Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2495
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: 186439
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:147856 original size:1 final size:1
Alignment explanation
Indices: 147850--147937 Score: 68
Period size: 1 Copynumber: 88.0 Consensus size: 1
147840 AAATCTTCAC
* * ** * * * **
147850 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
147915 TTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTT
147938 CCAATTGCCA
Statistics
Matches: 67, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (1 bp):
T
Found at i:147896 original size:30 final size:30
Alignment explanation
Indices: 147850--147939 Score: 146
Period size: 31 Copynumber: 3.0 Consensus size: 30
147840 AAATCTTCAC
147850 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCT
1 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCT
147880 TTTTTTGTTTTGTTTTTTTTTTCTTTTTCCT
1 TTTTTT-TTTTGTTTTTTTTTTCTTTTTCCT
*
147911 TTTTTTTTGTT-TTGTTTTTTTCTTTTTCC
1 TTTTTTTT-TTGTTTTTTTTTTCTTTTTCC
147940 AATTGCCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
30 25 0.44
31 32 0.56
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (30 bp):
TTTTTTTTTTGTTTTTTTTTTCTTTTTCCT
Found at i:157279 original size:21 final size:21
Alignment explanation
Indices: 157245--157325 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
157235 GATGCAATGG
*
157245 TTGGATGAAAAAAATGTATTTT
1 TTGGATG-AAAAAATATATTTT
157267 TTGGATGAAAAAATATATTTT
1 TTGGATGAAAAAATATATTTT
*
157288 TTGGATGAAAAAATACATTTT
1 TTGGATGAAAAAATATATTTT
**
157309 TTTTATGAAAAAATATA
1 TTGGATGAAAAAATATA
157326 ACTTTTAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 47 0.87
22 7 0.13
ACGTcount: A:0.44, C:0.01, G:0.14, T:0.41
Consensus pattern (21 bp):
TTGGATGAAAAAATATATTTT
Found at i:158218 original size:19 final size:20
Alignment explanation
Indices: 158184--158222 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
158174 CATATTAAAA
*
158184 TTTATATAAATATATAATAT
1 TTTAAATAAATATATAATAT
158204 TTTAAATAAAT-TATAATAT
1 TTTAAATAAATATATAATAT
158223 ATAATCTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAATAAATATATAATAT
Found at i:159027 original size:2 final size:2
Alignment explanation
Indices: 159020--159063 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
159010 TGCTGGATTG
* * *
159020 TA TA TA TA TA TA TG TG TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
159062 TA
1 TA
159064 GGAGTTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:159041 original size:14 final size:14
Alignment explanation
Indices: 159018--159060 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
159008 TTTGCTGGAT
159018 TGTATATATATATA
1 TGTATATATATATA
*
159032 TGTGTATATATATA
1 TGTATATATATATA
159046 TGTATATATATATA
1 TGTATATATATATA
159060 T
1 T
159061 ATAGGAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
TGTATATATATATA
Found at i:163117 original size:3 final size:3
Alignment explanation
Indices: 163109--163156 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
163099 ACTTGCTGAT
* *
163109 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GGA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
163157 ATCGTAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:163781 original size:14 final size:14
Alignment explanation
Indices: 163751--163788 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
163741 CAATATATTA
*
163751 TTAAATATAAATAT
1 TTAAATAAAAATAT
163765 TT-AATAAAAATATT
1 TTAAATAAAAATA-T
163779 TTAAATAAAA
1 TTAAATAAAA
163789 TAAAATATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 5 0.24
15 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAATAAAAATAT
Found at i:163789 original size:14 final size:14
Alignment explanation
Indices: 163745--163790 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
163735 ACCTATCAAT
163745 ATATTATTAAATATAA
1 ATATT-TTAAATA-AA
163761 ATA-TTT-AATAAAA
1 ATATTTTAAAT-AAA
163774 ATATTTTAAATAAA
1 ATATTTTAAATAAA
163788 ATA
1 ATA
163791 AAATATTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 8 0.30
14 12 0.44
15 4 0.15
16 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATTTTAAATAAA
Found at i:164447 original size:34 final size:33
Alignment explanation
Indices: 164404--164628 Score: 256
Period size: 34 Copynumber: 6.7 Consensus size: 33
164394 GGTTTGGTAA
*
164404 AAATCACCATTTAATCAACAATGGCAACCTACC
1 AAATCACCATTTAATCAACAATGGTAACCTACC
* *
164437 AAATCTACCATTTAGTCAACAATGGTAAGCC-ATC
1 AAATC-ACCATTTAATCAACAATGGTAA-CCTACC
* *
164471 AAATCACCCATTTAATCAATAATGGTAAGCTACC
1 AAATCA-CCATTTAATCAACAATGGTAACCTACC
** *
164505 AAATTTCTCATTTAATCAACAATGGTAAGCTACC
1 AAATCAC-CATTTAATCAACAATGGTAACCTACC
* * * *
164539 AAATCTCCCATTTAGTCAATAATGGCAAACC-ACC
1 AAATC-ACCATTTAATCAACAATGG-TAACCTACC
*
164573 AAATCACCCATTTAATCAACAATGGTAAACTACC
1 AAATCA-CCATTTAATCAACAATGGTAACCTACC
164607 AAATCACCATTTAATCAACAAT
1 AAATCACCATTTAATCAACAAT
164629 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 27 0.17
34 129 0.80
35 6 0.04
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (33 bp):
AAATCACCATTTAATCAACAATGGTAACCTACC
Found at i:164552 original size:102 final size:101
Alignment explanation
Indices: 164404--164628 Score: 342
Period size: 102 Copynumber: 2.2 Consensus size: 101
164394 GGTTTGGTAA
* *
164404 AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCA
1 AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCA
* * *
164469 TCAAATCACCCATTTAATCAATAATGGTAAGCTACC
66 CCAAATCACCCATTTAATCAACAATGGTAAACTACC
** * * * *
164505 AAATTTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAATAATGGCAAACC
1 AAATCAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACC
164570 ACCAAATCACCCATTTAATCAACAATGGTAAACTACC
65 ACCAAATCACCCATTTAATCAACAATGGTAAACTACC
164607 AAATCACCATTTAATCAACAAT
1 AAATCACCATTTAATCAACAAT
164629 TCTCCCACTT
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 20 0.18
102 90 0.82
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (101 bp):
AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCA
CCAAATCACCCATTTAATCAACAATGGTAAACTACC
Found at i:169101 original size:34 final size:33
Alignment explanation
Indices: 169035--169254 Score: 185
Period size: 34 Copynumber: 6.5 Consensus size: 33
169025 TGGTAAAAAC
* *
169035 CACCACTTAATCAACAAT-G-ACAACCTACCAAAT
1 CACCATTTAATCAACAATAGTA-AA-CTATCAAAT
* * *
169068 CTACCATTTAGTCAACAATAGTAAGCCATCAAAT
1 C-ACCATTTAATCAACAATAGTAAACTATCAAAT
* *
169102 CACCTATTTAATCAATAATAGTAAACTACCAAAT
1 CACC-ATTTAATCAACAATAGTAAACTATCAAAT
** * *
169136 TTCTCATTTAATCAACAATGGTAAGCTATCAAAT
1 CAC-CATTTAATCAACAATAGTAAACTATCAAAT
* * * * * *
169170 CTCTCATTTAGTCAATAATGGCAAACCA-CTAAAT
1 CAC-CATTTAATCAACAATAGTAAACTATC-AAAT
*
169204 CACCCATTTAATCAACAATAGTAAATTATCAAAT
1 CA-CCATTTAATCAACAATAGTAAACTATCAAAT
169238 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
169255 GTACTCCCCA
Statistics
Matches: 150, Mismatches: 29, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
33 20 0.13
34 124 0.83
35 5 0.03
36 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.28
Consensus pattern (33 bp):
CACCATTTAATCAACAATAGTAAACTATCAAAT
Found at i:169135 original size:68 final size:68
Alignment explanation
Indices: 169041--169251 Score: 225
Period size: 68 Copynumber: 3.1 Consensus size: 68
169031 AAACCACCAC
* * * *
169041 TTAATCAACAAT-GACAACCTACCAAATCTACCATTTAGTCAACAATAGTAAGCCATCAAATCAC
1 TTAATCAATAATAG-CAAACTACCAAATCTACCATTTAATCAACAATAGTAAGCTATCAAATCAC
169105 CTAT
65 CTAT
* * * *
169109 TTAATCAATAATAGTAAACTACCAAAT-TTCTCATTTAATCAACAATGGTAAGCTATCAAATC-T
1 TTAATCAATAATAGCAAACTACCAAATCTAC-CATTTAATCAACAATAGTAAGCTATCAAATCAC
169172 CTCAT
65 CT-AT
* * * * **
169177 TTAGTCAATAATGGCAAACCACTAAATC-ACCCATTTAATCAACAATAGTAAATTATCAAATCAC
1 TTAATCAATAATAGCAAACTACCAAATCTA-CCATTTAATCAACAATAGTAAGCTATCAAATCAC
169241 C-AT
65 CTAT
169244 TTAATCAA
1 TTAATCAA
169252 CAAGTACTCC
Statistics
Matches: 118, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
67 13 0.11
68 102 0.86
69 3 0.03
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (68 bp):
TTAATCAATAATAGCAAACTACCAAATCTACCATTTAATCAACAATAGTAAGCTATCAAATCACC
TAT
Found at i:169217 original size:102 final size:101
Alignment explanation
Indices: 169035--169254 Score: 264
Period size: 102 Copynumber: 2.2 Consensus size: 101
169025 TGGTAAAAAC
* * *
169035 CACCACTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATAGTAAGCCATCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCATCAA
* *
169100 ATCACCTATTTAATCAATAATAGTAAACTACCAAAT
66 ATCACCCATTTAATCAACAATAGTAAACTACCAAAT
** ** * * * *
169136 TTCTCATTTAATCAACAATGGTAAGCTATCAAATCT-CTCATTTAGTCAATAATGGCAAACCA-C
1 CAC-CATTTAATCAACAATGACAACCTACCAAATCTAC-CATTTAGTCAACAATAGCAAACCATC
* *
169199 TAAATCACCCATTTAATCAACAATAGTAAATTATCAAAT
64 -AAATCACCCATTTAATCAACAATAGTAAACTACCAAAT
169238 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
169255 GTACTCCCCA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
101 17 0.17
102 82 0.83
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.28
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCATCAA
ATCACCCATTTAATCAACAATAGTAAACTACCAAAT
Found at i:171476 original size:2 final size:2
Alignment explanation
Indices: 171469--171494 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
171459 AACATATGTA
171469 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
171495 GAAGTATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:173038 original size:13 final size:14
Alignment explanation
Indices: 173014--173042 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
173004 AAAAAAATCA
173014 TAAATATTAAAATT
1 TAAATATTAAAATT
173028 TAAAT-TTAAAATT
1 TAAATATTAAAATT
173041 TA
1 TA
173043 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATATTAAAATT
Found at i:181602 original size:1 final size:1
Alignment explanation
Indices: 181596--181671 Score: 71
Period size: 1 Copynumber: 76.0 Consensus size: 1
181586 CTTTCCACCC
* * * * * * * *
181596 AAAAAAACAAAACAAAAAAACACAAAAAAAAAAAAACAAAACAAAAAAACAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
181661 ATAAAAAAAAA
1 AAAAAAAAAAA
181672 TAGAAGGGTC
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.88, C:0.09, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:181628 original size:29 final size:29
Alignment explanation
Indices: 181596--181671 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 29
181586 CTTTCCACCC
*
181596 AAAAAAACAAAACAAAAAAACACAAAAAA
1 AAAAAAACAAAACAAAAAAACAAAAAAAA
181625 AAAAAAACAAAACAAAAAAACAAAAAAAA
1 AAAAAAACAAAACAAAAAAACAAAAAAAA
*
181654 AAAGAAAATAAAA-AAAAA
1 AAA-AAAACAAAACAAAAA
181672 TAGAAGGGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 36 0.82
30 8 0.18
ACGTcount: A:0.88, C:0.09, G:0.01, T:0.01
Consensus pattern (29 bp):
AAAAAAACAAAACAAAAAAACAAAAAAAA
Found at i:181666 original size:12 final size:12
Alignment explanation
Indices: 181595--181669 Score: 89
Period size: 13 Copynumber: 6.0 Consensus size: 12
181585 CCTTTCCACC
181595 CAAAAAAACAAAA
1 CAAAAAAA-AAAA
*
181608 CAAAAAAACACAA
1 CAAAAAAA-AAAA
181621 -AAAAAAAAAAA
1 CAAAAAAAAAAA
181632 CAAAACAAAAAAA
1 CAAAA-AAAAAAA
181645 CAAAAAAAAAAA
1 CAAAAAAAAAAA
*
181657 GAAAATAAAAAAA
1 CAAAA-AAAAAAA
181670 AATAGAAGGG
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
11 3 0.05
12 22 0.39
13 31 0.55
ACGTcount: A:0.87, C:0.11, G:0.01, T:0.01
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:182961 original size:28 final size:29
Alignment explanation
Indices: 182879--184228 Score: 1789
Period size: 28 Copynumber: 47.4 Consensus size: 29
182869 AGAATGTTCT
182879 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
182908 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
182937 CTCTTTTCAAAG-CCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
182965 C-CCTTTCAAAGCCCCCAACTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
182993 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183021 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
183050 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
183079 CTCTTTTCAAAGCCCAGAAGTTAGTGG-A
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183107 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183135 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183163 C-CCTTTCAAAGCCCATAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183191 CTCCTTTCAAAGCCCAC-AGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
183219 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183248 CT-ATTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183276 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183305 C-CCTTTCAAAGCCCACAAGTTAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183333 C-CCTTTCAGAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
183361 C-CCTTTCGAAGCCCACAAGTTAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
183389 C-CATTGCGAAGCCCACAATTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183417 CT-CTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183445 C-CCTTTTAAAGCTCACACAAGTCAGTGGCA
1 CTCCTTTCAAAGC-C-CACAAGTCAGTGGCA
*
183475 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
183504 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183533 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183561 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183589 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183618 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
183647 CCCCTTTTAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
183676 CTCTTTTCAAAGCCC-CAAGTTAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183704 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183732 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
183761 CTCTTTTCAAAGCCCACAAATCCGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
**
183790 CTATTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
183819 CTCTTTTCAAAGCCCACAAATCAGTGGCG
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183848 CTCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183876 C-CCTTTCAAAG-CC-C-AGTTAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
183901 C-CCTTTCAGAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
183929 C-CCTTTCGAAGCCCACAAGTTAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
183957 C-CATTGCGAAGCCCACAATTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
183985 CT-CTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
184013 C-CCTTTTAAAGCTTACACAAGTCAGTGGCA
1 CTCCTTTCAAAGC--CCACAAGTCAGTGGCA
* * *
184043 CTCCTTTTAAAGCTCACGCAAGTC-GTGGTA
1 CTCCTTTCAAAGC-C-CACAAGTCAGTGGCA
*
184073 C-CTTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
184101 CT-CTTTCAAAGCCCACAAGTCAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
184129 CTCCTTTCAAAGCCCACGAGTTAGTGGCA
1 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
184158 -TTCTTTCAAAGCCCACGCACGTTAGTGGCA
1 CTCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
184188 C-CCTTTTAAAGCCCATGCAAGTCAATGGCAA
1 CTCCTTTCAAAGCCCA--CAAGTCAGTGGC-A
184219 C-CCTTTCAAA
1 CTCCTTTCAAA
184229 TCACCACTGT
Statistics
Matches: 1186, Mismatches: 104, Indels: 60
0.88 0.08 0.04
Matches are distributed among these distances:
25 20 0.02
26 3 0.00
27 58 0.05
28 544 0.46
29 450 0.38
30 73 0.06
31 38 0.03
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
CTCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:184025 original size:568 final size:567
Alignment explanation
Indices: 182881--184228 Score: 2164
Period size: 568 Copynumber: 2.4 Consensus size: 567
182871 AATGTTCTCT
* *
182881 CCTTTCAAAGC-C-CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTT
1 CCTTTTAAAGCTCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTT
* *
182944 CAAAG-CCACAAGTCAGTGGCACCCTTTCAAAGCCCCCAACTCAGTGGCACCCTTTCAAAGCCCA
66 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA
*
183008 CAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCA
131 CAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCA
* * *
183073 GTGGCACTCTTTTCAAAGCCCAGAAGTTAGTGGACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
195 GTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
*
183138 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCACTCCTTTCAAAG
260 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
* * *
183203 CCCACAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTATTTCAAAGCCCACAAGT
325 CCCACAATCAGTGGCACTATTTTCAAAGCCCACAAATCAGTGGCACTATTTCAAAGCCCACAAAT
183268 CAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA
390 CAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA
183333 CCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTTAGTGGCACCATTGCGA
455 CCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTTAGTGGCACCATTGCGA
183398 AGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC
520 AGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC
183446 CCTTTTAAAGCTCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTT
1 CCTTTTAAAGCTCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTT
*
183511 CAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA
66 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA
183576 CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCA
131 CAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCA
* *
183641 GTGGCACCCCTTTT-AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC-CAAGTTAGTGGCA
195 GTGGCA-CCCTTTTCAAAGCCCACAAGTCAGTGG-AC-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
183704 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
257 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * *
183769 AAAGCCCACAAATCCGTGGCACTATTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
321 AAAGCCCAC-AATCAGTGGCACTATTTTCAAAGCCCACAAATCAGTGGCACT-ATTTCAAAGCCC
*
183834 ACAAATCAGTGGCGCTCTTTTC-AAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-C-AGTTA
384 ACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTA
183895 GTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTTAGTGGCACCA
449 GTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTTAGTGGCACCA
183960 TTGCGAAGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC
514 TTGCGAAGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
184014 CCTTTTAAAGCTTACACAAGTCAGTGGCACTCCTTTTAAAGCTCACGCAAGTC-GTGGTAC-CTT
1 CCTTTTAAAGCTCACACAAGTCAGTGGCACTCCTTTCAAAGC-C-CACAAATCAGTGGCACTCTT
*
184077 TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
64 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGC
* * * * * *
184142 CCACGAGTTAGTGGCATTCTTTCAAAGCCCACGCACGTTAGTGGCACCCTTTT-AAAGCCCATGC
128 CCACAAGTCAGTGGCACTCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCA--C
*
184206 AAGTCAATGGCAACCC-TTTCAAA
189 AAGTCAGTGGC-ACCCTTTTCAAA
184229 TCACCACTGT
Statistics
Matches: 730, Mismatches: 34, Indels: 32
0.92 0.04 0.04
Matches are distributed among these distances:
565 10 0.01
566 1 0.00
567 56 0.08
568 371 0.51
569 92 0.13
570 82 0.11
571 86 0.12
572 32 0.04
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (567 bp):
CCTTTTAAAGCTCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTT
CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA
CAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAG
TGGCACCCTTTTCAAAGCCCACAAGTCAGTGGACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
CCACAATCAGTGGCACTATTTTCAAAGCCCACAAATCAGTGGCACTATTTCAAAGCCCACAAATC
AGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCAC
CCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTTAGTGGCACCATTGCGAA
GCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:184741 original size:20 final size:19
Alignment explanation
Indices: 184716--184770 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
184706 CATTTTTCAA
184716 TATCGATACATGTATGAATG
1 TATCGATACAT-TATGAATG
* * *
184736 TATCGATATATTCTACAATG
1 TATCGATACATTAT-GAATG
184756 TATCGATACATTATG
1 TATCGATACATTATG
184771 TCTTTTTACC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TATCGATACATTATGAATG
Found at i:185713 original size:21 final size:21
Alignment explanation
Indices: 185682--185733 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
185672 TAGCCTTTGC
*
185682 CATGC-TTTTTTTTTATGTTT
1 CATGCATTTTTTATTATGTTT
185702 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTATTATGTTT
185723 CATGCATTTTT
1 CATGCATTTTT
185734 AACATGTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.15, C:0.12, G:0.10, T:0.63
Consensus pattern (21 bp):
CATGCATTTTTTATTATGTTT
Found at i:185740 original size:20 final size:21
Alignment explanation
Indices: 185696--185740 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
185686 CTTTTTTTTT
**
185696 ATGTTTCATGCATTTTTTATT
1 ATGTTTCATGCATTTTTTAAC
185717 ATGTTTCATGCA-TTTTTAAC
1 ATGTTTCATGCATTTTTTAAC
185737 ATGT
1 ATGT
185741 CCAGCATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (21 bp):
ATGTTTCATGCATTTTTTAAC
Done.