Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1390
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: 40718
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:96 original size:13 final size:14
Alignment explanation
Indices: 80--121 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
70 TTATCATAGA
80 TTTTTATAAATATT
1 TTTTTATAAATATT
94 TTTTTA-AAATAAATTT
1 TTTTTATAAAT--A-TT
110 TTTTTATAAATA
1 TTTTTATAAATA
122 CGGTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.17
14 6 0.25
15 2 0.08
16 8 0.33
17 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTATAAATATT
Found at i:107 original size:17 final size:17
Alignment explanation
Indices: 85--121 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
75 ATAGATTTTT
85 ATAAATATTTTTTTA-AA
1 ATAAAT-TTTTTTTATAA
102 ATAAATTTTTTTTATAA
1 ATAAATTTTTTTTATAA
119 ATA
1 ATA
122 CGGTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAAATTTTTTTTATAA
Found at i:474 original size:36 final size:33
Alignment explanation
Indices: 397--474 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
387 TTAAAAAATT
**
397 AAAATATTAATTATATATTTTTATAAAAATAAA
1 AAAATATTTTTTATATATTTTTATAAAAATAAA
*
430 AAAGTATTTTTTATATTATTTTT-TAATAAAATAAA
1 AAAATATTTTTTATA-TATTTTTAT-A-AAAATAAA
465 AAATATATTT
1 AAA-ATATTT
475 AATTACATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 13 0.35
34 8 0.22
35 11 0.30
36 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
AAAATATTTTTTATATATTTTTATAAAAATAAA
Found at i:521 original size:22 final size:23
Alignment explanation
Indices: 487--537 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
477 TTACATTTAA
* *
487 AAAAAATTTACATTAAATAAATT
1 AAAAAATTAACATTAAAGAAATT
* *
510 AAAAAA-TAACATTTAAGGAATT
1 AAAAAATTAACATTAAAGAAATT
532 AAAAAA
1 AAAAAA
538 ATTTACCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAAAATTAACATTAAAGAAATT
Found at i:535 original size:111 final size:112
Alignment explanation
Indices: 327--536 Score: 250
Period size: 111 Copynumber: 1.9 Consensus size: 112
317 ATTAAAAGAA
* **
327 TTTATTATTACTTTTTAATAAAATTAGGAATAATATTTAATTAAATTTAAAAAAATTACATTAAA
1 TTTATTATTACTTTTTAATAAAATAAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAAA
* * ****
392 AAATTAAAATATTAATTATATATTTTTATAAAAATAAAAAAGTATTT
66 AAATTAAAAAATAAATTATATAGGAATATAAAAATAAAAAAGTATTT
* *
439 TTTA-TATTATTTTTTAATAAAATAAAAAAT-ATATTTAATTACATTTAAAAAAAATTTACATTA
1 TTTATTATTACTTTTTAATAAAATAAAAAATAATATTTAATTAAATTT-AAAAAAA-TTACATTA
502 AATAAATTAAAAAATAACATT-TA-AGGAAT-TAAAAA
64 AA-AAATTAAAAAATAA-ATTATATAGGAATATAAAAA
537 AATTTACCAT
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
110 15 0.18
111 35 0.42
112 16 0.19
113 14 0.17
114 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (112 bp):
TTTATTATTACTTTTTAATAAAATAAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAAA
AAATTAAAAAATAAATTATATAGGAATATAAAAATAAAAAAGTATTT
Found at i:1135 original size:125 final size:121
Alignment explanation
Indices: 835--1177 Score: 324
Period size: 124 Copynumber: 2.7 Consensus size: 121
825 TCATAAAACT
* * *
835 TTTTTAATTTAAAATTTTTATTTTTAAAACACTAATAATTAATATTTTAATTTGTTAACTGTACA
1 TTTTT-ATTTAAATTTTTTATTTTTAAAA-AC-ATTAATTAATATTTTAATTTGTTAATTGTA-A
* * *
900 -TTTTAAATTTAAATTAAATATTATTTGTTATTTTATTAGAAATTATAATAAAACCTTTTTA
62 TTTTTAAACTT-AATTAAATATTATTT-TTATTGTATTAGAAATTATAATAAAACCTTTTGA
* * *
961 CTTTTA---AAATTTTTTCTTTTTATAAAAACATAATAATTTAA-ATTTTAATTTCGGTAATTGT
1 TTTTTATTTAAATTTTTT-ATTTT-TAAAAACAT--TAA-TTAATATTTTAATTT-GTTAATTGT
*
1022 AATTTGTTAAACTTAATT-AATATTATTTTTAATTGTATTA-AAATACTAATAATAAACCCTTTT
60 AATTT-TTAAACTTAATTAAATATTATTTTT-ATTGTATTAGAAAT--T-ATAATAAAACCTTTT
1085 GA
120 GA
* **
1087 TTTTTATTTTAAATTTTTTATTATTAAAAA-ATTAATTAATATTTTAATTTGTTAATAATAAGTT
1 TTTTTA-TTTAAATTTTTTATTTTTAAAAACATTAATTAATATTTTAATTTGTTAATTGTAA-TT
*
1151 TTTAAAAGTTAATTAAATATTATTTTT
64 TTT-AAACTTAATTAAATATTATTTTT
1178 TATTAAAAAT
Statistics
Matches: 180, Mismatches: 17, Indels: 40
0.76 0.07 0.17
Matches are distributed among these distances:
122 9 0.05
123 12 0.07
124 51 0.28
125 45 0.25
126 43 0.24
127 2 0.01
128 6 0.03
129 3 0.02
130 9 0.05
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (121 bp):
TTTTTATTTAAATTTTTTATTTTTAAAAACATTAATTAATATTTTAATTTGTTAATTGTAATTTT
TAAACTTAATTAAATATTATTTTTATTGTATTAGAAATTATAATAAAACCTTTTGA
Found at i:1212 original size:29 final size:27
Alignment explanation
Indices: 1149--1213 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
1139 TAATAATAAG
*
1149 TTTTTAAAAGTTAATTAAATATTATTT
1 TTTTTAAAAATTAATTAAATATTATTT
1176 TTTATTAAAAATATAATT-AATAATTATTAT
1 TTT-TTAAAAAT-TAATTAAAT-ATTATT-T
1206 TTTTTAAA
1 TTTTTAAA
1214 TTTTTAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 10 0.30
29 16 0.48
30 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTTTAAAAATTAATTAAATATTATTT
Found at i:1903 original size:11 final size:11
Alignment explanation
Indices: 1867--1915 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1857 TTATTACTTT
*
1867 TTATCTATAAA
1 TTATTTATAAA
* *
1878 TTATTTTTAAT
1 TTATTTATAAA
1889 TTATTTATAAA
1 TTATTTATAAA
*
1900 TTATATA-AAA
1 TTATTTATAAA
1910 TTATTT
1 TTATTT
1916 TTATTAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 8 0.26
11 23 0.74
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:2172 original size:16 final size:17
Alignment explanation
Indices: 2153--2184 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2143 TAATCATCAT
2153 AAATTTT-ATAACTTTC
1 AAATTTTAATAACTTTC
2169 AAATTTTAATAACTTT
1 AAATTTTAATAACTTT
2185 TTTTCGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTTAATAACTTTC
Found at i:5536 original size:70 final size:70
Alignment explanation
Indices: 5462--5595 Score: 223
Period size: 70 Copynumber: 1.9 Consensus size: 70
5452 ATTTTTCAGC
* * * *
5462 TTTTCTATCAAAAGGAATCTGATTCTCAAATATAATTTATGCATTAGTCTAATCTTTATAGTCTT
1 TTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTATAGTCTT
5527 TCTTT
66 TCTTT
*
5532 TTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTATAGTCT
1 TTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTATAGTCT
5596 GACATTTACA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (70 bp):
TTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTATAGTCTT
TCTTT
Found at i:5634 original size:91 final size:87
Alignment explanation
Indices: 5521--5765 Score: 330
Period size: 91 Copynumber: 2.8 Consensus size: 87
5511 TAATCTTTAT
5521 AGTCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATC
1 AGTCTTTC-TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATC
* *
5586 CTTATAGTCTGACATTTACAATCAATC
65 CTTACAATCTGACATTT---A-CAATC
* * *
5613 AGTCTTTCTTTTTTCTATAAAAAAAAATCCGATTCTCAGATATAATTTATGCATTAGTCTAATCC
1 AGTCTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCC
* *
5678 TTACAATTTGATATTTACAATC
66 TTACAATCTGACATTTACAATC
** * * *
5700 AGTC-AACTTTTTTCTATAAAAAAGAATTTGATTCTCAGATATAATTCATACATTAGTATAATCC
1 AGTCTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCC
5764 TT
66 TT
5766 GCAGTCTTTA
Statistics
Matches: 138, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
86 54 0.39
87 9 0.07
88 1 0.01
91 66 0.48
92 8 0.06
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.42
Consensus pattern (87 bp):
AGTCTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCC
TTACAATCTGACATTTACAATC
Found at i:5809 original size:69 final size:69
Alignment explanation
Indices: 5706--5910 Score: 322
Period size: 69 Copynumber: 3.0 Consensus size: 69
5696 AATCAGTCAA
* *
5706 CTTTTTTCTATAAAAAAGAATTTGATTCTCAGATATAATTCATACATTAGTATAATCCTTGCAGT
1 CTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAGT
5771 CTTT
66 CTTT
* *
5775 ATTTTTTTCTATAAAAAAG-ATCTGATTCTCAGATATAATTCATACATTAGTCTAATCCTTACAG
1 -CTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAG
5839 TCTTT
65 TCTTT
* * * *
5844 CTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTGTAGT
1 CTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAGT
5909 CT
66 CT
5911 GACATTTACA
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
68 17 0.14
69 90 0.73
70 17 0.14
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.43
Consensus pattern (69 bp):
CTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAGT
CTTT
Found at i:5948 original size:94 final size:93
Alignment explanation
Indices: 5839--6197 Score: 496
Period size: 92 Copynumber: 3.9 Consensus size: 93
5829 ATCCTTACAG
*
5839 TCTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTT
1 TCTTT-TTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTT
* *
5904 GTAGTCTGACATTTACAATTAATCAGTCTT
65 GCAATCTGACATTTACAA-TAATCAGTCTT
* * *
5934 TCTTTTTTTTTCTATAAAAAAGAATCCGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTG
1 TCTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTG
*
5999 CAATCTGACATTTAC---AATCAGTC-A
66 CAATCTGACATTTACAATAATCAGTCTT
* * * *
6023 ACTTTTTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTTATGCATTAGTCTAATCCTTG
1 TCTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTG
* * * * *
6088 TAGTCTAACATTTACAATCAGTCA-ACTT
66 CAATCTGACATTTACAAT-AATCAGTCTT
*
6116 T-TCTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTG
1 TCTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTG
6180 CAATCTGACATTTACAAT
66 CAATCTGACATTTACAAT
6198 CAATTCTCAG
Statistics
Matches: 233, Mismatches: 26, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
89 72 0.31
90 8 0.03
92 75 0.32
93 4 0.02
94 69 0.30
95 5 0.02
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (93 bp):
TCTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTG
CAATCTGACATTTACAATAATCAGTCTT
Found at i:6077 original size:89 final size:90
Alignment explanation
Indices: 5840--6199 Score: 524
Period size: 89 Copynumber: 3.9 Consensus size: 90
5830 TCCTTACAGT
*
5840 CTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTG
1 CTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTG
* * * * *
5905 TAGTCTGACATTTACAATTAATCAGT
66 CAATCTGACATTTACAATCAGTCA-A
* * *
5931 CTTTCTTTTTTTTTCTATAAAAAAGAATCCGATTTTCAGATATAATTCATGCATTAGTCTAATCC
1 CTTTC---TTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCC
5996 TTGCAATCTGACATTTACAATCAGTCAA
63 TTGCAATCTGACATTTACAATCAGTCAA
* * *
6024 CTTT-TTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTTATGCATTAGTCTAATCCTTG
1 CTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTG
* * *
6088 TAGTCTAACATTTACAATCAGTCAA
66 CAATCTGACATTTACAATCAGTCAA
6113 CTTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCT
1 C-TTTC-TTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCT
6178 TGCAATCTGACATTTACAATCA
64 TGCAATCTGACATTTACAATCA
6200 ATTCTCAGAT
Statistics
Matches: 241, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
89 79 0.33
90 3 0.01
91 5 0.02
92 74 0.31
93 4 0.02
94 76 0.32
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (90 bp):
CTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTG
CAATCTGACATTTACAATCAGTCAA
Found at i:6231 original size:57 final size:57
Alignment explanation
Indices: 6143--6258 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
6133 AAAGAATCTG
* * *
6143 ATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAATCTGACATTTACAATCA
1 ATTCTCAAATATAATTAATGCATTAGTCTAATCCTTACAATATGACATTTACAATCA
* *
6200 ATTCTCAGATATAATTAATGCATTAGTCTAATCCTTACAGTATGACATTTACAATCA
1 ATTCTCAAATATAATTAATGCATTAGTCTAATCCTTACAATATGACATTTACAATCA
6257 AT
1 AT
6259 CAACTTTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (57 bp):
ATTCTCAAATATAATTAATGCATTAGTCTAATCCTTACAATATGACATTTACAATCA
Found at i:6351 original size:89 final size:90
Alignment explanation
Indices: 6200--6374 Score: 273
Period size: 89 Copynumber: 2.0 Consensus size: 90
6190 TTTACAATCA
* *
6200 ATTCTCAGATATAATTAATGCATTAGTCTAATCCTTACAGTATGACATTTACAATCAATCAACTT
1 ATTCTCAAATATAATTAATACATTAGTCTAATCCTTACAGTATGACATTTACAATCAATCAACTT
*
6265 TTC-TTTTTTTCTATAAAAAAATTG
66 TTCTTTTTTTTCCATAAAAAAATTG
* * *
6289 ATTCTCAAATATAATTCATACATTAGTCTAATCCTTGA-ATTCTGACATTTACAATCAATCAACT
1 ATTCTCAAATATAATTAATACATTAGTCTAATCCTT-ACAGTATGACATTTACAATCAATCAACT
6353 TTTCTTTTTTTTCCATAAAAAA
65 TTTCTTTTTTTTCCATAAAAAA
6375 GAATCTGATT
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 61 0.78
90 17 0.22
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (90 bp):
ATTCTCAAATATAATTAATACATTAGTCTAATCCTTACAGTATGACATTTACAATCAATCAACTT
TTCTTTTTTTTCCATAAAAAAATTG
Found at i:7352 original size:122 final size:122
Alignment explanation
Indices: 7073--7338 Score: 402
Period size: 122 Copynumber: 2.2 Consensus size: 122
7063 ATTTTAAATA
* *
7073 AAAATAAAAAAGGTTTATTATTAT--TTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAA
1 AAAATAAAAAA-GTTTTTTATTATAATTTTTAATAAAATAAAAAATAATATTTAATTAAGTTTAA
7136 AAAATTACATTAACAAATTAAAATTTAATTATTATGTTTTTATAAAAATAAAAATTTT
65 AAAATTACATTAACAAATTAAAATTTAATTATTATGTTTTTATAAAAATAAAAATTTT
*
7194 AAAATAAAAAGGTTTTTTATTATAATTTTTAATAAAATAAAAAATAATATTTAATTCAA-TTTAA
1 AAAATAAAAAAGTTTTTTATTATAATTTTTAATAAAATAAAAAATAATATTTAATT-AAGTTTAA
* *
7258 AAATTTACATTAACAAATTAAACTATTAATTATTATG-TTTT-T-AAAATAAAAATTTT
65 AAAATTACATTAACAAATTAAAAT-TTAATTATTATGTTTTTATAAAAATAAAAATTTT
*
7314 AAATTAAAAAAG-TTTTTATTATAAT
1 AAAATAAAAAAGTTTTTTATTATAAT
7339 AATATTTTTT
Statistics
Matches: 134, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
119 13 0.10
120 35 0.26
121 11 0.08
122 61 0.46
123 14 0.10
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (122 bp):
AAAATAAAAAAGTTTTTTATTATAATTTTTAATAAAATAAAAAATAATATTTAATTAAGTTTAAA
AAATTACATTAACAAATTAAAATTTAATTATTATGTTTTTATAAAAATAAAAATTTT
Found at i:7359 original size:14 final size:14
Alignment explanation
Indices: 7339--7376 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
7329 TTATTATAAT
7339 AATATTTTTTA-AA
1 AATATTTTTTAGAA
*
7352 ACATATTTTTGAGAA
1 A-ATATTTTTTAGAA
7367 AATATTTTTT
1 AATATTTTTT
7377 TCGTCAGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 1 0.05
14 17 0.81
15 3 0.14
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (14 bp):
AATATTTTTTAGAA
Found at i:7671 original size:22 final size:22
Alignment explanation
Indices: 7600--7672 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
7590 GAATAAAATG
* *
7600 TTTTTTAATTGAATAATGATAAAT
1 TTTTTTAATTG-TTAATG-TAATT
* * *
7624 TTTTTTAATTCCTTAA-ATATTAT
1 TTTTTTAATT-GTTAATGTAAT-T
7647 TTTTTTAATTGTTAATGTAATT
1 TTTTTTAATTGTTAATGTAATT
7669 TTTT
1 TTTT
7673 AAAATTTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
22 11 0.29
23 14 0.37
24 13 0.34
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTTTTAATTGTTAATGTAATT
Found at i:8832 original size:28 final size:29
Alignment explanation
Indices: 8790--8850 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
8780 GTTGTCTCCT
*
8790 AATTTAAATTTTAAA-AATTTTTTATTTA
1 AATTTAAATTTTAAATAATTTATTATTTA
8818 AATTT-AATTTATAAATTTAATTTATTATTTA
1 AATTTAAATTT-TAAA--TAATTTATTATTTA
8849 AA
1 AA
8851 ATATTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 5 0.18
28 9 0.32
31 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTTAAATTTTAAATAATTTATTATTTA
Found at i:8897 original size:6 final size:6
Alignment explanation
Indices: 8873--8921 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
8863 AATAAATAAT
8873 AATTTA AA-TT- AATTT- AATTTA AATTATTA AATTTA ATATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AA-T-TTA AATTTA A-ATTTA AATTTA
8921 A
1 A
8922 TTAAATATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 2 0.05
5 9 0.24
6 14 0.37
7 8 0.21
8 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:8935 original size:37 final size:38
Alignment explanation
Indices: 8869--8944 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
8859 ATTTAATAAA
* * *
8869 TAATAATTTAAATTAATTTAATTTAAATT-ATTAAATT
1 TAATAATTTAAATTAATTAAATATAAATTAAATAAATT
*
8906 TAAT-ATTTAAATTTAATTAAATATGAATTAAATAAATT
1 TAATAATTTAAA-TTAATTAAATATAAATTAAATAAATT
8944 T
1 T
8945 CTTGATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 7 0.21
37 18 0.55
38 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (38 bp):
TAATAATTTAAATTAATTAAATATAAATTAAATAAATT
Found at i:10822 original size:20 final size:20
Alignment explanation
Indices: 10787--10829 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
10777 AATATATTTT
10787 AATAAAATATATTTATAA-A
1 AATAAAATATATTTATAATA
*
10806 AATAAATTATCATTTATAATA
1 AATAAAATAT-ATTTATAATA
10827 AAT
1 AAT
10830 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 8 0.38
21 4 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAAATATATTTATAATA
Found at i:10914 original size:91 final size:87
Alignment explanation
Indices: 10776--10962 Score: 286
Period size: 91 Copynumber: 2.1 Consensus size: 87
10766 AATGAATATA
* * *
10776 TAATATATTTTAATAAAATATATTTATAAAAATAAATTATCATTTATAATAAATTTAAAAATTAA
1 TAATATATTTTAACAAAATATATTTATAAAAATAAATTACCACTTATAATAAATTTAAAAATTAA
10841 TTCAATTAATCTATTAAATTACTTTT
66 TTC---T-ATCTATTAAATTACTTTT
*
10867 TAATAT-TTTTAACAAAATATATTTCATAAAAATAAATTACCACTTATAATAAATTTAAAATTTA
1 TAATATATTTTAACAAAATATATTT-ATAAAAATAAATTACCACTTATAATAAATTTAAAAATTA
10931 ATTCTATCTATTAAATTACTTTT
65 ATTCTATCTATTAAATTACTTTT
10954 TAATATATT
1 TAATATATT
10963 ATATCTAATA
Statistics
Matches: 90, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
87 24 0.27
88 3 0.03
90 17 0.19
91 46 0.51
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (87 bp):
TAATATATTTTAACAAAATATATTTATAAAAATAAATTACCACTTATAATAAATTTAAAAATTAA
TTCTATCTATTAAATTACTTTT
Found at i:11096 original size:32 final size:34
Alignment explanation
Indices: 11031--11097 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
11021 TACTTTTATA
*
11031 AAAAATAATAAAATAATTAAATTTTTTAATATATT
1 AAAAATAATAAAATAA-TAAATTTTTGAATATATT
11066 AAAAATAATAAAAT-A-AAA-TTTTGAATTATATT
1 AAAAATAATAAAATAATAAATTTTTGAA-TATATT
11098 GTACTTGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 6 0.20
32 9 0.30
34 1 0.03
35 14 0.47
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (34 bp):
AAAAATAATAAAATAATAAATTTTTGAATATATT
Found at i:11891 original size:2 final size:2
Alignment explanation
Indices: 11884--11930 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
11874 TGTAAGCGTT
11884 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11926 TC TC T
1 TC TC T
11931 AATTCATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:17227 original size:15 final size:15
Alignment explanation
Indices: 17207--17235 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17197 CCTTAGAAAA
17207 AAAAATAACAATAAT
1 AAAAATAACAATAAT
17222 AAAAATAACAATAA
1 AAAAATAACAATAA
17236 AATTTGGGGA
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:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAACAATAAT
Found at i:22491 original size:6 final size:6
Alignment explanation
Indices: 22480--22504 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22470 GGGTTGATTA
22480 TAAGAC TAAGAC TAAGAC TAAGAC T
1 TAAGAC TAAGAC TAAGAC TAAGAC T
22505 CAGTTAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (6 bp):
TAAGAC
Found at i:25608 original size:19 final size:19
Alignment explanation
Indices: 25581--25633 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
25571 AAGTAAAATA
* *
25581 CTAATTAATATTAAAGAGC
1 CTAAATAATATAAAAGAGC
* *
25600 CTAAATAATCTAAAATAGC
1 CTAAATAATATAAAAGAGC
*
25619 CTAGATAATTATAAA
1 CTAAATAA-TATAAA
25634 GGTTAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (19 bp):
CTAAATAATATAAAAGAGC
Found at i:31039 original size:18 final size:19
Alignment explanation
Indices: 30999--31042 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
30989 AATCAGCTCG
*
30999 ATTTAAAATAGTAATTTTT
1 ATTTAAAATAGTAATTTTA
31018 ATTTAAAATAGT-ATTTTA
1 ATTTAAAATAGTAATTTTA
31036 ATTTAAA
1 ATTTAAA
31043 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTTAAAATAGTAATTTTA
Found at i:31058 original size:15 final size:15
Alignment explanation
Indices: 31038--31067 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31028 GTATTTTAAT
*
31038 TTAAATTTAAAAATA
1 TTAAATATAAAAATA
31053 TTAAATATAAAAATA
1 TTAAATATAAAAATA
31068 ATATTATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAATATAAAAATA
Found at i:31472 original size:17 final size:17
Alignment explanation
Indices: 31452--31486 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31442 TTTAATGAAA
31452 TGTTTT-ATTTATTTATT
1 TGTTTTGATTTA-TTATT
31469 TGTTTTGATTTATTATT
1 TGTTTTGATTTATTATT
31486 T
1 T
31487 ATTTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (17 bp):
TGTTTTGATTTATTATT
Found at i:32102 original size:29 final size:29
Alignment explanation
Indices: 32069--32127 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
32059 ATAATTCTTA
32069 ATTATATAAATATA-AATATAATATAAATT
1 ATTATATAAATA-AGAATATAATATAAATT
* *
32098 ATTATATAAATAAGAATATGATATATATT
1 ATTATATAAATAAGAATATAATATAAATT
32127 A
1 A
32128 AATATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
ATTATATAAATAAGAATATAATATAAATT
Found at i:32557 original size:50 final size:50
Alignment explanation
Indices: 32454--32554 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 50
32444 ATAAATTGAT
*
32454 AATTAAATTTAATATTATATAATTATATTTGTTACAAACATAAATTTTTA
1 AATTAAATTTAATATTATATAATTATATTCGTTACAAACATAAATTTTTA
*
32504 AATT-AATTTGATATATATATAATTATA-TCGATTA-AAA-ATAATATTTTTA
1 AATTAAATTTAATAT-TATATAATTATATTCG-TTACAAACATAA-ATTTTTA
32553 AA
1 AA
32555 ATTTTAGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
48 4 0.09
49 23 0.50
50 19 0.41
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (50 bp):
AATTAAATTTAATATTATATAATTATATTCGTTACAAACATAAATTTTTA
Found at i:32841 original size:13 final size:13
Alignment explanation
Indices: 32823--32868 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
32813 TTTAATTTTT
32823 TTTATTATTAATA
1 TTTATTATTAATA
32836 TTTATTA-TAATTA
1 TTTATTATTAA-TA
* *
32849 ATTA-TAATAATA
1 TTTATTATTAATA
32861 TTTATTAT
1 TTTATTAT
32869 ATTTATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:32862 original size:25 final size:24
Alignment explanation
Indices: 32831--32877 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
32821 TTTTTATTAT
32831 TAATATTTATTATAATTAATTATAA
1 TAATATTTATTAT-ATTAATTATAA
*
32856 TAATATTTATTATATTTATTAT
1 TAATATTTATTATATTAATTAT
32878 TATCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATATTTATTATATTAATTATAA
Found at i:33796 original size:27 final size:26
Alignment explanation
Indices: 33737--33804 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
33727 TATGTAATGG
* *
33737 TATATTATTAAAA--AATATAAAATT
1 TATATTTTTAAAATTAATATAAAAAT
*
33761 TAAATTTTTTAAAATTAATATAAATAAT
1 TATA-TTTTTAAAATTAATATAAA-AAT
33789 TATATTTTTAATAATT
1 TATATTTTTAA-AATT
33805 TATTTGATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 3 0.09
25 8 0.23
27 15 0.43
28 9 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATATTTTTAAAATTAATATAAAAAT
Found at i:36205 original size:15 final size:16
Alignment explanation
Indices: 36156--36205 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
36146 GTTTTATATT
*
36156 ATATTATATATATTTA
1 ATATTATATATAATTA
* *
36172 A-AATATATATAAATA
1 ATATTATATATAATTA
36187 ATATTATAT-TAATTA
1 ATATTATATATAATTA
36202 ATAT
1 ATAT
36206 AAAATAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 21 0.75
16 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTATATATAATTA
Found at i:36657 original size:5 final size:5
Alignment explanation
Indices: 36647--36676 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
36637 TAAGGTCAAA
*
36647 AATAT AATAT AATAT AATAT AACAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT
36677 GCTCACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:38420 original size:14 final size:16
Alignment explanation
Indices: 38398--38441 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
38388 TATACGAATA
38398 TATTAAAATTTATAAG
1 TATTAAAATTTATAAG
38414 -A-TAAAA-TTATAAAG
1 TATTAAAATTTAT-AAG
38428 TATTAAAATTTATA
1 TATTAAAATTTATA
38442 TAAATATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 2 0.08
16 6 0.25
17 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
TATTAAAATTTATAAG
Found at i:39543 original size:35 final size:35
Alignment explanation
Indices: 39495--39561 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
39485 AATCAACCAA
39495 ATAAACTTTTAAAAATATA-ATTATTTTTATTATTT
1 ATAAACTTTTAAAAATATATATT-TTTTTATTATTT
*
39530 ATAAA-TTTATAAAAATTTATATTTTTTTATTA
1 ATAAACTTT-TAAAAATATATATTTTTTTATTA
39562 ATGATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 3 0.10
35 23 0.79
36 3 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (35 bp):
ATAAACTTTTAAAAATATATATTTTTTTATTATTT
Found at i:40407 original size:15 final size:15
Alignment explanation
Indices: 40387--40421 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40377 TATTATCACG
* *
40387 ATTAATTATAAAAAT
1 ATTAATAATAAAAAA
40402 ATTAATAATAAAAAA
1 ATTAATAATAAAAAA
40417 ATTAA
1 ATTAA
40422 AATTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAATAATAAAAAA
Done.