAA-----CAACT--TTGAAAT
1 TTTGTTTTGAGAGAAAAATGTCTCAAGTGAAACAAAA
**
440996 TGTTGTTCCGA-AGAAAAATGTCTCAAGTGAAACAAAA
1 T-TTGTTTTGAGAGAAAAATGTCTCAAGTGAAACAAAA
* * * *
441033 TTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACGACAT
1 TTTGTTTTGAGAGAAAAATGTCTCAAGTGAAAC-AAAA
*
441071 TTTGTTTCGAGAGAAA
1 TTTGTTTTGAGAGAAA
441087 CAACACCCAA
Statistics
Matches: 120, Mismatches: 27, Indels: 19
0.72 0.16 0.11
Matches are distributed among these distances:
29 4 0.03
30 13 0.11
31 3 0.03
35 4 0.03
36 13 0.11
37 67 0.56
38 16 0.13
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (37 bp):
TTTGTTTTGAGAGAAAAATGTCTCAAGTGAAACAAAA
Found at i:445592 original size:15 final size:15
Alignment explanation
Indices: 445574--445605 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
445564 TCAACCATAC
*
445574 AAAATTCTAAGGAAA
1 AAAATTCTAAAGAAA
445589 AAAATTCTAAAGAAA
1 AAAATTCTAAAGAAA
445604 AA
1 AA
445606 TATAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (15 bp):
AAAATTCTAAAGAAA
Found at i:446307 original size:30 final size:31
Alignment explanation
Indices: 446272--446330 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
446262 ATATCATGCT
* * *
446272 ATAATATTATATACAAAGT-AATATATAATA
1 ATAATAATATAAACAAAATAAATATATAATA
446302 ATAATAATATAAACAAAATAAATATATAA
1 ATAATAATATAAACAAAATAAATATATAA
446331 AACATAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (31 bp):
ATAATAATATAAACAAAATAAATATATAATA
Found at i:450388 original size:18 final size:19
Alignment explanation
Indices: 450367--450407 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
450357 AAAATGAGAG
* *
450367 AAATTCAGAAAA-TGTCAA
1 AAATTAAGAAAATTCTCAA
450385 AAA-TAAGAAAATTCTCAA
1 AAATTAAGAAAATTCTCAA
450403 AAATT
1 AAATT
450408 TTATACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.37
18 11 0.58
19 1 0.05
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (19 bp):
AAATTAAGAAAATTCTCAA
Found at i:451428 original size:80 final size:77
Alignment explanation
Indices: 451297--451458 Score: 213
Period size: 80 Copynumber: 2.1 Consensus size: 77
451287 ACGGAATCCC
* * *
451297 TGCAAGTAATATGAAGGACAACTTCTCAATTTACATTGAGGTCAAATTTATAAC-AGATATTTAG
1 TGCAAGTAAAATGAAGGACAACTTCTCAATTTACATTCAGATCAAATTTATAACTA-ATATTTA-
451361 AGACCA-CTGCTAAT
64 AGA-CAGCTGCTAAT
451375 TGCAAGTAAAATGAAGGACTAAACTTCTCAAATTT-CATTCAGATCAAATTTATAACTAATATTT
1 TGCAAGTAAAATGAAGGAC--AACTTCTC-AATTTACATTCAGATCAAATTTATAACTAATATTT
*
451439 AAGACAGCTGCTCAT
63 AAGACAGCTGCTAAT
451454 TGCAA
1 TGCAA
451459 CATAATCTAA
Statistics
Matches: 75, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
78 20 0.27
79 15 0.20
80 34 0.45
81 6 0.08
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (77 bp):
TGCAAGTAAAATGAAGGACAACTTCTCAATTTACATTCAGATCAAATTTATAACTAATATTTAAG
ACAGCTGCTAAT
Found at i:457028 original size:8 final size:8
Alignment explanation
Indices: 457015--457053 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
457005 TCATTTTCAG
457015 GAATTTGA
1 GAATTTGA
457023 GAATTT-A
1 GAATTTGA
* *
457030 GAGTTTGG
1 GAATTTGA
457038 GAATTTGA
1 GAATTTGA
457046 GAATTTGA
1 GAATTTGA
457054 AAGATTGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (8 bp):
GAATTTGA
Found at i:457347 original size:127 final size:127
Alignment explanation
Indices: 457120--457425 Score: 564
Period size: 127 Copynumber: 2.4 Consensus size: 127
457110 TCTATAATCG
457120 TTCACTATTCATATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCATATGAAGGCGCGTTCCCGGGG-CGCGCCTTCCATTATTTCGTCAGAGAATATGT
457185 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
65 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
457248 TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTT
1 TTCACTATTCATATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTT
457313 ATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 ATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
457375 TTCACTATTCATATGAAGGCGCGTTCCCGGGG-GCGCGC--CCATTATTTCGTC
1 TTCACTATTCATATGAAGGCGCGTTCCCGGGGCGCGC-CTTCCATTATTTCGTC
457426 GTTATCATTG
Statistics
Matches: 175, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
125 13 0.07
126 4 0.02
127 127 0.73
128 31 0.18
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (127 bp):
TTCACTATTCATATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTT
ATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Done.