Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2411
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: 206453
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
File 2 of 2
Found at i:157058 original size:3 final size:3
Alignment explanation
Indices: 157050--157082 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
157040 ATGATTTGAA
157050 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
157083 TTCGTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:159143 original size:21 final size:20
Alignment explanation
Indices: 159080--159158 Score: 64
Period size: 21 Copynumber: 4.2 Consensus size: 20
159070 TTTAAAATTT
*
159080 ATATAATATGAAT-TATT-A
1 ATATAATATAAATATATTAA
159098 ATAT-AT-TAAA-AT-TTAA
1 ATATAATATAAATATATTAA
*
159114 ATA-AATATAAATATCTTAA
1 ATATAATATAAATATATTAA
* *
159133 ATATAATTATAATTATATAAA
1 ATATAA-TATAAATATATTAA
159154 ATATA
1 ATATA
159159 TGAACATGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
15 2 0.04
16 10 0.20
17 6 0.12
18 6 0.12
19 7 0.14
20 2 0.04
21 16 0.33
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (20 bp):
ATATAATATAAATATATTAA
Found at i:159476 original size:76 final size:77
Alignment explanation
Indices: 159372--159524 Score: 247
Period size: 76 Copynumber: 2.0 Consensus size: 77
159362 GTTTTTAAGC
* *
159372 ATTCAATCCTACAAACCTTTTATTTTTTTTGAGTTCATTTAGGTCCTCAAAGAGCCTTAGTTTCG
1 ATTCAATCCTACAAACCTTTTATTTTTTTCGAGTTCATTTAGGTCCTCAAAGAGCCTGAGTTTCG
159437 TCG-CTACTGTA
66 TCGCCTACTGTA
* *
159448 ATTCAATGCC-ACAGACCTTTTATTTTTTTCGAGTTCATTTAGGTCCTCAATGAGCCTGAGTTTC
1 ATTCAAT-CCTACAAACCTTTTATTTTTTTCGAGTTCATTTAGGTCCTCAAAGAGCCTGAGTTTC
159512 GTCGCCTACTGTA
65 GTCGCCTACTGTA
159525 GATTGTTCCC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
76 61 0.86
77 10 0.14
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (77 bp):
ATTCAATCCTACAAACCTTTTATTTTTTTCGAGTTCATTTAGGTCCTCAAAGAGCCTGAGTTTCG
TCGCCTACTGTA
Found at i:165770 original size:35 final size:35
Alignment explanation
Indices: 165716--165837 Score: 181
Period size: 35 Copynumber: 3.5 Consensus size: 35
165706 ATTAATATAG
* *
165716 AAGAAATAAAGCTGTTGCAAACAGCAGCAATGAAT
1 AAGAAATAAAGCTGCTGCAAACGGCAGCAATGAAT
* *
165751 AAAAAATAAAGCTGCTGCAAATGGCAGCAATGAAT
1 AAGAAATAAAGCTGCTGCAAACGGCAGCAATGAAT
* * *
165786 AAGAAATAAAGCTGTTACAAACGGCAGCAATGAAG
1 AAGAAATAAAGCTGCTGCAAACGGCAGCAATGAAT
165821 AAGAAATAAAGCTGCTG
1 AAGAAATAAAGCTGCTG
165838 AGATTCAATG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 76 1.00
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.16
Consensus pattern (35 bp):
AAGAAATAAAGCTGCTGCAAACGGCAGCAATGAAT
Found at i:166705 original size:20 final size:20
Alignment explanation
Indices: 166680--166718 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
166670 ATATAGAGGT
**
166680 ATGATGCTTGATTTTGTTGC
1 ATGATGCTAAATTTTGTTGC
166700 ATGATGCTAAATTTTGTTG
1 ATGATGCTAAATTTTGTTG
166719 AAATTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.49
Consensus pattern (20 bp):
ATGATGCTAAATTTTGTTGC
Found at i:178673 original size:16 final size:15
Alignment explanation
Indices: 178648--178690 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
178638 TTCAAATACC
*
178648 ATATTTAATAACTAAA
1 ATATTAAATAA-TAAA
178664 ATATTAAATATATAAA
1 ATATTAAATA-ATAAA
*
178680 ATATAAAATAA
1 ATATTAAATAA
178691 ACAAAGAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATTAAATAATAAA
Found at i:178744 original size:20 final size:20
Alignment explanation
Indices: 178719--178769 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
178709 AAAAGAAAAT
178719 ACATAAAAATTTAAAATAAA
1 ACATAAAAATTTAAAATAAA
*
178739 ACATAAATATTTAAAATAAA
1 ACATAAAAATTTAAAATAAA
*
178759 ACATGAAAATT
1 ACATAAAAATT
178770 CAATTGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (20 bp):
ACATAAAAATTTAAAATAAA
Found at i:182101 original size:3 final size:3
Alignment explanation
Indices: 182093--182127 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
182083 AACTTGGCAG
182093 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
182128 ACGAATCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:182566 original size:12 final size:12
Alignment explanation
Indices: 182549--182574 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
182539 GGAGCTTAGT
182549 ATTTATTTATTC
1 ATTTATTTATTC
182561 ATTTATTTATTC
1 ATTTATTTATTC
182573 AT
1 AT
182575 CGGGTGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATTTATTC
Found at i:183072 original size:24 final size:24
Alignment explanation
Indices: 183040--183089 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
183030 AATTTCCACT
183040 TTCACTTTGATTTCAGCCTCATTA
1 TTCACTTTGATTTCAGCCTCATTA
183064 TTCACTTTGATTTCAGCCTCATTA
1 TTCACTTTGATTTCAGCCTCATTA
183088 TT
1 TT
183090 TCTCTTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (24 bp):
TTCACTTTGATTTCAGCCTCATTA
Found at i:185428 original size:20 final size:20
Alignment explanation
Indices: 185403--185450 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
185393 TAAACCCTCA
*
185403 AATTTTTAA-TAATTTTACTT
1 AATTTTTAATTAAATTTA-TT
185423 AATTTTTAATTAAATTTATT
1 AATTTTTAATTAAATTTATT
*
185443 AATATTTA
1 AATTTTTA
185451 TTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTTTAATTAAATTTATT
Found at i:186914 original size:55 final size:55
Alignment explanation
Indices: 186822--186948 Score: 152
Period size: 55 Copynumber: 2.3 Consensus size: 55
186812 GTTCAATAGT
**
186822 TTAA-TTTTCGTGAAAAAATATTTATTCTAGTAATGATGATTTCTCTTCTAATAA
1 TTAATTTTTCGTGAAAAAATATTTATTCTAGTAATGATGATTTCTAATCTAATAA
* * * *
186876 TTAATTTTTCGTGAAGAGATA-TTACTTTTAG-AAGTGATGATTTTTAATCTAATAA
1 TTAATTTTTCGTGAAAAAATATTTA-TTCTAGTAA-TGATGATTTCTAATCTAATAA
*
186931 TTAATTTTTCATGAAAAA
1 TTAATTTTTCGTGAAAAA
186949 TTGTTTTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
54 9 0.15
55 52 0.85
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (55 bp):
TTAATTTTTCGTGAAAAAATATTTATTCTAGTAATGATGATTTCTAATCTAATAA
Found at i:187689 original size:26 final size:26
Alignment explanation
Indices: 187659--187717 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
187649 TCATATGGTT
187659 TTAACTTAATCAACTCTTTTAACTCG
1 TTAACTTAATCAACTCTTTTAACTCG
* *
187685 TTAACTAAATCAACTCTTTTAATTCG
1 TTAACTTAATCAACTCTTTTAACTCG
*
187711 TTGACTT
1 TTAACTT
187718 GTATGGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (26 bp):
TTAACTTAATCAACTCTTTTAACTCG
Found at i:187926 original size:42 final size:43
Alignment explanation
Indices: 187880--187965 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
187870 GTCATGCAAT
** *
187880 AAATAAATCTATAAAATAC-TTAATTATTTAAAATATT-TTAAA
1 AAATAAATAAATAAAATACATTAA-AATTTAAAATATTATTAAA
* *
187922 AAATATATAAATAATATACATTAAAATTTAAAATATTATTAAA
1 AAATAAATAAATAAAATACATTAAAATTTAAAATATTATTAAA
187965 A
1 A
187966 TATATATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 27 0.73
43 10 0.27
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (43 bp):
AAATAAATAAATAAAATACATTAAAATTTAAAATATTATTAAA
Found at i:187954 original size:32 final size:30
Alignment explanation
Indices: 187916--187975 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
187906 TTTAAAATAT
187916 TTTAAAAAATATATAAATAATATACATTAAAA
1 TTTAAAAAAT-TATAAA-AATATACATTAAAA
* * *
187948 TTTAAAATATTATTAAAATATATATTAA
1 TTTAAAAAATTATAAAAATATACATTAA
187976 CAATAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.44
31 5 0.20
32 9 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (30 bp):
TTTAAAAAATTATAAAAATATACATTAAAA
Found at i:188209 original size:9 final size:9
Alignment explanation
Indices: 188195--188228 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
188185 GTCTCCATTT
188195 TATTTAAGA
1 TATTTAAGA
188204 TATTTAAGA
1 TATTTAAGA
188213 TTATTTAA-A
1 -TATTTAAGA
188222 TATTTAA
1 TATTTAA
188229 TTAATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 7 0.29
9 10 0.42
10 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (9 bp):
TATTTAAGA
Found at i:188620 original size:3 final size:3
Alignment explanation
Indices: 188612--188644 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
188602 ATGAATTAAA
188612 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
188645 GTTGTTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:189922 original size:42 final size:41
Alignment explanation
Indices: 189845--189930 Score: 100
Period size: 42 Copynumber: 2.1 Consensus size: 41
189835 GTTGGACTCA
*
189845 ATGTATCAAACTATTCACAACGTATAGATAAATGAACAGTG
1 ATGTATCAAACTATTCACAACGCATAGATAAATGAACAGTG
* * * * * *
189886 ATGTATCGATACTATTTACAATGCATCGATACATGAATAGTG
1 ATGTATC-AAACTATTCACAACGCATAGATAAATGAACAGTG
189928 ATG
1 ATG
189931 AACAGTGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 7 0.19
42 30 0.81
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (41 bp):
ATGTATCAAACTATTCACAACGCATAGATAAATGAACAGTG
Found at i:191195 original size:21 final size:20
Alignment explanation
Indices: 191171--191215 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
191161 TGTAGAAAAT
191171 AGCAAGACAAACATTT-ATGAA
1 AGCAA-ACAAA-ATTTCATGAA
*
191192 AGCAAACATAATTTCATGAA
1 AGCAAACAAAATTTCATGAA
191212 AGCA
1 AGCA
191216 TGAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (20 bp):
AGCAAACAAAATTTCATGAA
Found at i:191564 original size:21 final size:21
Alignment explanation
Indices: 191540--191585 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
191530 TTTTTCTAAG
191540 TACAAATACGTATT-GTATCAA
1 TACAAATAC-TATTAGTATCAA
* *
191561 TACATATACTATTAGTATTAA
1 TACAAATACTATTAGTATCAA
191582 TACA
1 TACA
191586 CAAGGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (21 bp):
TACAAATACTATTAGTATCAA
Found at i:191751 original size:53 final size:53
Alignment explanation
Indices: 191664--191802 Score: 224
Period size: 53 Copynumber: 2.6 Consensus size: 53
191654 ACAGATTGCA
* *
191664 TAGTATCGATACACACAAATATGTATCGATACAGGACATTGGTAGTAGCCAAAT
1 TAGTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAAT
*
191718 TAGTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAAT
1 TAGTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAAT
* *
191771 TTGTATCGATACACAAAATATGTATCGATACA
1 TAGTATCGATACACACAATATGTATCGATACA
191803 TTGGAAGTAG
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 64 0.80
54 16 0.20
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (53 bp):
TAGTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAAT
Found at i:191903 original size:22 final size:22
Alignment explanation
Indices: 191848--191923 Score: 100
Period size: 21 Copynumber: 3.4 Consensus size: 22
191838 ACTATTCATT
191848 ACTGTTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
191870 ACT-TTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
* * *
191891 ACTGTTCACGTATCGTTAAAAATC
1 ACTGTTCATGTATCG--ATACATC
191915 ACTGTTCAT
1 ACTGTTCAT
191924 CACTATTCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.45
22 13 0.28
24 13 0.28
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (22 bp):
ACTGTTCATGTATCGATACATC
Found at i:192477 original size:34 final size:35
Alignment explanation
Indices: 192414--192480 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
192404 CTAAGTGATT
192414 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
192450 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
192481 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:194766 original size:21 final size:21
Alignment explanation
Indices: 194741--194795 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
194731 CACTTGCAAC
*
194741 TCATTTCTTTTCTCTTCTAAT
1 TCATTTATTTTCTCTTCTAAT
*
194762 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCTTCTAAT
* *
194783 TCACTTAATTTCT
1 TCATTTATTTTCT
194796 TTTTAAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (21 bp):
TCATTTATTTTCTCTTCTAAT
Found at i:196882 original size:19 final size:20
Alignment explanation
Indices: 196858--196932 Score: 82
Period size: 19 Copynumber: 3.7 Consensus size: 20
196848 CCGTTAGACT
196858 CAATGTATCGA-ACTATTCA
1 CAATGTATCGATACTATTCA
**
196877 CAATGTATCGATAC-ATGAA
1 CAATGTATCGATACTATTCA
196896 CAATGATGTATCGATACTATTCA
1 C-A--ATGTATCGATACTATTCA
*
196919 CAATGCATCGATAC
1 CAATGTATCGATAC
196933 ATGAATAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 15 0.33
20 14 0.30
22 13 0.28
23 4 0.09
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (20 bp):
CAATGTATCGATACTATTCA
Found at i:196973 original size:20 final size:20
Alignment explanation
Indices: 196933--196973 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
196923 GCATCGATAC
* *
196933 ATGAATAGTTATGAACGGTG
1 ATGAATAGTGATGAACAGTG
*
196953 ATGAATAGTGATGAATAGTG
1 ATGAATAGTGATGAACAGTG
196973 A
1 A
196974 AAATGAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.29, T:0.29
Consensus pattern (20 bp):
ATGAATAGTGATGAACAGTG
Found at i:197019 original size:13 final size:13
Alignment explanation
Indices: 197001--197025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
196991 TGCCAGTTTT
197001 ATGTATCGATACA
1 ATGTATCGATACA
197014 ATGTATCGATAC
1 ATGTATCGATAC
197026 TAAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:198716 original size:37 final size:33
Alignment explanation
Indices: 198660--198774 Score: 119
Period size: 35 Copynumber: 3.3 Consensus size: 33
198650 AAACATAATT
*
198660 ATATAAATA-CAATATATGTAAAAATATTAAATA
1 ATATAAATATTAATATATGTAAAAAT-TTAAATA
*
198693 CATGATACAATATTAATATATGTATAAAATTTATATA
1 -AT-ATA-AATATTAATATATGTA-AAAATTTAAATA
198730 ATATAAATTATTAATATAT-T-AAAATTTAAATAA
1 ATATAAA-TATTAATATATGTAAAAATTTAAAT-A
198763 ATATAAAATATT
1 ATAT-AAATATT
198775 TTAAATATAA
Statistics
Matches: 71, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
32 10 0.14
33 9 0.13
34 8 0.11
35 17 0.24
36 6 0.08
37 16 0.23
38 5 0.07
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (33 bp):
ATATAAATATTAATATATGTAAAAATTTAAATA
Found at i:198736 original size:16 final size:17
Alignment explanation
Indices: 198680--198784 Score: 67
Period size: 16 Copynumber: 6.1 Consensus size: 17
198670 AATATATGTA
*
198680 AAAATATTAAATACATGAT
1 AAAATATTATATA-AT-AT
* *
198699 ACAATATTAATATATGTAT
1 AAAATATT-ATATA-ATAT
198718 AAAAT-TTATATAATAT
1 AAAATATTATATAATAT
*
198734 AAATTATTA-AT-ATATT
1 AAAATATTATATAATA-T
*
198750 AAAAT-TTAAATAAATAT
1 AAAATATTATAT-AATAT
*
198767 AAAATATTTTA-AATAT
1 AAAATATTATATAATAT
198783 AA
1 AA
198785 TTATGATAAG
Statistics
Matches: 69, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
15 6 0.09
16 23 0.33
17 14 0.20
18 8 0.12
19 13 0.19
20 5 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAATATTATATAATAT
Found at i:198758 original size:15 final size:17
Alignment explanation
Indices: 198705--198771 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
198695 TGATACAATA
*
198705 TTAATATATGTATAAAAT
1 TTAATATA-ATATAAAAT
*
198723 TT-ATATAATATAAATT
1 TTAATATAATATAAAAT
198739 ATTAATAT-AT-TAAAAT
1 -TTAATATAATATAAAAT
198755 TTAA-ATAAATATAAAAT
1 TTAATAT-AATATAAAAT
198772 ATTTTAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.05
15 4 0.10
16 14 0.34
17 15 0.37
18 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
TTAATATAATATAAAAT
Found at i:198782 original size:49 final size:49
Alignment explanation
Indices: 198715--198818 Score: 117
Period size: 49 Copynumber: 2.1 Consensus size: 49
198705 TTAATATATG
*
198715 TATAAAATTTATATAATATAAATTATTAATATATTAAAAT-T-TAAATA-AA
1 TATAAAATTTATATAATAT-AATTA-TAATA-AGTAAAATATATAAATATAA
* *
198764 TATAAAATATTTTA-AATATAATTATGATAAGTAAAATATATAAATATAA
1 TATAAAAT-TTATATAATATAATTATAATAAGTAAAATATATAAATATAA
198813 TATAAA
1 TATAAA
198819 TAAATGAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
46 7 0.15
47 5 0.10
48 11 0.23
49 21 0.44
50 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (49 bp):
TATAAAATTTATATAATATAATTATAATAAGTAAAATATATAAATATAA
Found at i:203086 original size:24 final size:24
Alignment explanation
Indices: 203059--203106 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
203049 CGTTACACAC
*
203059 AAATATAATATGAA-AAAATAATTA
1 AAATATAATAT-AACAAAAAAATTA
203083 AAATATAATATAACAAAAAAATTA
1 AAATATAATATAACAAAAAAATTA
203107 TATAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATATAATATAACAAAAAAATTA
Found at i:204289 original size:20 final size:20
Alignment explanation
Indices: 204264--204301 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
204254 AAAATCATAA
204264 TAATATTATTACATAAAACT
1 TAATATTATTACATAAAACT
* *
204284 TAATATTGTTACGTAAAA
1 TAATATTATTACATAAAA
204302 GTTTTAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (20 bp):
TAATATTATTACATAAAACT
Found at i:204878 original size:2 final size:2
Alignment explanation
Indices: 204867--204910 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
204857 CCACACATGC
* * * *
204867 AT AT AA AT AT AT AT AT AT AT AT AT AT GT GT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
204909 AT
1 AT
204911 GTGTTTATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:204899 original size:18 final size:18
Alignment explanation
Indices: 204878--204924 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
204868 TATAAATATA
204878 TATATATATATATATGTG
1 TATATATATATATATGTG
*
204896 TATATATACATATATGTG
1 TATATATATATATATGTG
* *
204914 TTTATTTATAT
1 TATATATATAT
204925 GATCTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (18 bp):
TATATATATATATATGTG
Found at i:204899 original size:20 final size:20
Alignment explanation
Indices: 204876--204924 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
204866 CATATAAATA
204876 TATATATATATATATATGTG
1 TATATATATATATATATGTG
* * *
204896 TATATATACATATATGTGTT
1 TATATATATATATATATGTG
*
204916 TATTTATAT
1 TATATATAT
204925 GATCTTAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (20 bp):
TATATATATATATATATGTG
Found at i:205349 original size:21 final size:20
Alignment explanation
Indices: 205325--205386 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
205315 AACTAGCAGT
*
205325 AACACCAACAACAACCGAAGC
1 AACACCAACAACAAAC-AAGC
* *
205346 AACACCAGCAGCAAACAAGC
1 AACACCAACAACAAACAAGC
*
205366 AACAACAAGCAA-AAAC-AGC
1 AACACCAA-CAACAAACAAGC
205385 AA
1 AA
205387 GCTAGACACC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.15
20 14 0.41
21 15 0.44
ACGTcount: A:0.56, C:0.32, G:0.11, T:0.00
Consensus pattern (20 bp):
AACACCAACAACAAACAAGC
Done.