Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009013.1 Hibiscus syriacus cultivar Beakdansim tig00112401_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: 323053
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:240547 original size:12 final size:12
Alignment explanation
Indices: 240530--240562 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
240520 CATTCAATAT
240530 TCACATTTCATA
1 TCACATTTCATA
*
240542 TCACATTCCATA
1 TCACATTTCATA
240554 TCA-ATTTCA
1 TCACATTTCA
240563 CATTCCCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (12 bp):
TCACATTTCATA
Found at i:243494 original size:20 final size:20
Alignment explanation
Indices: 243460--243509 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
243450 GTTATACTAC
* * *
243460 GTTGAAAATTAATGTTTGAGT
1 GTTG-AAATTGATGTTAGAAT
243481 GTTGAAATTGATGTTAGAAT
1 GTTGAAATTGATGTTAGAAT
243501 G-TGAAATTG
1 GTTGAAATTG
243510 GATCATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 8 0.31
20 14 0.54
21 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (20 bp):
GTTGAAATTGATGTTAGAAT
Found at i:244088 original size:26 final size:27
Alignment explanation
Indices: 244035--244088 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
244025 ATGTTATTTA
*
244035 TCATATATTTGACATGTTTTAAATATG
1 TCATATATTTGACATGTTTTAAACATG
244062 TCATATATTTGA-ATGTTTTAAACATG
1 TCATATATTTGACATGTTTTAAACATG
244088 T
1 T
244089 TAATTCGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (27 bp):
TCATATATTTGACATGTTTTAAACATG
Found at i:244357 original size:69 final size:69
Alignment explanation
Indices: 244238--244366 Score: 195
Period size: 69 Copynumber: 1.9 Consensus size: 69
244228 GCATATCGGA
* * *
244238 TTAGCACTATAGTGTATACCCAAGACACTTAGTACAGGTGGTGGGAACGACCTTATGTGTCATAT
1 TTAGCACTAGAGTGTATACCCAAGACACTTAGTACAGATGGTAGGAACGACCTTATGTGTCATAT
244303 TGAT
66 TGAT
** * *
244307 TTAGCACTAGAGTGTATACCCAAGACACTTAGTGTATATGGTAGGCACGACCTTATGTGT
1 TTAGCACTAGAGTGTATACCCAAGACACTTAGTACAGATGGTAGGAACGACCTTATGTGT
244367 ATTCGCACTG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (69 bp):
TTAGCACTAGAGTGTATACCCAAGACACTTAGTACAGATGGTAGGAACGACCTTATGTGTCATAT
TGAT
Found at i:251137 original size:16 final size:17
Alignment explanation
Indices: 251104--251137 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
251094 GAATTTATGG
*
251104 GAACAACTAAATAAATA
1 GAACAAATAAATAAATA
251121 GAACAAATAAA-AAATA
1 GAACAAATAAATAAATA
251137 G
1 G
251138 CGGTATGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.15
Consensus pattern (17 bp):
GAACAAATAAATAAATA
Found at i:260625 original size:24 final size:24
Alignment explanation
Indices: 260598--260695 Score: 153
Period size: 24 Copynumber: 4.1 Consensus size: 24
260588 AAACCGAGAT
*
260598 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
260622 ATCA-AATATCATAACAGAATCCAG
1 ATCAGAA-ATCAGAACAGAATTCAG
260646 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
260670 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
260694 AT
1 AT
260696 AAAACATTCA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
23 2 0.03
24 64 0.94
25 2 0.03
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:260658 original size:12 final size:12
Alignment explanation
Indices: 260598--260695 Score: 83
Period size: 12 Copynumber: 8.2 Consensus size: 12
260588 AAACCGAGAT
*
260598 ATCAGAAATCAA
1 ATCAGAAATCAG
* *
260610 AACAGAATTCAG
1 ATCAGAAATCAG
*
260622 ATCA-AATATCAT
1 ATCAGAA-ATCAG
*
260634 AACAG-AATCCAG
1 ATCAGAAAT-CAG
260646 ATCAGAAATCAG
1 ATCAGAAATCAG
* *
260658 AACAGAATTCAG
1 ATCAGAAATCAG
260670 ATCAGAAATCAG
1 ATCAGAAATCAG
* *
260682 AACAGAATTCAG
1 ATCAGAAATCAG
260694 AT
1 AT
260696 AAAACATTCA
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
11 4 0.06
12 59 0.89
13 3 0.05
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.18
Consensus pattern (12 bp):
ATCAGAAATCAG
Found at i:262677 original size:20 final size:19
Alignment explanation
Indices: 262631--262679 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
262621 AAAATTTAGT
*
262631 GGAAGAGAATATTTTCTAA
1 GGAAGAAAATATTTTCTAA
262650 GGAGAGAAAATATTTT-TCAA
1 GGA-AGAAAATATTTTCT-AA
262670 GAGAAGAAAA
1 G-GAAGAAAA
262680 ATTATTGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 20 0.77
21 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.22, T:0.24
Consensus pattern (19 bp):
GGAAGAAAATATTTTCTAA
Found at i:264357 original size:22 final size:22
Alignment explanation
Indices: 264332--264374 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
264322 AATTGGATTG
*
264332 TTAGCTTATTC-TCTTTTTAGTC
1 TTAG-TTATTCTTCTTCTTAGTC
*
264354 TTAGTTTTTCTTCTTCTTAGT
1 TTAGTTATTCTTCTTCTTAGT
264375 TTTCGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.16, G:0.09, T:0.63
Consensus pattern (22 bp):
TTAGTTATTCTTCTTCTTAGTC
Found at i:264382 original size:22 final size:22
Alignment explanation
Indices: 264343--264384 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
264333 TAGCTTATTC
*
264343 TCTTTTTAGTCTTAGTTTTTCT
1 TCTTCTTAGTCTTAGTTTTTCT
* *
264365 TCTTCTTAGTTTTCGTTTTT
1 TCTTCTTAGTCTTAGTTTTT
264385 AACTTTTTAC
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:0.07, C:0.14, G:0.10, T:0.69
Consensus pattern (22 bp):
TCTTCTTAGTCTTAGTTTTTCT
Found at i:267936 original size:55 final size:55
Alignment explanation
Indices: 267848--267956 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
267838 AAGTAAAATG
* * *
267848 GTTTACTTAAGACGACAATTGTATCCTTTCAAAGAATCATTTCAAGAATTGAACT
1 GTTTACTTAAGACGACAACTGCATCCTTACAAAGAATCATTTCAAGAATTGAACT
*
267903 GTTTACTTAAGACTACAACTGCATCCTTACAAAGAATCATTTCAAGAATTGAAC
1 GTTTACTTAAGACGACAACTGCATCCTTACAAAGAATCATTTCAAGAATTGAAC
267957 GACTAATTGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (55 bp):
GTTTACTTAAGACGACAACTGCATCCTTACAAAGAATCATTTCAAGAATTGAACT
Found at i:272104 original size:60 final size:60
Alignment explanation
Indices: 271990--272108 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
271980 AATAGTCGCA
* * * *
271990 TGATTATTTTATAACTTTTAATAGACGAGGGATTGAACAAAATAATATCTTATAATTAAT
1 TGATTATTTTATAACTTTTAATAGACGAGGAATTGAACAAAACAATACCATATAATTAAT
* ** * *
272050 TGATTATTTTATAATTTTTAATAGTTGATGAACTT-AACAAAACAGTACCATATAATTAA
1 TGATTATTTTATAACTTTTAATAGACGAGGAA-TTGAACAAAACAATACCATATAATTAA
272109 GGAACATTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (60 bp):
TGATTATTTTATAACTTTTAATAGACGAGGAATTGAACAAAACAATACCATATAATTAAT
Found at i:277425 original size:44 final size:45
Alignment explanation
Indices: 277305--277430 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
277295 TATAAAATCC
* *
277305 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
277350 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
277397 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
277431 GTATGCTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 24 0.33
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:277631 original size:59 final size:59
Alignment explanation
Indices: 277539--277667 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 59
277529 CGTAGTGCTA
* * ** *
277539 TCCCGAATATGACACATAAGGTCATGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAAGTATCCTTAAGTACAG
* * ** *
277598 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAAGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAAGTATCCTTAAGTACAG
277657 TCCCGAATATG
1 TCCCGAATATG
277668 CAGCCTGCTG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAAGTATCCTTAAGTACAG
Found at i:285081 original size:59 final size:58
Alignment explanation
Indices: 284946--285082 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 58
284936 ATAAGCACCG
* * **
284946 TAGTGCTATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
* **
285005 AAGTACAGTCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
*
285064 TAGTGTATTCCCAAATATG
1 TAGTGTA-TCCCGAATATG
285083 CAGCCTGCTG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.02
59 64 0.98
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
Found at i:294488 original size:23 final size:23
Alignment explanation
Indices: 294439--294492 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
294429 TATATTTTTA
**
294439 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAG
*
294462 ATATTATAATAATATAAT-ATAAG
1 ATATTATAATAAAATAATCA-AAG
294485 ATATTATA
1 ATATTATA
294493 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAG
Found at i:294636 original size:24 final size:23
Alignment explanation
Indices: 294609--294677 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
294599 ATATTTAATA
294609 TTAATAAA-ATAATTTAATAATATT
1 TTAATAAAGAT-ATTTAA-AATATT
*
294633 TTAATAAAGATATTTAAAATATA
1 TTAATAAAGATATTTAAAATATT
* * * *
294656 CTAATTAATATTTTTAAAATAT
1 TTAATAAAGATATTTAAAATAT
294678 AATATAACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 23 0.59
24 14 0.36
25 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (23 bp):
TTAATAAAGATATTTAAAATATT
Found at i:294797 original size:14 final size:14
Alignment explanation
Indices: 294778--294821 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
294768 TTCCAGAAAT
294778 ATAATTCATTTTTC
1 ATAATTCATTTTTC
*
294792 ATAATTCAATTTTC
1 ATAATTCATTTTTC
*
294806 AATAATTTATTTTTC
1 -ATAATTCATTTTTC
294821 A
1 A
294822 GAGTTCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAATTCATTTTTC
Found at i:294810 original size:15 final size:14
Alignment explanation
Indices: 294778--294832 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
294768 TTCCAGAAAT
*
294778 ATAATTCATTTTTC
1 ATAATTCAATTTTC
294792 ATAATTCAATTTTC
1 ATAATTCAATTTTC
* *
294806 AATAATTTATTTTTC
1 -ATAATTCAATTTTC
* *
294821 AGAGTTCAATTT
1 ATAATTCAATTT
294833 CAAAAATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.53
Consensus pattern (14 bp):
ATAATTCAATTTTC
Found at i:294843 original size:29 final size:29
Alignment explanation
Indices: 294780--294841 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
294770 CCAGAAATAT
* * *
294780 AATTCATTTTTCATAATTCAATTTTCAAT
1 AATTTATTTTTCAGAATTCAATTTTCAAA
*
294809 AATTTATTTTTCAGAGTTCAA-TTTCAAA
1 AATTTATTTTTCAGAATTCAATTTTCAAA
294837 AATTT
1 AATTT
294842 TAATTTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.50
Consensus pattern (29 bp):
AATTTATTTTTCAGAATTCAATTTTCAAA
Found at i:296391 original size:3 final size:3
Alignment explanation
Indices: 296383--296408 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
296373 CGTCCCAATG
296383 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
296409 TTGTGCATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:298625 original size:82 final size:82
Alignment explanation
Indices: 298478--298647 Score: 243
Period size: 82 Copynumber: 2.1 Consensus size: 82
298468 TTTCTCTTGA
* *
298478 ATCAATATTAATTTTTAAGACGAAATAGATATATCTCTTCATTTCAATTGGAGTAATAAAAGACT
1 ATCATTATTAATTTTTAAGACGAAATAGATATATCTCTTCATTTCAATTAGAGTAATAAAAGACT
298543 ACTTTAAGGCATGAGAG
66 ACTTTAAGGCATGAGAG
* *** *
298560 ATCATTATTGATTTTTAAGACGAAATA-ATGATATCTCTTCATTTTGGTTAGAGTAATAAATGAC
1 ATCATTATTAATTTTTAAGACGAAATAGAT-ATATCTCTTCATTTCAATTAGAGTAATAAAAGAC
*
298624 TACTTTAAGGCATGATAG
65 TACTTTAAGGCATGAGAG
*
298642 GTCATT
1 ATCATT
298648 TATTCTCAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 2 0.03
82 76 0.97
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (82 bp):
ATCATTATTAATTTTTAAGACGAAATAGATATATCTCTTCATTTCAATTAGAGTAATAAAAGACT
ACTTTAAGGCATGAGAG
Found at i:305793 original size:36 final size:37
Alignment explanation
Indices: 305768--305850 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
305758 CTTGAGATTA
*
305768 CTTTCTTAAAAACAAATTTTGTCTCACTTAAGACAAT
1 CTTTCTTAAAAACAAATTTCGTCTCACTTAAGACAAT
* * * *
305805 TTTTCTTAAAAATAAATTTCGTCACACTTAAGACAGT
1 CTTTCTTAAAAACAAATTTCGTCTCACTTAAGACAAT
*
305842 CTTCCTTAA
1 CTTTCTTAA
305851 GACACACACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (37 bp):
CTTTCTTAAAAACAAATTTCGTCTCACTTAAGACAAT
Found at i:305813 original size:37 final size:37
Alignment explanation
Indices: 305769--305839 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
305759 TTGAGATTAC
* *
305769 TTTCTTAAAAACAAATTTTGTCTCACTTAAGACAATT
1 TTTCTTAAAAACAAATTTCGTCACACTTAAGACAATT
*
305806 TTTCTTAAAAATAAATTTCGTCACACTTAAGACA
1 TTTCTTAAAAACAAATTTCGTCACACTTAAGACA
305840 GTCTTCCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (37 bp):
TTTCTTAAAAACAAATTTCGTCACACTTAAGACAATT
Found at i:306235 original size:67 final size:67
Alignment explanation
Indices: 306158--306571 Score: 415
Period size: 67 Copynumber: 6.0 Consensus size: 67
306148 AACAAAATTG
* * *
306158 ATAAACCTTTGAGATTGATTCTCTCAAAACAAAGTTTTGTCTCGCCTGAGACAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
306223 AC
66 AC
* * * *
306225 TTAAACCTTTGGGATTGTTTCTCTCGAAACAAAGTTTTATCTCAG-TTGAGACAATTTCTCTTGA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTC-GCTTGAGACAGTTTCTCTTGA
306289 AAC
65 AAC
*
306292 ATAAACCTTTGAGATTGTTTCTCTCGAAACAACGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
306357 AC
66 AC
* *
306359 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAA-TTTTGTCTCGCTTGAGACAGTTTCT-TTCGA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTT-GA
306422 AAC
65 AAC
*** * * * * * * *
306425 AAGTTTTGTCTCTTTTAAGATAGTTTCTCTTGAAATAAA-TTTTGTCTTGCTTGAGACAATTTAT
1 -A---TAAAC-C-TTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCT
*
306489 TTTGAAAC
60 CTTGAAAC
* ** * *
306497 A-AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTT
1 ATAA------AC-CT-TTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTT
306561 CTCTTGAAAC
58 CTCTTGAAAC
306571 A
1 A
306572 AAAATTTGTC
Statistics
Matches: 294, Mismatches: 35, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
65 2 0.01
66 31 0.11
67 149 0.51
68 1 0.00
70 2 0.01
71 2 0.01
72 50 0.17
73 28 0.10
74 29 0.10
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (67 bp):
ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
AC
Found at i:306292 original size:37 final size:37
Alignment explanation
Indices: 306241--306610 Score: 291
Period size: 37 Copynumber: 10.5 Consensus size: 37
306231 CTTTGGGATT
* * *
306241 GTTTCTCTCGAAACAAAGTTTTATCTCAGTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTGTTGAGACA
* * **
306278 ATTTCTCTTGAAACATAA------AC-CT-TTGAGATT
1 GTTTCTCTTGAAACA-AAGTTTTGTCTCTGTTGAGACA
* *
306308 GTTTCTCTCGAAACAACGTTTTGTCTC-GCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTG-TTGAGACA
* **
306345 GTTTCTCTTGAAACATAA------AC-CT-TTGAGATT
1 GTTTCTCTTGAAACA-AAGTTTTGTCTCTGTTGAGACA
*
306375 GTTTCCCTTGAAACAAA-TTTTGTCTC-GCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTG-TTGAGACA
* * *
306411 GTTTCT-TTCGAAAC-AAGTTTTGTCTCTTTTAAGATA
1 GTTTCTCTT-GAAACAAAGTTTTGTCTCTGTTGAGACA
*
306447 GTTTCTCTTGAAATAAA-TTTTGTCT-TGCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTG-TTGAGACA
* * * *
306483 ATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTGTTGAGACA
*
306520 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTGTTGAGACA
** * *
306557 GTTTCTCTTGAAACAAAAATTTGTCTCTCTTGAGATA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTGTTGAGACA
306594 GTTTCTCTTGAAACAAA
1 GTTTCTCTTGAAACAAA
306611 TTATCCCTAA
Statistics
Matches: 265, Mismatches: 40, Indels: 56
0.73 0.11 0.16
Matches are distributed among these distances:
29 3 0.01
30 39 0.15
31 2 0.01
32 2 0.01
34 1 0.00
35 7 0.03
36 69 0.26
37 138 0.52
38 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (37 bp):
GTTTCTCTTGAAACAAAGTTTTGTCTCTGTTGAGACA
Found at i:306313 original size:30 final size:30
Alignment explanation
Indices: 306279--306389 Score: 87
Period size: 30 Copynumber: 3.5 Consensus size: 30
306269 GTTGAGACAA
306279 TTTCTCTTGAAACATAAACCTTTGAGATTG
1 TTTCTCTTGAAACATAAACCTTTGAGATTG
* *** * **
306309 TTTCTCTCGAAACAACGTTTTGTCTCGCTTGAGACAG
1 TTTCTCTTGAAAC-A----TAAAC-C-TTTGAGATTG
306346 TTTCTCTTGAAACATAAACCTTTGAGATTG
1 TTTCTCTTGAAACATAAACCTTTGAGATTG
*
306376 TTTCCCTTGAAACA
1 TTTCTCTTGAAACA
306390 AATTTTGTCT
Statistics
Matches: 59, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
30 32 0.54
31 2 0.03
32 2 0.03
35 2 0.03
36 2 0.03
37 19 0.32
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (30 bp):
TTTCTCTTGAAACATAAACCTTTGAGATTG
Found at i:306415 original size:36 final size:36
Alignment explanation
Indices: 306308--306612 Score: 322
Period size: 37 Copynumber: 8.5 Consensus size: 36
306298 CTTTGAGATT
* * *
306308 GTTTCTCTCGAAACAACGTTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAA-ATTTTGTCTCTCTTGAGACA
* **
306345 GTTTCTCTTGAAACATAA-----AC-CT-TTGAGATT
1 GTTTCTCTTGAAACA-AATTTTGTCTCTCTTGAGACA
* *
306375 GTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * *
306411 GTTTCT-TTCGAAACAAGTTTTGTCTCTTTTAAGATA
1 GTTTCTCTT-GAAACAAATTTTGTCTCTCTTGAGACA
*
306447 GTTTCTCTTGAAATAAATTTTGTCT-TGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCT-CTTGAGACA
* * *
306483 ATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
306520 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* *
306557 GTTTCTCTTGAAACAAAAATTTGTCTCTCTTGAGATA
1 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
306594 GTTTCTCTTGAAACAAATT
1 GTTTCTCTTGAAACAAATT
306613 ATCCCTAAAG
Statistics
Matches: 222, Mismatches: 32, Indels: 29
0.78 0.11 0.10
Matches are distributed among these distances:
29 2 0.01
30 20 0.09
31 1 0.00
32 1 0.00
34 1 0.00
35 4 0.02
36 76 0.34
37 112 0.50
38 5 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:306559 original size:20 final size:20
Alignment explanation
Indices: 306499--306560 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 20
306489 TTTGAAACAA
306499 AGTTTTGTCTCTCTTGAGAC
1 AGTTTTGTCTCTCTTGAGAC
*
306519 AG---T-T-TCTCTTGAAAC
1 AGTTTTGTCTCTCTTGAGAC
306534 AAAGTTTTGTCTCTCTTGAGAC
1 --AGTTTTGTCTCTCTTGAGAC
306556 AGTTT
1 AGTTT
306561 CTCTTGAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 10 0.30
16 1 0.03
17 3 0.09
20 8 0.24
21 1 0.03
22 10 0.30
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (20 bp):
AGTTTTGTCTCTCTTGAGAC
Found at i:306857 original size:139 final size:139
Alignment explanation
Indices: 306607--307032 Score: 541
Period size: 139 Copynumber: 3.1 Consensus size: 139
306597 TCTCTTGAAA
* * * *
306607 CAAATTATCCCTAAAGACAGCTAGATGTCCTCATCAAGTAGGAACAATGTCGTCAACCGACCAGA
1 CAAATTATCCCTAAAGATAGCTAGACGTCCTCATCAAGTAGGAACAATGTCGTCCACCGACTAGA
* * *** * * **
306672 TCTTCTCATCACGTGGGAGTAACATCATCCTTATATAACCAGACTTCCTCATCATATAGGAACCG
66 TCTTCTCATCACGTAGGAGCAGTGTCATCCTTAGATAACTAGACTTCCTCATCACGTAGGAACCG
*
306737 TGTTATCTT
131 TGTTATCTC
* *
306746 CAAATTATCCCTAAAGATAGCTAGACGTCCTCATCATGTAGGAACATTGTCGTCCACCGACTAGA
1 CAAATTATCCCTAAAGATAGCTAGACGTCCTCATCAAGTAGGAACAATGTCGTCCACCGACTAGA
* *
306811 TCTCCTCATCACGTAGGAGCAGTGTCATCCTCAGATAACTAGACTTCCTCATCACGTAGGAACCG
66 TCTTCTCATCACGTAGGAGCAGTGTCATCCTTAGATAACTAGACTTCCTCATCACGTAGGAACCG
*
306876 TGTTGTCTC
131 TGTTATCTC
* * * * * *
306885 CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAAAAATGTCTTCCACTGA-TAAG
1 CAAATTATCCCTAAAGATAGCTAGACGTCCTCATCAAGTAGGAACAATGTCGTCCACCGACT-AG
* * *
306949 ATATTCTCATCACATAGGAGCAGTGTCATCCTTAGACAA-TCAGACTTCCTCATCACGTAGGAAC
65 ATCTTCTCATCACGTAGGAGCAGTGTCATCCTTAGATAACT-AGACTTCCTCATCACGTAGGAAC
* *
307013 CGTGTTGTCAC
129 CGTGTTATCTC
*
307024 TAAATTATC
1 CAAATTATC
307033 TTCAAATTGA
Statistics
Matches: 252, Mismatches: 33, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
138 2 0.01
139 250 0.99
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (139 bp):
CAAATTATCCCTAAAGATAGCTAGACGTCCTCATCAAGTAGGAACAATGTCGTCCACCGACTAGA
TCTTCTCATCACGTAGGAGCAGTGTCATCCTTAGATAACTAGACTTCCTCATCACGTAGGAACCG
TGTTATCTC
Found at i:308646 original size:8 final size:8
Alignment explanation
Indices: 308633--308667 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
308623 TTTCATTTCA
308633 TATTTTTT
1 TATTTTTT
308641 TATTTTTTT
1 TA-TTTTTT
308650 TATTTTTT
1 TATTTTTT
308658 TATTTTTT
1 TATTTTTT
308666 TA
1 TA
308668 ATTTGTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TATTTTTT
Found at i:308649 original size:9 final size:9
Alignment explanation
Indices: 308635--308671 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
308625 TCATTTCATA
308635 TTTTTTTAT
1 TTTTTTTAT
308644 TTTTTTTA-
1 TTTTTTTAT
308652 TTTTTTTAT
1 TTTTTTTAT
*
308661 TTTTTTAAT
1 TTTTTTTAT
308670 TT
1 TT
308672 GTTAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:308653 original size:17 final size:17
Alignment explanation
Indices: 308633--308671 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
308623 TTTCATTTCA
308633 TATTTTTTTATTTTTTT
1 TATTTTTTTATTTTTTT
308650 TATTTTTTTATTTTTTT
1 TATTTTTTTATTTTTTT
*
308667 AATTT
1 TATTT
308672 GTTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
TATTTTTTTATTTTTTT
Found at i:311069 original size:6 final size:6
Alignment explanation
Indices: 311058--311087 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
311048 ATAGTTTCTC
311058 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
311088 CTTTTTGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:314579 original size:19 final size:18
Alignment explanation
Indices: 314555--314641 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 18
314545 ATTTCGCCTG
314555 AATGAAGAAAAAAAGGAAA
1 AATGAAGAAAAAAA-GAAA
* *
314574 AATGAAAAATAAAAATAAA
1 AATGAAGAA-AAAAAGAAA
*
314593 AA--AAGAAAAGAA-AAA
1 AATGAAGAAAAAAAGAAA
*
314608 AATG-AGAAAAATAGAAA
1 AATGAAGAAAAAAAGAAA
*
314625 AA-GAA-AGAAAAAGAAA
1 AATGAAGAAAAAAAGAAA
314641 A
1 A
314642 GAGAATAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
15 5 0.09
16 22 0.40
17 10 0.18
19 13 0.24
20 5 0.09
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (18 bp):
AATGAAGAAAAAAAGAAA
Found at i:314588 original size:14 final size:14
Alignment explanation
Indices: 314563--314630 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 14
314553 TGAATGAAGA
*
314563 AAAAAAGGAAAAAT
1 AAAAAATGAAAAAT
*
314577 GAAAAAT-AAAAAT
1 AAAAAATGAAAAAT
*
314590 AAAAAAAGAAAAGA-
1 AAAAAATGAAAA-AT
314604 AAAAAATGAGAAAAAT
1 AAAAAAT--GAAAAAT
314620 AGAAAAA-GAAA
1 A-AAAAATGAAA
314631 GAAAAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
13 11 0.26
14 19 0.44
15 2 0.05
16 6 0.14
17 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.07
Consensus pattern (14 bp):
AAAAAATGAAAAAT
Found at i:314618 original size:30 final size:31
Alignment explanation
Indices: 314562--314654 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 31
314552 CTGAATGAAG
* *
314562 AAAAA-AAGGAAAAATGAAAA-ATAAAAATAA
1 AAAAAGAAAGAAAAA-GAAAAGAGAAAAATAA
* *
314592 AAAAAGAAA-AGAAAA-AAATGAGAAAAATAG
1 AAAAAGAAAGA-AAAAGAAAAGAGAAAAATAA
314622 AAAAAGAAAGAAAAAGAAAAGAGAATAAATAA
1 AAAAAGAAAGAAAAAGAAAAGAGAA-AAATAA
314654 A
1 A
314655 GGGGGTTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
29 3 0.06
30 27 0.53
31 15 0.29
32 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (31 bp):
AAAAAGAAAGAAAAAGAAAAGAGAAAAATAA
Done.