Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007881.1 Hibiscus syriacus cultivar Beakdansim tig00110259_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: 148206
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4614 original size:14 final size:14
Alignment explanation
Indices: 4597--4632 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4587 TAAAAACAGA
*
4597 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
4611 AAATTAGAGGAATG
1 AAATTAAAGGAATG
4625 AAATTAAA
1 AAATTAAA
4633 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:9794 original size:20 final size:20
Alignment explanation
Indices: 9769--9808 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9759 CGTTGGGCTT
9769 GATACTACTGTAGCAGTATC
1 GATACTACTGTAGCAGTATC
* *
9789 GATACTATTGTAGTAGTATC
1 GATACTACTGTAGCAGTATC
9809 AGTATCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
GATACTACTGTAGCAGTATC
Found at i:9894 original size:20 final size:20
Alignment explanation
Indices: 9837--9897 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
9827 GATGTTTTTT
* *
9837 AGTATCGGTACTATTCACAC
1 AGTATCGATACTATTCATAC
9857 AGTATCGATACTATTCATAC
1 AGTATCGATACTATTCATAC
*
9877 AGTATTGATACTATTCATAC
1 AGTATCGATACTATTCATAC
9897 A
1 A
9898 ATAATATTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTATTCATAC
Found at i:16160 original size:43 final size:42
Alignment explanation
Indices: 16037--16392 Score: 264
Period size: 42 Copynumber: 8.3 Consensus size: 42
16027 TTTTATCGTA
* *
16037 ATAATTGAGGCCTCTAATTTTTGT-AATCCTAC-TTTTATCTTT
1 ATAATTGAAGCC-CTAATTTTT-TCAATCCTACTTTTTACCTTT
* * * * *
16079 ATAATTGATGCCTTTAATTTTTTTAATCCCACTCTTTTACATTT
1 ATAATTGAAGCC-CTAATTTTTTCAATCCTACT-TTTTACCTTT
*
16123 ATGATTGATAGCCCTAATTTTTTCAATCCTACTTTTTACCTTT
1 ATAATTGA-AGCCCTAATTTTTTCAATCCTACTTTTTACCTTT
* *
16166 ATAATTG-AGCTCCTAAATTTTTCAAT-CTCACTTTCTACCTTT
1 ATAATTGAAGC-CCTAATTTTTTCAATCCT-ACTTTTTACCTTT
* * *
16208 ATAATTGAGGCCCCTAATTTATT-AATCAC-ATTTTTTACCTTT
1 ATAATTGAAG-CCCTAATTTTTTCAATC-CTACTTTTTACCTTT
* *
16250 ATAATTGAGACCCCTGA-TTTTTCAAT-CTCACTTTTTACCTTT
1 ATAATTGA-AGCCCTAATTTTTTCAATCCT-ACTTTTTACCTTT
* * *
16292 AAAATTGAGGACCCTAAATTTTTT-AAT-CTCATTTTTTACCTTT
1 ATAATTGAAG-CCCT-AATTTTTTCAATCCT-ACTTTTTACCTTT
* ** * * * *
16335 ATAATTGAGATCTTTAAGTTTTTGAATCGTACTTTTTTACTTTT
1 ATAATTGA-AGCCCTAATTTTTTCAATCCTAC-TTTTTACCTTT
*
16379 ATAATTTAAGCCCT
1 ATAATTGAAGCCCT
16393 TTAGTTTAAT
Statistics
Matches: 251, Mismatches: 42, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
40 1 0.00
41 10 0.04
42 120 0.48
43 60 0.24
44 57 0.23
45 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (42 bp):
ATAATTGAAGCCCTAATTTTTTCAATCCTACTTTTTACCTTT
Found at i:16270 original size:84 final size:86
Alignment explanation
Indices: 16155--16344 Score: 296
Period size: 84 Copynumber: 2.2 Consensus size: 86
16145 TCAATCCTAC
* * *
16155 TTTTTACCTTTATAATTGAG-CTCCTAAATTTTTCAATCTCACTTTCTACCTTTATAATTGAGGC
1 TTTTTACCTTTATAATTGAGACCCCTAAATTTTTCAATCTCACTTTCTACCTTTAAAATTGAGGA
16219 CCCT-AATTTATTAATCACAT
66 CCCTAAATTTATTAATCACAT
* *
16239 TTTTTACCTTTATAATTGAGACCCCT-GATTTTTCAATCTCACTTTTTACCTTTAAAATTGAGGA
1 TTTTTACCTTTATAATTGAGACCCCTAAATTTTTCAATCTCACTTTCTACCTTTAAAATTGAGGA
* *
16303 CCCTAAATTTTTTAATCTCAT
66 CCCTAAATTTATTAATCACAT
16324 TTTTTACCTTTATAATTGAGA
1 TTTTTACCTTTATAATTGAGA
16345 TCTTTAAGTT
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
84 58 0.60
85 39 0.40
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.46
Consensus pattern (86 bp):
TTTTTACCTTTATAATTGAGACCCCTAAATTTTTCAATCTCACTTTCTACCTTTAAAATTGAGGA
CCCTAAATTTATTAATCACAT
Found at i:24056 original size:29 final size:29
Alignment explanation
Indices: 24001--24061 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
23991 CCTAACTGGC
*
24001 TGAACCGATCAACCCGTTGACTCGACCGT
1 TGAACCGATCAACCCGTTGACTCGACCAT
*
24030 TGAACC-AGTCAACCTGTTGAC-CAGACCAT
1 TGAACCGA-TCAACCCGTTGACTC-GACCAT
24059 TGA
1 TGA
24062 TTTTGACCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (29 bp):
TGAACCGATCAACCCGTTGACTCGACCAT
Found at i:24631 original size:30 final size:30
Alignment explanation
Indices: 24595--24692 Score: 135
Period size: 30 Copynumber: 3.3 Consensus size: 30
24585 ATTCCAGTCT
24595 TGACATCTGCATAGGATTAATTCCCCGTTC
1 TGACATCTGCATAGGATTAATTCCCCGTTC
** *
24625 TGACATCCACATAGGATTAATTCCTCGTTC
1 TGACATCTGCATAGGATTAATTCCCCGTTC
* *
24655 TGACATATGCAT-GATATTAATTCCCCGTTC
1 TGACATCTGCATAG-GATTAATTCCCCGTTC
24685 TGACATCT
1 TGACATCT
24693 ATATGGGACT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 1 0.02
30 57 0.98
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (30 bp):
TGACATCTGCATAGGATTAATTCCCCGTTC
Found at i:24674 original size:60 final size:59
Alignment explanation
Indices: 24595--24732 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
24585 ATTCCAGTCT
* *
24595 TGACATCTGCAT-AGGATTAATTCCCCGTTCTGACATCCACATAGGATTAATTCCTCGTTC
1 TGACATATGCATGA-GATTAATTCCCCGTTCTGACATCCACATAGGACTAATTCC-CGTTC
* * * * * *
24655 TGACATATGCATGATATTAATTCCCCGTTCTGACATCTATATGGGACTAGTTCCCTTTC
1 TGACATATGCATGAGATTAATTCCCCGTTCTGACATCCACATAGGACTAATTCCCGTTC
*
24714 TGACATATGTATGAGATTA
1 TGACATATGCATGAGATTA
24733 TATCCTCATT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 21 0.31
60 45 0.67
61 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (59 bp):
TGACATATGCATGAGATTAATTCCCCGTTCTGACATCCACATAGGACTAATTCCCGTTC
Found at i:24709 original size:30 final size:30
Alignment explanation
Indices: 24595--24719 Score: 126
Period size: 30 Copynumber: 4.2 Consensus size: 30
24585 ATTCCAGTCT
* *
24595 TGACATCTGCATAGGATTAATTCCCCGTTC
1 TGACATCTACATGGGATTAATTCCCCGTTC
* * *
24625 TGACATCCACATAGGATTAATTCCTCGTTC
1 TGACATCTACATGGGATTAATTCCCCGTTC
* * **
24655 TGACATATGCATGATATTAATTCCCCGTTC
1 TGACATCTACATGGGATTAATTCCCCGTTC
* * * *
24685 TGACATCTATATGGGACTAGTT-CCCTTTC
1 TGACATCTACATGGGATTAATTCCCCGTTC
24714 TGACAT
1 TGACAT
24720 ATGTATGAGA
Statistics
Matches: 77, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
29 12 0.16
30 65 0.84
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (30 bp):
TGACATCTACATGGGATTAATTCCCCGTTC
Found at i:29605 original size:29 final size:28
Alignment explanation
Indices: 29541--29626 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 28
29531 ACTGAATTAG
* * * *
29541 TTGAATCGGTCAACCCGTTAACCTGATCG
1 TTGAACCGGTCAA-CCGTTGACCTGACCA
* *
29570 TTAAACCGGTCAACCAGTTGACTTGACCA
1 TTGAACCGGTCAACC-GTTGACCTGACCA
* *
29599 TTGAACCGATCAACTCGTTGACCCGACC
1 TTGAACCGGTCAAC-CGTTGACCTGACC
29627 GTTAATCGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
28 2 0.04
29 42 0.93
30 1 0.02
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (28 bp):
TTGAACCGGTCAACCGTTGACCTGACCA
Found at i:31653 original size:20 final size:20
Alignment explanation
Indices: 31624--31666 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
31614 ATTCCACCAC
31624 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
31644 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
31664 ATG
1 ATG
31667 AGCTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:32048 original size:30 final size:30
Alignment explanation
Indices: 32007--32184 Score: 214
Period size: 30 Copynumber: 5.9 Consensus size: 30
31997 TGTATTTCCG
* * *
32007 ATCTCCATGGGACTAATTCCCCGTTTTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * *
32037 ATCTGCATGGGATTAATTTCCTGTTTTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* *
32067 ATCTGCATGGGATTAATTTCCCATTCTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * *
32097 ATCTGTATGGGATTAGTTCCCCATTCTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * *
32127 ATCTGTATGAGATTAGTTCCCCGTTCTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
32157 ATCTGCATGGGATT-ATATCCCCGTTCTG
1 ATCTGCATGGGATTAAT-TCCCCGTTCTG
32185 TTTATCTGTG
Statistics
Matches: 132, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
29 1 0.01
30 131 0.99
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (30 bp):
ATCTGCATGGGATTAATTCCCCGTTCTGAC
Found at i:32771 original size:13 final size:13
Alignment explanation
Indices: 32748--32786 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
32738 TTAATTGAGT
32748 TTTTATTAATTAAA
1 TTTT-TTAATTAAA
32762 TTTTTTAATTAAA
1 TTTTTTAATTAAA
*
32775 TTATTTAATTAA
1 TTTTTTAATTAA
32787 TGTCGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTTAATTAAA
Found at i:39458 original size:2 final size:2
Alignment explanation
Indices: 39235--39438 Score: 166
Period size: 2 Copynumber: 101.5 Consensus size: 2
39225 GGGTGTTACA
39235 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
* * *
39277 AT AT AT AT AT AT AT AT AT AT AA AC AT AT AT AA AGT AT A- AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT
* * * *
39320 AT AA ACT AT AT A- AT AT AA AT AT AT AA ACT AT AT AT AT AT AT AC
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * * * *
39363 AC AT AT GT AT AT AT GT AT GT AT AA AGT AT AT A- AT AT AT AA AC
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
39405 AT AT A- AA AA AT AA AT AT AT AT AT A- AGT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
39439 AACACACAAA
Statistics
Matches: 164, Mismatches: 27, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
1 5 0.03
2 153 0.93
3 6 0.04
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (2 bp):
AT
Found at i:39963 original size:23 final size:22
Alignment explanation
Indices: 39895--39977 Score: 57
Period size: 23 Copynumber: 3.7 Consensus size: 22
39885 TTAAATTATT
* **
39895 AATTAATTATTATATAAAAAATA
1 AATTAATT-TTAAATAATTAATA
39918 AATTAAATTTATAAAT-ATT--TA
1 AATT-AATTT-TAAATAATTAATA
39939 AATTAATTTTAAATAATCTAATAA
1 AATTAATTTTAAATAAT-TAAT-A
*
39963 AATT-ATGTTAAATAA
1 AATTAATTTTAAATAA
39978 ATATATTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.10
20 7 0.14
21 7 0.14
23 17 0.35
24 13 0.27
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
AATTAATTTTAAATAATTAATA
Found at i:40199 original size:16 final size:16
Alignment explanation
Indices: 40180--40213 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40170 TTATAATTTA
40180 TAAGTCAGATAAATAT
1 TAAGTCAGATAAATAT
*
40196 TAAGTCCGATAAATAT
1 TAAGTCAGATAAATAT
40212 TA
1 TA
40214 GATCGGTTCA
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:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (16 bp):
TAAGTCAGATAAATAT
Found at i:45423 original size:13 final size:13
Alignment explanation
Indices: 45405--45433 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
45395 CACTGGTTTA
45405 GTGAAGGAGTTGG
1 GTGAAGGAGTTGG
45418 GTGAAGGAGTTGG
1 GTGAAGGAGTTGG
45431 GTG
1 GTG
45434 TTCAGCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.55, T:0.24
Consensus pattern (13 bp):
GTGAAGGAGTTGG
Found at i:55412 original size:181 final size:184
Alignment explanation
Indices: 55128--55462 Score: 459
Period size: 182 Copynumber: 1.8 Consensus size: 184
55118 TTCAAAGATA
* * *
55128 AAACTCATTTTACCATTCACTTAAATATGTATTATTTTAATTTGAATTAAACAAAAATATAATTA
1 AAACTCATTCTACCATTCACTTAAATATGTATTATTTTAACTTGAAATAAACAAAAATATAATTA
* * *
55193 TCTTTAATATTCAAAGTTAAAAAGGTAACAAATACC-TTTTAAGTTGA-TATATTCAAAA-AGTA
66 TCTTT-ATATTCAAAATTAAAAAGATAACAAATACCTTTTTAAATTGACT-TATT-AAAAGAGTA
* *
55255 ATTATCCTACTAATCTTTAAATTAAATAATATATTTAATTTGCAATGGTCAAAAGGT
128 ATTATCCTACTAATATTCAAATTAAATAATATATTTAATTTGCAATGGTCAAAAGGT
* * **
55312 AAACTCCTTCTACCATTCAAACTT-AATA-GTATTA-TTTAACTTGAAATATACAAGTATATAAT
1 AAACTCATTCTACCATTC--ACTTAAATATGTATTATTTTAACTTGAAATAAACAAAAATATAAT
*
55374 TATCTTT-TATTCAAAATTAAAAAGATAACAATTACCTTTTTAAATTGACTTATTAAAAGAGTAA
64 TATCTTTATATTCAAAATTAAAAAGATAACAAATACCTTTTTAAATTGACTTATTAAAAGAGTAA
55438 TTATCCTACTAATATTCAAATTAAA
129 TTATCCTACTAATATTCAAATTAAA
55463 AATTATCTTT
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
181 30 0.23
182 42 0.32
183 31 0.23
184 22 0.17
185 4 0.03
186 4 0.03
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.39
Consensus pattern (184 bp):
AAACTCATTCTACCATTCACTTAAATATGTATTATTTTAACTTGAAATAAACAAAAATATAATTA
TCTTTATATTCAAAATTAAAAAGATAACAAATACCTTTTTAAATTGACTTATTAAAAGAGTAATT
ATCCTACTAATATTCAAATTAAATAATATATTTAATTTGCAATGGTCAAAAGGT
Found at i:56671 original size:84 final size:85
Alignment explanation
Indices: 56531--56706 Score: 311
Period size: 84 Copynumber: 2.1 Consensus size: 85
56521 TGCGAAATAT
*
56531 ATCCATTTGTCGTTGATGTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATAG
1 ATCCATTTGCCGTTGATGTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATAG
56596 TAGAAT-A-AAAAAAATACA
66 TAGAATAATAAAAAAATACA
*
56614 ATCCATTTGCCGTTGATATTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATA
1 ATCCATTTGCCGTTGAT-GTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATA
56679 GTAGAATAATAAAAAAATACA
65 GTAGAATAATAAAAAAATACA
56700 ATCCATT
1 ATCCATT
56707 GTTTAGGATT
Statistics
Matches: 88, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
83 16 0.18
84 53 0.60
85 1 0.01
86 18 0.20
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (85 bp):
ATCCATTTGCCGTTGATGTTTAAATATCAAATTCCAACTAGCATCAGTCTATCATTCTAAAATAG
TAGAATAATAAAAAAATACA
Found at i:65553 original size:25 final size:24
Alignment explanation
Indices: 65505--65574 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
65495 GAAAATAAAA
65505 ATAAAATAT-TTTAAATTAAGTTAAC
1 ATAAAATATATTT-AA-TAAGTTAAC
*
65530 AGTAAAATATATTTAATAAGTTAAT
1 A-TAAAATATATTTAATAAGTTAAC
65555 ATAAAA-ATATTT--TAAGTTAA
1 ATAAAATATATTTAATAAGTTAA
65575 TATATAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 8 0.19
23 6 0.14
24 5 0.12
25 10 0.24
26 10 0.24
27 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (24 bp):
ATAAAATATATTTAATAAGTTAAC
Found at i:65585 original size:23 final size:22
Alignment explanation
Indices: 65521--65583 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 22
65511 TATTTTAAAT
*
65521 TAAGTTAACAGTAAAATATATTTAA
1 TAAGTTAATA-TAAAA-ATATTT-A
65546 TAAGTTAATATAAAAATATTT-
1 TAAGTTAATATAAAAATATTTA
65567 TAAGTTAATATATAAAA
1 TAAGTTAATATA-AAAA
65584 ATTATATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 12 0.33
22 4 0.11
23 6 0.17
24 5 0.14
25 9 0.25
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
TAAGTTAATATAAAAATATTTA
Found at i:65648 original size:16 final size:18
Alignment explanation
Indices: 65627--65660 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
65617 GTTCATAATT
65627 TTTTATT-TTTTT-AAAA
1 TTTTATTATTTTTGAAAA
65643 TTTTATTATTTTTGAAAA
1 TTTTATTATTTTTGAAAA
65661 ATTATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTATTATTTTTGAAAA
Found at i:65661 original size:19 final size:18
Alignment explanation
Indices: 65623--65663 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
65613 CCCGGTTCAT
**
65623 AATTTTTTATTTTTTTAA
1 AATTTTTTATTTTTGAAA
65641 AATTTTATTATTTTTGAAA
1 AATTTT-TTATTTTTGAAA
65660 AATT
1 AATT
65664 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
AATTTTTTATTTTTGAAA
Found at i:65869 original size:39 final size:39
Alignment explanation
Indices: 65826--65931 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 39
65816 TTTAAAAAAT
65826 AATTTAGAACGTTAATGTGAAATAATTTAAGAAA-TTAAG
1 AATTTAGAACGTTAATGTGAAATAATTTAA-AAACTTAAG
* *
65865 AATTTAGAACGTT-ATGGTGTCAA-AATTTAAAAACTTAAT
1 AATTTAGAACGTTAAT-GTG-AAATAATTTAAAAACTTAAG
*
65904 ATTTTAGAACGTTAGA-GTGAAATAATTT
1 AATTTAGAACGTTA-ATGTGAAATAATTT
65932 GAGGATTATG
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
38 7 0.12
39 47 0.82
40 2 0.04
41 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (39 bp):
AATTTAGAACGTTAATGTGAAATAATTTAAAAACTTAAG
Found at i:66364 original size:31 final size:31
Alignment explanation
Indices: 66322--66396 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
66312 TAACTCGGGA
* *
66322 TGACCAAATCTTAATTAAATAAAAATGAAAG
1 TGACCATATCTTAATTAAATAAAAACGAAAG
*
66353 TGACCATATCTTAATTAAATAAAAACGTAAG
1 TGACCATATCTTAATTAAATAAAAACGAAAG
*
66384 TGGCCATATCTTA
1 TGACCATATCTTA
66397 TGTATTTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (31 bp):
TGACCATATCTTAATTAAATAAAAACGAAAG
Found at i:78846 original size:155 final size:154
Alignment explanation
Indices: 78560--78869 Score: 611
Period size: 155 Copynumber: 2.0 Consensus size: 154
78550 TACAAGCAAG
78560 ACATGAGCTTTAAAGCATCATATAAACTTATGTTGAAGCTAAACAAAGAAAATGCACAGCTTCAG
1 ACATGAGCTTTAAAGCATCATATAAACTTATGTTGAAGCTAAACAAAGAAAATGCACAGCTTCAG
78625 ATAAATTATTTCTTATCCCAACTAATCAAAGGTGGTCAACTCAATATCCTTGCACTCAGATTAAG
66 ATAAATTATTTCTTATCCCAACTAATCAAAGGTGGTCAACTCAATATCCTTGCACTCAGATTAAG
78690 CATCAAAAGATATTATGAATTCAA
131 CATCAAAAGATATTATGAATTCAA
78714 ACATGGAGCTTTAAAGCATCATATAAACTTATGTTGAAGCTAAACAAAGAAAATGCACAGCTTCA
1 ACAT-GAGCTTTAAAGCATCATATAAACTTATGTTGAAGCTAAACAAAGAAAATGCACAGCTTCA
78779 GATAAATTATTTCTTATCCCAACTAATCAAAGGTGGTCAACTCAATATCCTTGCACTCAGATTAA
65 GATAAATTATTTCTTATCCCAACTAATCAAAGGTGGTCAACTCAATATCCTTGCACTCAGATTAA
78844 GCATCAAAAGATATTATGAATTCAA
130 GCATCAAAAGATATTATGAATTCAA
78869 A
1 A
78870 TTTACCAAAG
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
154 4 0.03
155 151 0.97
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (154 bp):
ACATGAGCTTTAAAGCATCATATAAACTTATGTTGAAGCTAAACAAAGAAAATGCACAGCTTCAG
ATAAATTATTTCTTATCCCAACTAATCAAAGGTGGTCAACTCAATATCCTTGCACTCAGATTAAG
CATCAAAAGATATTATGAATTCAA
Found at i:80233 original size:32 final size:32
Alignment explanation
Indices: 80197--80262 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
80187 ATTATTTTTA
80197 TATAAAAGCATCAATTAGAATTGTAACGAACT
1 TATAAAAGCATCAATTAGAATTGTAACGAACT
80229 TATAAAAGCATCAATTAGAATTGTAACGAACT
1 TATAAAAGCATCAATTAGAATTGTAACGAACT
80261 TA
1 TA
80263 CAAGTTGGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (32 bp):
TATAAAAGCATCAATTAGAATTGTAACGAACT
Found at i:84903 original size:72 final size:75
Alignment explanation
Indices: 84783--84923 Score: 261
Period size: 72 Copynumber: 1.9 Consensus size: 75
84773 CAGCAACTTC
84783 TGGGAAGAAAGGTATTTGTGTTTCTGTTTATCCTTTCTTTGACCAAGATTAGAAAAGATGAAAGG
1 TGGGAAGAAAGGTATTTGTGTTTCTGTTTATCCTTTCTTTGACCAAGATTAGAAAAGATGAAAGG
84848 GTAATCCTAG
66 GTAATCCTAG
84858 TGGGAAGAAA-GTA-TTGT-TTTCTGTTTATCCTTTCTTTGACCAAGATTAGAAAAGATGAAAGG
1 TGGGAAGAAAGGTATTTGTGTTTCTGTTTATCCTTTCTTTGACCAAGATTAGAAAAGATGAAAGG
84920 GTAA
66 GTAA
84924 ATCACTTCCC
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
72 49 0.74
73 4 0.06
74 3 0.05
75 10 0.15
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (75 bp):
TGGGAAGAAAGGTATTTGTGTTTCTGTTTATCCTTTCTTTGACCAAGATTAGAAAAGATGAAAGG
GTAATCCTAG
Found at i:101180 original size:22 final size:22
Alignment explanation
Indices: 101155--101213 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
101145 AAGTGTCTCG
101155 ACACTGATACAAAAGTGCATTC
1 ACACTGATACAAAAGTGCATTC
* *
101177 ACACTGATTCAAATGTGCATTC
1 ACACTGATACAAAAGTGCATTC
*
101199 TCACTGATACTAAAA
1 ACACTGATAC-AAAA
101214 TGCCTTAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (22 bp):
ACACTGATACAAAAGTGCATTC
Found at i:101375 original size:11 final size:11
Alignment explanation
Indices: 101359--101394 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
101349 TTATCACACA
101359 TATCTTATTAT
1 TATCTTATTAT
*
101370 TATCTTATTGT
1 TATCTTATTAT
*
101381 TATCTTGTTAT
1 TATCTTATTAT
101392 TAT
1 TAT
101395 TATCATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (11 bp):
TATCTTATTAT
Found at i:104685 original size:56 final size:56
Alignment explanation
Indices: 104593--104761 Score: 198
Period size: 56 Copynumber: 3.0 Consensus size: 56
104583 TGATACTGCC
* * * * *
104593 AAAAGCCCAAAACTAATGCAACAAGCTCCTCATGCACTCTCAAATCCAAGAAGCAG
1 AAAACCCCAAAGCTAATGCAACAAGTTCCTTATGCACTCTCACATCCAAGAAGCAG
** * * *
104649 AAAATTCCAAAGCTAATGCAACAAGTTCCTTATGCACACTCGCATCCAAGAACCAG
1 AAAACCCCAAAGCTAATGCAACAAGTTCCTTATGCACTCTCACATCCAAGAAGCAG
* * *
104705 -AAACCCCAAAAG-TAATGCAACAAATTCCTTATTCACTCTCACATCCAAAAAGCAG
1 AAAACCCC-AAAGCTAATGCAACAAGTTCCTTATGCACTCTCACATCCAAGAAGCAG
104760 AA
1 AA
104762 GGCACAGTTA
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
55 42 0.45
56 52 0.55
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.18
Consensus pattern (56 bp):
AAAACCCCAAAGCTAATGCAACAAGTTCCTTATGCACTCTCACATCCAAGAAGCAG
Found at i:104733 original size:55 final size:55
Alignment explanation
Indices: 104598--104761 Score: 195
Period size: 55 Copynumber: 3.0 Consensus size: 55
104588 CTGCCAAAAG
* * * * *
104598 CCCAAAACTAATGCAACAAGCTCCTCATGCACTCTCAAATCCAAGAAGCAGAAAAT
1 CCCAAAAGTAATGCAACAAGTTCCTTATGCACTCTCACATCCAAGAAGCAG-AAAC
* * * *
104654 TCC-AAAGCTAATGCAACAAGTTCCTTATGCACACTCGCATCCAAGAACCAGAAAC
1 CCCAAAAG-TAATGCAACAAGTTCCTTATGCACTCTCACATCCAAGAAGCAGAAAC
* * *
104709 CCCAAAAGTAATGCAACAAATTCCTTATTCACTCTCACATCCAAAAAGCAGAA
1 CCCAAAAGTAATGCAACAAGTTCCTTATGCACTCTCACATCCAAGAAGCAGAA
104762 GGCACAGTTA
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
55 47 0.52
56 43 0.48
ACGTcount: A:0.41, C:0.30, G:0.10, T:0.18
Consensus pattern (55 bp):
CCCAAAAGTAATGCAACAAGTTCCTTATGCACTCTCACATCCAAGAAGCAGAAAC
Found at i:108204 original size:81 final size:81
Alignment explanation
Indices: 108105--108253 Score: 228
Period size: 81 Copynumber: 1.8 Consensus size: 81
108095 TGTGAGTAAT
* * * *
108105 TATATATATATATAGTAGATGTATCGAATAATTTACAGTAACTTGTAAAATATAAAATTATT-TT
1 TATATATAAATATAGTAGATGTATCGAATAAGTTACAATAAATTGTAAAATATAAAATTATTATT
108169 TTTATATATGTATATA
66 TTTATATATGTATATA
* *
108185 TATATATAAAATATAGTAGATGTATTGAATAAGTTACAATAAATTTTAAAATATAAAATTATTAT
1 TATATAT-AAATATAGTAGATGTATCGAATAAGTTACAATAAATTGTAAAATATAAAATTATTAT
108250 TTTT
65 TTTT
108254 TGTCAAGTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 7 0.11
81 49 0.80
82 5 0.08
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (81 bp):
TATATATAAATATAGTAGATGTATCGAATAAGTTACAATAAATTGTAAAATATAAAATTATTATT
TTTATATATGTATATA
Found at i:108803 original size:17 final size:18
Alignment explanation
Indices: 108763--108809 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
108753 TGACTGTTTG
108763 ATTTTAAATTTTATTTTAT
1 ATTTT-AATTTTATTTTAT
* *
108782 -TTTTTATTTTATTTTCT
1 ATTTTAATTTTATTTTAT
108799 ATTTTAATTTT
1 ATTTTAATTTT
108810 CTGAAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTAATTTTATTTTAT
Found at i:111546 original size:16 final size:15
Alignment explanation
Indices: 111525--111556 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
111515 AAATATGAAA
111525 CCTAAACTAAACTAAT
1 CCTAAACTAAAC-AAT
111541 CCTAAACTAAACAAT
1 CCTAAACTAAACAAT
111556 C
1 C
111557 ACTCAACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (15 bp):
CCTAAACTAAACAAT
Found at i:112600 original size:55 final size:54
Alignment explanation
Indices: 112525--112754 Score: 193
Period size: 55 Copynumber: 4.2 Consensus size: 54
112515 GTCAGGATAA
* * *
112525 ATAAGACTTGAA-ACATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGT
1 ATAAGACTCGAACA-ATCTTCAAA-AACGAGCCTGCTCTCTATTCCTTCAGAG-AGT
* * * * *
112580 ATAAGACTCGAGCAATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGT
1 ATAAGACTCGAACAATCTTCA-AAAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
* *
112635 ATAAGACTTGAACAATCTTCAATAAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAGACTCGAACAATCTTC-A-AAAACGAG-CCTGCTCTCTATTCCTTCAGAGAGT
* * *
112691 AT-AGAACTCGAAAAATCTTCAATAAAC-AGGTCC-GCTCCCTATTCTTTCAGAGAGT
1 ATAAG-ACTCGAACAATCTTCAA-AAACGA-G-CCTGCTCTCTATTCCTTCAGAGAGT
*
112746 ATAGGACTC
1 ATAAGACTC
112755 AATCTCTAAC
Statistics
Matches: 146, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
54 1 0.01
55 95 0.65
56 49 0.34
57 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (54 bp):
ATAAGACTCGAACAATCTTCAAAAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
Found at i:112685 original size:56 final size:56
Alignment explanation
Indices: 112558--113009 Score: 268
Period size: 51 Copynumber: 8.6 Consensus size: 56
112548 TGACGAGCCT
* * * *
112558 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAGCAATCTTC-ATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * *
112613 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * *
112669 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAT-AAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAACGGGTCC
* * * * *
112724 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATC-TCTAA-CAAACGTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTC-AATAAAACGGGTCC
* ** **
112775 GCTCCCTA-TCCGTTCAGGGAGTAT-AGAACTCG----ATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAACGGGTCC
* ** **
112826 GCTCCCTATTCATTCAGAGAGTAT-AGAACTCG----ATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
112877 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
112928 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* *
112979 GCTCCCTATTCATTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
113010 AATCTTCAAC
Statistics
Matches: 354, Mismatches: 27, Indels: 35
0.85 0.06 0.08
Matches are distributed among these distances:
50 5 0.01
51 221 0.62
52 5 0.01
55 72 0.20
56 51 0.14
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (56 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
Found at i:112783 original size:51 final size:51
Alignment explanation
Indices: 112608--113023 Score: 510
Period size: 51 Copynumber: 8.0 Consensus size: 51
112598 TCATAAAATG
* * * ** *
112608 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACG
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACT
* * * * ** *
112664 GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACA
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACT
* * * *
112719 GGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATC-TCTAACAAACG
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTC-AACGAACT
* * * * * *
112770 TGTTCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* *
112821 TGTCCGCTCCCTATTCATTCAGAGAGTATAGAACTCGATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
112872 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
112923 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
112974 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAAC
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAAC
113024 GAATTTGCTT
Statistics
Matches: 327, Mismatches: 27, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
50 2 0.01
51 246 0.75
52 3 0.01
55 38 0.12
56 38 0.12
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:114174 original size:7 final size:7
Alignment explanation
Indices: 114162--114206 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
114152 TTATTTCTCT
114162 TTTTTCA
1 TTTTTCA
114169 TTTTTC-
1 TTTTTCA
*
114175 TCTTTTTA
1 T-TTTTCA
114183 TTTTTC-
1 TTTTTCA
114189 TTTTTCA
1 TTTTTCA
114196 TTTTT-A
1 TTTTTCA
114202 TTTTT
1 TTTTT
114207 TCTTCCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
6 13 0.39
7 19 0.58
8 1 0.03
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTCA
Found at i:114179 original size:27 final size:27
Alignment explanation
Indices: 114150--114243 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 27
114140 TGAACCCTCC
114150 TTTTATTTCTCTTTTTTCATTTTTCTCT
1 TTTTATTTCTC-TTTTTCATTTTTCTCT
* *
114178 TTTTATTTTTCTTTTTCATTTTTAT-T
1 TTTTATTTCTCTTTTTCATTTTTCTCT
* * *
114204 TTTT-CTTCCCTTTTCCATTTTT-TCT
1 TTTTATTTCTCTTTTTCATTTTTCTCT
*
114229 TCTTTTTTTC-CTTTT
1 T-TTTATTTCTCTTTT
114244 CGTTTTTTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
24 1 0.02
25 16 0.29
26 13 0.23
27 16 0.29
28 10 0.18
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTATTTCTCTTTTTCATTTTTCTCT
Found at i:114180 original size:14 final size:14
Alignment explanation
Indices: 114149--114200 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
114139 TTGAACCCTC
*
114149 CTTTT-ATTTCTCT
1 CTTTTCATTTTTCT
*
114162 TTTTTCATTTTTCT
1 CTTTTCATTTTTCT
*
114176 CTTTTTATTTTTCT
1 CTTTTCATTTTTCT
114190 -TTTTCATTTTT
1 CTTTTCATTTTT
114201 ATTTTTTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
13 14 0.42
14 19 0.58
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (14 bp):
CTTTTCATTTTTCT
Found at i:114206 original size:20 final size:21
Alignment explanation
Indices: 114161--114210 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
114151 TTTATTTCTC
*
114161 TTTTTTCATTTTTCTCTTTTTA
1 TTTTTTC-TTTTTCTATTTTTA
114183 -TTTTTCTTTTTC-ATTTTTA
1 TTTTTTCTTTTTCTATTTTTA
114202 TTTTTTCTT
1 TTTTTTCTT
114211 CCCTTTTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTCTTTTTCTATTTTTA
Found at i:114237 original size:44 final size:42
Alignment explanation
Indices: 114189--114286 Score: 99
Period size: 44 Copynumber: 2.3 Consensus size: 42
114179 TTTATTTTTC
* * *
114189 TTTTTCATTTTTATTTTTT-CTTCCCTTTTCCATTTTTTCTTCTT
1 TTTTTCATTTTTATTTTTTCCAT-CATTTTCC-TTTTTTC-TCAT
* **
114233 TTTTTCCTTTTCGTTTTTTCCATCATTTTCCTTTTTTCTCAT
1 TTTTTCATTTTTATTTTTTCCATCATTTTCCTTTTTTCTCAT
*
114275 TTTCTCATTTTT
1 TTTTTCATTTTT
114287 TTCTCTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
42 12 0.27
43 7 0.16
44 23 0.52
45 2 0.05
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.70
Consensus pattern (42 bp):
TTTTTCATTTTTATTTTTTCCATCATTTTCCTTTTTTCTCAT
Found at i:114269 original size:34 final size:34
Alignment explanation
Indices: 114214--114278 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
114204 TTTTCTTCCC
* * * *
114214 TTTTCCATTTTTTCTTCTTTTTTTCCTTTTCGTT
1 TTTTCCATATTTTCCTCTTTTTCTCATTTTCGTT
114248 TTTTCCATCATTTTCCT-TTTTTCTCATTTTC
1 TTTTCCAT-ATTTTCCTCTTTTTCTCATTTTC
114279 TCATTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
34 20 0.77
35 6 0.23
ACGTcount: A:0.06, C:0.23, G:0.02, T:0.69
Consensus pattern (34 bp):
TTTTCCATATTTTCCTCTTTTTCTCATTTTCGTT
Found at i:114274 original size:16 final size:16
Alignment explanation
Indices: 114230--114278 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 16
114220 ATTTTTTCTT
*
114230 CTTTTTT-TCCTTTTC
1 CTTTTTTCTCATTTTC
*
114245 GTTTTTTCCATCATTTTC
1 CTTTTTT-C-TCATTTTC
114263 CTTTTTTCTCATTTTC
1 CTTTTTTCTCATTTTC
114279 TCATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 8 0.29
17 1 0.04
18 13 0.46
ACGTcount: A:0.06, C:0.24, G:0.02, T:0.67
Consensus pattern (16 bp):
CTTTTTTCTCATTTTC
Found at i:114295 original size:26 final size:26
Alignment explanation
Indices: 114150--114295 Score: 74
Period size: 26 Copynumber: 5.5 Consensus size: 26
114140 TGAACCCTCC
* *
114150 TTTTATTTCTCTTTTTTCATTTTTCTCT
1 TTTT-TTTCTCTTTTCTCA-TTTTCTCA
*
114178 TTTTATTTTTCTTTT-TCATTTT-T-A
1 TTTT-TTTCTCTTTTCTCATTTTCTCA
*
114202 TTTTTTCTTCCCTTTTC-CATTTTTTCTTC-
1 -TTTTT-TTCTCTTTTCTCA--TTTTC-TCA
*
114231 TTTTTTTC-CTTTTCGT-TTTTTC-CA
1 TTTTTTTCTCTTTTC-TCATTTTCTCA
* * *
114255 TCATTTTCCTTTTTTCTCATTTTCTCA
1 T-TTTTTTCTCTTTTCTCATTTTCTCA
114282 TTTTTTTCTCTTTT
1 TTTTTTTCTCTTTT
114296 ATTTCTTCTT
Statistics
Matches: 91, Mismatches: 12, Indels: 32
0.67 0.09 0.24
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 25 0.27
26 30 0.33
27 13 0.14
28 19 0.21
29 1 0.01
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.73
Consensus pattern (26 bp):
TTTTTTTCTCTTTTCTCATTTTCTCA
Found at i:124059 original size:48 final size:46
Alignment explanation
Indices: 123951--124060 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 46
123941 CCATGCTTTG
123951 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
* *
123998 TTGTTCAAAAAA-AAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAAT---CCTAACCGCATGATATCTAATTCGCATGC
124046 ATTTATTCGAAAAAA
1 --TTATTC-AAAAAA
124061 CGAAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
45 4 0.07
46 5 0.09
47 6 0.11
48 28 0.52
50 5 0.09
51 6 0.11
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
Found at i:125860 original size:16 final size:15
Alignment explanation
Indices: 125839--125870 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
125829 AAATATGAAA
125839 CCTAAACTAAACTAAT
1 CCTAAACTAAAC-AAT
125855 CCTAAACTAAACAAT
1 CCTAAACTAAACAAT
125870 C
1 C
125871 ACTCAACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (15 bp):
CCTAAACTAAACAAT
Found at i:133633 original size:15 final size:15
Alignment explanation
Indices: 133581--133624 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
133571 TCAAAAGAAA
* *
133581 AGAA-AGAAAGGTAC
1 AGAAGAGAAATGTCC
133595 AGAAGAGAAATGTCC
1 AGAAGAGAAATGTCC
133610 AGAAGAGAAATGTCC
1 AGAAGAGAAATGTCC
133625 TTAAGAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.50, C:0.11, G:0.27, T:0.11
Consensus pattern (15 bp):
AGAAGAGAAATGTCC
Found at i:142373 original size:21 final size:21
Alignment explanation
Indices: 142342--142390 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
142332 AAACTGACTA
*
142342 ATAATTAATATTATAGATAATT
1 ATAA-TAATATTATAAATAATT
*
142364 TTAATAATATTATAAATAATT
1 ATAATAATATTATAAATAATT
142385 ATAATA
1 ATAATA
142391 CGAGTGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATAATAATATTATAAATAATT
Done.