Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_762
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: 47527
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:258 original size:46 final size:47
Alignment explanation
Indices: 135--553 Score: 512
Period size: 46 Copynumber: 9.1 Consensus size: 47
125 GCCCTTCGGA
* * * * * * *
135 TTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGCCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* * * *
182 CTGTCACTTATATATCACTTCCACATTCATCACATCGGCCATTAGGCC
1 TTATCACATATATA-CACTTTCACATTCATCACATCGGCCATTAGGCC
230 TTATCACATATATAC-CTTTCACATTCATCACATCGGCCATTA-GCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* *
275 CTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
322 -TATCACATATATATACACTTTCACATTCATCACATCGG-CATTAGG-C
1 TTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
368 TTATCACATATATATACACTTTCACATTCATCACATC-GCCATTA-GCC
1 TTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
415 TTAT-ACATATATACACTTTCACATTCATCACA-CGGCCATTAGGCC
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* *
460 CTATCACATTATATACACTTTCA-ATTCATCACATC-GCCATTAGACC
1 TTATCACA-TATATACACTTTCACATTCATCACATCGGCCATTAGGCC
*
506 ATATCACA-ATAATA-ACTTTCA-A-TCATCA-A-CGGCCATTAGGCC
1 TTATCACATAT-ATACACTTTCACATTCATCACATCGGCCATTAGGCC
548 TTATCA
1 TTATCA
554 TCATTTCATA
Statistics
Matches: 334, Mismatches: 23, Indels: 35
0.85 0.06 0.09
Matches are distributed among these distances:
41 1 0.00
42 16 0.05
43 7 0.02
44 43 0.13
45 25 0.07
46 94 0.28
47 82 0.25
48 66 0.20
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
Found at i:409 original size:140 final size:140
Alignment explanation
Indices: 136--553 Score: 531
Period size: 140 Copynumber: 3.0 Consensus size: 140
126 CCCTTCGGAT
* * * * * * * * *
136 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGCCCCTGTCACTTATATAT-CAC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAG-GCCTATCACATATATATACAC
*
200 TTCCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATAC-CTTTCACATTCATCACAT
65 TTTCACATTCATCACATCGG-CATTAGG-CTTATCACAATATATACACTTTCACATTCATCACAT
263 CGGCCATTAGCCC
128 CGGCCATTAGCCC
*
276 TATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATATACACT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATATACACT
341 TTCACATTCATCACATCGGCATTAGGCTTATCACATATATATACACTTTCACATTCATCACATC-
66 TTCACATTCATCACATCGGCATTAGGCTTATCACA-ATATATACACTTTCACATTCATCACATCG
*
405 GCCATTAGCCT
130 GCCATTAGCCC
416 TAT-ACATATATACACTTTCACATTCATCACA-CGGCCATTAGGCCCTATCACAT-TATATACAC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CCTATCACATATATATACAC
* * *
478 TTTCA-ATTCATCACATCGCCATTAGACCATATCACAATA-ATA-ACTTTCA-A-TCATCA-A-C
65 TTTCACATTCATCACATCGGCATTAG-GCTTATCACAATATATACACTTTCACATTCATCACATC
*
536 GGCCATTAGGCCT
129 GGCCATTA-GCCC
549 TATCA
1 TATCA
554 TCATTTCATA
Statistics
Matches: 253, Mismatches: 16, Indels: 24
0.86 0.05 0.08
Matches are distributed among these distances:
131 1 0.00
132 8 0.03
133 13 0.05
134 2 0.01
135 7 0.03
136 3 0.01
137 22 0.09
138 41 0.16
139 58 0.23
140 79 0.31
141 19 0.08
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (140 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATATACACT
TTCACATTCATCACATCGGCATTAGGCTTATCACAATATATACACTTTCACATTCATCACATCGG
CCATTAGCCC
Found at i:457 original size:91 final size:96
Alignment explanation
Indices: 135--553 Score: 529
Period size: 91 Copynumber: 4.6 Consensus size: 96
125 GCCCTTCGGA
* * * * * * * * *
135 TTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGCCCCTGTCACTTATATAT-CA
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACA
*
199 CTTCCACATTCATCACATCGGCCATTAGGCC
66 CTTTCACATTCATCACATCGGCCATTAGGCC
*
230 TTATCACATATATAC-CTTTCACATTCATCACATCGGCCATTA-GCCCTATCAC--ATATACACA
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACA
291 CTTTCACATTCATCACATCGGCCATTAGGCC
66 CTTTCACATTCATCACATCGGCCATTAGGCC
*
322 -TATCACATATATATACACTTTCACATTCATCACATCGG-CATTAGG-CTTATCACATATATATA
1 TTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATA
384 CACTTTCACATTCATCACATC-GCCATTA-GCC
64 CACTTTCACATTCATCACATCGGCCATTAGGCC
415 TTAT-ACATATATACACTTTCACATTCATCACA-CGGCCATTAGGCCCTATCACAT-TATATACA
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACA
*
477 CTTTCA-ATTCATCACATC-GCCATTAGACC
66 CTTTCACATTCATCACATCGGCCATTAGGCC
* *
506 ATATCACA-ATAATA-ACTTTCA-A-TCATCA-A-CGGCCATTAGGCCTTATCA
1 TTATCACATAT-ATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCA
554 TCATTTCATA
Statistics
Matches: 295, Mismatches: 16, Indels: 33
0.86 0.05 0.10
Matches are distributed among these distances:
88 19 0.06
89 6 0.02
90 23 0.08
91 72 0.24
92 47 0.16
93 33 0.11
94 54 0.18
95 41 0.14
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.32
Consensus pattern (96 bp):
TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACA
CTTTCACATTCATCACATCGGCCATTAGGCC
Found at i:4241 original size:40 final size:40
Alignment explanation
Indices: 3989--4461 Score: 452
Period size: 40 Copynumber: 11.8 Consensus size: 40
3979 TATAACACCA
* * * *
3989 GCACAAATGCTCCTCGGGACTTAGCCCGGATACATCAA-TA
1 GCACAAATGC-CTTCGGGTCTTAGCCCGGATATATCAATTC
*** * * * *
4029 GCACAAATGCTCTTCGTAACTTAGTCCGGATACATC-ACTA
1 GCACAAATGC-CTTCGGGTCTTAGCCCGGATATATCAATTC
* * ** * * * *
4069 GCACGAATGTTCTTCGGAACTTAGTCCGGATACATC-ACTA
1 GCACAAATG-CCTTCGGGTCTTAGCCCGGATATATCAATTC
* ** * * * *
4109 GCACGAATGCTCTTCGGAACTTAGTCCGGATACATC-ACTA
1 GCACAAATGC-CTTCGGGTCTTAGCCCGGATATATCAATTC
* ** * * * ***
4149 GCACGAATGCTCTTCGGAACTTAGTCCGGATATAACCACAA
1 GCACAAATGC-CTTCGGGTCTTAGCCCGGATATATCAATTC
* * * * * *
4190 GCTCAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
*
4230 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT-
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAA-TTC
*
4270 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAATTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
*
4310 GCACAAATGCCTTCGGGTCTTATCCCGGATATATCAATTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
*
4350 GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
4390 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
4430 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
4462 CATTCAAATG
Statistics
Matches: 391, Mismatches: 36, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
39 3 0.01
40 377 0.96
41 11 0.03
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
Found at i:4847 original size:29 final size:29
Alignment explanation
Indices: 4808--4886 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
4798 CTTAATAATC
*
4808 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
4838 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
4867 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
4887 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:7160 original size:49 final size:49
Alignment explanation
Indices: 6938--7376 Score: 689
Period size: 49 Copynumber: 9.1 Consensus size: 49
6928 CCCTTCGGGA
* * * * *
6938 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
6985 C-TGTCACTTATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7033 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCACTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7080 CCTATCAC--ATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7127 CCTATCACATATATATACACTTTCACATTCATCAAATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7176 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7225 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7272 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7321 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7370 CTTATCA
1 CTTATCA
7377 TCATTTCATA
Statistics
Matches: 365, Mismatches: 20, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
46 6 0.02
47 137 0.38
48 31 0.08
49 191 0.52
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:7186 original size:96 final size:97
Alignment explanation
Indices: 6938--7376 Score: 678
Period size: 96 Copynumber: 4.6 Consensus size: 97
6928 CCCTTCGGGA
* * * * * *
6938 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-CCTGTCACTTATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC-TATATAT
*
7000 ACACTTCCACATTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7033 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCAC-ATATACA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACTATATATA
7095 CACTTTCACATTCATCACATCGGCCATTAGGC
66 CACTTTCACATTCATCACATCGGCCATTAGGC
* * *
7127 CCTATCACATATATATACACTTTCACATTCATCAAATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC-TATATAT
7192 ACACTTTCACATTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
7225 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC-TATATAT
7288 ACACTTTCACATTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
7321 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCA
7377 TCATTTCATA
Statistics
Matches: 319, Mismatches: 16, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
94 45 0.14
95 39 0.12
96 145 0.45
98 90 0.28
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (97 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACTATATATA
CACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:7234 original size:145 final size:145
Alignment explanation
Indices: 6938--7376 Score: 740
Period size: 145 Copynumber: 3.0 Consensus size: 145
6928 CCCTTCGGGA
* * * * * * * *
6938 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-CCTGTCACTTATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
*
7002 ACTTCCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
*
7065 CATCGGCCACTAGGC
131 CATCGGCCATTAGGC
* *
7080 CCTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
*
7145 ACTTTCACATTCATCAAATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
7210 CATCGGCCATTAGGC
131 CATCGGCCATTAGGC
7225 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
7290 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
7355 CATCGGCCATTAGGC
131 CATCGGCCATTAGGC
7370 CTTATCA
1 CTTATCA
7377 TCATTTCATA
Statistics
Matches: 278, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
142 38 0.14
143 53 0.19
145 187 0.67
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (145 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
CATCGGCCATTAGGC
Found at i:10305 original size:6 final size:6
Alignment explanation
Indices: 10282--10356 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 6
10272 GATTTCGATC
* * ** * **
10282 TCTTTT TCCTTC TCTTTT TCTTTT TCACTT TCCTTT TCAATT TCATTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC-TTTT
10331 TCTTTT TCTTATT CTCTTTT TACTTT
1 TCTTTT TCTT-TT -TCTTTT T-CTTT
10357 CTTTCACACT
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
6 37 0.70
7 12 0.23
8 4 0.08
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (6 bp):
TCTTTT
Found at i:12490 original size:22 final size:21
Alignment explanation
Indices: 12462--12507 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
12452 CTTCCATACG
12462 ATGTATTAA-GCCATGCATGTAC
1 ATGTATTAATGCCATGC-T-TAC
12484 ATGTATTAATGCCATGCTTAC
1 ATGTATTAATGCCATGCTTAC
12505 ATG
1 ATG
12508 CATGTGTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 10 0.43
23 7 0.30
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATGTATTAATGCCATGCTTAC
Found at i:12717 original size:15 final size:16
Alignment explanation
Indices: 12692--12723 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12682 ACCTACAAAG
12692 AAATAAAAACATAATT
1 AAATAAAAACATAATT
12708 AAAT-AAAACATAATT
1 AAATAAAAACATAATT
12723 A
1 A
12724 TTCATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAAAACATAATT
Found at i:14600 original size:27 final size:28
Alignment explanation
Indices: 14570--14622 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
14560 GGTGTTTTGA
14570 TAAA-TCTACAAACCAA-GGATATTTCGT
1 TAAATTCTACAAACCAATGG-TATTTCGT
*
14597 TAAATTCTGCAAACCAATGGTATTTC
1 TAAATTCTACAAACCAATGGTATTTC
14623 TGTAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 17 0.74
29 2 0.09
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (28 bp):
TAAATTCTACAAACCAATGGTATTTCGT
Found at i:14672 original size:27 final size:26
Alignment explanation
Indices: 14615--14730 Score: 151
Period size: 27 Copynumber: 4.3 Consensus size: 26
14605 GCAAACCAAT
* *
14615 GGTATTTCTGTAATTTTTGAAAGTCAAG
1 GGTATTTCTATAATTTTT-AAA-TCAGG
14643 GGTATTTCTATAATTTTGTAAATCAGG
1 GGTATTTCTATAATTTT-TAAATCAGG
14670 GGTATTTCTATAATTTTATAAATCAGG
1 GGTATTTCTATAATTTT-TAAATCAGG
* *
14697 GGTATTTCTGTAATTTCCTAAATCAGG
1 GGTATTTCTATAATTT-TTAAATCAGG
14724 GGTATTT
1 GGTATTT
14731 TGGTAATTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
27 61 0.75
28 19 0.23
29 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (26 bp):
GGTATTTCTATAATTTTTAAATCAGG
Found at i:14712 original size:54 final size:54
Alignment explanation
Indices: 14615--14843 Score: 185
Period size: 54 Copynumber: 4.3 Consensus size: 54
14605 GCAAACCAAT
**
14615 GGTATTTCTGTAATTTT-TGAAAGTCAAGGGTATTTCTATAATTTTGTAAATCAGG
1 GGTATTTCTGTAATTTTAT-AAA-TCAAGGGTATTTCTATAATTTCCTAAATCAGG
* * *
14670 GGTATTTCTATAATTTTATAAATCAGGGGTATTTCTGTAATTTCCTAAATCAGG
1 GGTATTTCTGTAATTTTATAAATCAAGGGTATTTCTATAATTTCCTAAATCAGG
* * * *
14724 GGTATTT-TGGTAATTTTACAAATCGAA-GGTATTTC---AA--TAC-AAGT-TGAG
1 GGTATTTCT-GTAATTTTATAAATC-AAGGGTATTTCTATAATTTCCTAAATCAG-G
* * * * *
14772 GGTATTTTTGTAATTTTACAAGTCGAGGGTATTTCAATAATTTCAC-AAATCAGG
1 GGTATTTCTGTAATTTTATAAATCAAGGGTATTTCTATAATTTC-CTAAATCAGG
14826 GGTATTT-TGGTAATTTTA
1 GGTATTTCT-GTAATTTTA
14844 CAACCTAGGG
Statistics
Matches: 144, Mismatches: 16, Indels: 29
0.76 0.08 0.15
Matches are distributed among these distances:
47 2 0.01
48 33 0.23
49 3 0.02
51 4 0.03
53 3 0.02
54 77 0.53
55 21 0.15
56 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (54 bp):
GGTATTTCTGTAATTTTATAAATCAAGGGTATTTCTATAATTTCCTAAATCAGG
Found at i:14746 original size:27 final size:26
Alignment explanation
Indices: 14615--14868 Score: 141
Period size: 27 Copynumber: 9.6 Consensus size: 26
14605 GCAAACCAAT
** *
14615 GGTATTTCTGTAATTTTTGAAAGTCAAG
1 GGTATTT-TGTAATTTTACAAA-TCAGG
* **
14643 GGTATTTCTATAATTTTGTAAATCAGG
1 GGTATTT-TGTAATTTTACAAATCAGG
* *
14670 GGTATTTCTATAATTTTATAAATCAGG
1 GGTATTT-TGTAATTTTACAAATCAGG
*
14697 GGTATTTCTGTAA-TTTCCTAAATCAGG
1 GGTATTT-TGTAATTTTAC-AAATCAGG
*
14724 GGTATTTTGGTAATTTTACAAATC-GAA
1 GGTATTTT-GTAATTTTACAAATCAG-G
* * *
14751 GGTA-TTT-CAA---TACAAGT-TGAG
1 GGTATTTTGTAATTTTACAAATCAG-G
*
14772 GGTATTTTTGTAATTTTACAAGTC-GAG
1 GGTA-TTTTGTAATTTTACAAATCAG-G
** *
14799 GGTATTTCAATAATTTCACAAATCAGG
1 GGTATTT-TGTAATTTTACAAATCAGG
*
14826 GGTATTTTGGTAATTTTAC-AACCTAGG
1 GGTATTTT-GTAATTTTACAAATC-AGG
14853 GGTATTTTGGTAATTT
1 GGTATTTT-GTAATTT
14869 GCAACCCAAG
Statistics
Matches: 188, Mismatches: 22, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
21 12 0.06
23 3 0.02
24 4 0.02
26 14 0.07
27 131 0.70
28 24 0.13
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.42
Consensus pattern (26 bp):
GGTATTTTGTAATTTTACAAATCAGG
Found at i:14884 original size:26 final size:27
Alignment explanation
Indices: 14828--14885 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
14818 AAATCAGGGG
* * *
14828 TATTTTGGTAATTTTACAACCTAGGGG
1 TATTTTGGTAATTTTACAACCCAAGGA
*
14855 TATTTTGGTAA-TTTGCAACCCAAGGA
1 TATTTTGGTAATTTTACAACCCAAGGA
14881 TATTT
1 TATTT
14886 CAGTAATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (27 bp):
TATTTTGGTAATTTTACAACCCAAGGA
Found at i:14914 original size:27 final size:27
Alignment explanation
Indices: 14882--14955 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
14872 ACCCAAGGAT
* *
14882 ATTTCAGTAATTCTATCCTACATGGGC
1 ATTTCAGTAATTCTACCCTACAAGGGC
*
14909 ATTTCAGTAATTCTACCCTACAAGGGT
1 ATTTCAGTAATTCTACCCTACAAGGGC
* *
14936 ATTTCAGTAATACTAGCCTA
1 ATTTCAGTAATTCTACCCTA
14956 AGATATGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCCTACAAGGGC
Found at i:15038 original size:17 final size:18
Alignment explanation
Indices: 15016--15051 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
15006 ATTTATCCAC
*
15016 TTGGGCCCATA-GGCCCA
1 TTGGGCCCACATGGCCCA
15033 TTGGGCCCACATGGCCCA
1 TTGGGCCCACATGGCCCA
15051 T
1 T
15052 CCCGGCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.36, G:0.28, T:0.19
Consensus pattern (18 bp):
TTGGGCCCACATGGCCCA
Found at i:15195 original size:15 final size:16
Alignment explanation
Indices: 15163--15196 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15153 CACCGTATGA
*
15163 CTGGCATTTCGGCATT
1 CTGGCATTTCGCCATT
15179 CTGGCATTT-GCCATT
1 CTGGCATTTCGCCATT
15194 CTG
1 CTG
15197 CAGCTAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (16 bp):
CTGGCATTTCGCCATT
Found at i:20631 original size:48 final size:48
Alignment explanation
Indices: 20519--20730 Score: 202
Period size: 46 Copynumber: 4.5 Consensus size: 48
20509 TACGTATGCC
* * *
20519 AGTGGAAGATATGTCTGGGACATGCATCGGCC---ACAT-TACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATAC-A-AGCT
* * * *
20565 AGTGTAAGACATATCTGGGACATGAATCGGCCTTGAGATATACTAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCT
* * * ** *
20613 AGTGTAAGACATGTCTGGGACATGCATCGACTTTCAGA-CGA-GAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCT
* ** *
20659 AGTGTAAGACATGTCTCGGACATGCATTAGCCTCGAGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCT
*
20707 AGTGTAAGACCTGTCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
20731 GCGTCAGCTT
Statistics
Matches: 132, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
46 62 0.47
47 2 0.02
48 62 0.47
49 3 0.02
50 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCT
Found at i:20672 original size:46 final size:45
Alignment explanation
Indices: 20519--20730 Score: 163
Period size: 48 Copynumber: 4.5 Consensus size: 45
20509 TACGTATGCC
* * ** *
20519 AGTGGAAGATATGTCTGGGACATGCATCGGCCACATTACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTTCA-GACGAGAGCT
* * * ** * *
20565 AGTGTAAGACATATCTGGGACATGAATCGGCCTTGAGATATACTAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTTCAGA-CGA-GAGCT
*
20613 AGTGTAAGACATGTCTGGGACATGCATCGACTTTCAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-TTCAGACGAGAGCT
* ** * ** *
20659 AGTGTAAGACATGTCTCGGACATGCATTAGCCTCGAGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTTC-AGA-CGA-GAGCT
*
20707 AGTGTAAGACCTGTCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
20731 GCGTCAGCTT
Statistics
Matches: 129, Mismatches: 30, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
45 2 0.02
46 60 0.47
47 6 0.05
48 61 0.47
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTTCAGACGAGAGCT
Found at i:20680 original size:94 final size:94
Alignment explanation
Indices: 20516--20730 Score: 279
Period size: 94 Copynumber: 2.3 Consensus size: 94
20506 TGATACGTAT
* * * *
20516 GCCAGTGGAAGATATGTCTGGGACATGCATCGGCCACATTACGAGAGCTAGTGTAAGACATATCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATGACGAGAGCTAGTGTAAGACATATCT
* * * *
20581 GGGACATGAATCGGCCTTGAGATATACTA
66 CGGACATGAATCAGCCTCGAGATATACAA
** *
20610 GCCAGTGTAAGACATGTCTGGGACATGCATCGACTTTCA-GACGAGAGCTAGTGTAAGACATGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGAC-CACATGACGAGAGCTAGTGTAAGACATATC
* *
20674 TCGGACATGCATTAGCCTCGAGATATACAA
65 TCGGACATGAATCAGCCTCGAGATATACAA
* *
20704 GCTAGTGTAAGACCTGTCTGGGACATG
1 GCCAGTGTAAGACATGTCTGGGACATG
20731 GCGTCAGCTT
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 103 0.98
95 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (94 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATGACGAGAGCTAGTGTAAGACATATCT
CGGACATGAATCAGCCTCGAGATATACAA
Found at i:23202 original size:40 final size:40
Alignment explanation
Indices: 23158--23233 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
23148 TACATAGCTG
*
23158 AAGCTAT-CTCAAACCGCACGCTAAGTGCCAAATTTAGCCA
1 AAGCTATAC-CAAACCGCACACTAAGTGCCAAATTTAGCCA
* *
23198 AAGCTATACCGAACCGCACACTAAGTGCCATATTTA
1 AAGCTATACCAAACCGCACACTAAGTGCCAAATTTA
23234 TTCGATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (40 bp):
AAGCTATACCAAACCGCACACTAAGTGCCAAATTTAGCCA
Found at i:25772 original size:15 final size:15
Alignment explanation
Indices: 25752--25805 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
25742 AGACACGCAG
25752 GTGTGTGTCTAGGCC
1 GTGTGTGTCTAGGCC
25767 GTGTGTGTGTCTAGGCC
1 --GTGTGTGTCTAGGCC
*
25784 GTGTATGTCTAGGCC
1 GTGTGTGTCTAGGCC
*
25799 ATGTGTG
1 GTGTGTG
25806 ATTCACGACC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 19 0.56
17 15 0.44
ACGTcount: A:0.09, C:0.17, G:0.39, T:0.35
Consensus pattern (15 bp):
GTGTGTGTCTAGGCC
Found at i:25774 original size:17 final size:16
Alignment explanation
Indices: 25752--25805 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 16
25742 AGACACGCAG
25752 GTGTGTGTCTAGGCCGT
1 GTGTGTGTCTAGGCC-T
25769 GTGTGTGTCTAGGCC-
1 GTGTGTGTCTAGGCCT
*
25784 GTGTATGTCTAGGCCAT
1 GTGTGTGTCTAGGCC-T
25801 GTGTG
1 GTGTG
25806 ATTCACGACC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 14 0.42
17 19 0.58
ACGTcount: A:0.09, C:0.17, G:0.39, T:0.35
Consensus pattern (16 bp):
GTGTGTGTCTAGGCCT
Found at i:30001 original size:40 final size:40
Alignment explanation
Indices: 29916--30095 Score: 208
Period size: 40 Copynumber: 4.5 Consensus size: 40
29906 GCTACTCATT
*
29916 CAAATGCCTTCGGGA-ATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
29955 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
29995 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
30034 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
30075 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
30096 TGGACATCAT
Statistics
Matches: 120, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 47 0.39
40 58 0.48
41 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:30083 original size:79 final size:79
Alignment explanation
Indices: 29916--30095 Score: 197
Period size: 79 Copynumber: 2.3 Consensus size: 79
29906 GCTACTCATT
** *
29916 CAAATGCCTTCGGGAATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCTGGA
1 CAAA-GCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCTGGA
* *
29981 TTTAGTAACTCGCAC
65 TATAGTAACTAGCAC
* *
29996 CAATGCCTTCGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC-G
1 CAAAGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTA-ACCTG
* *
30058 GATATGGTCACTTAGCA-
63 GATATAGTAAC-TAGCAC
30075 CAAAGCCTTCGGGACTTAGCC
1 CAAAGCCTTCGGG-CTTAGCC
30096 TGGACATCAT
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
78 4 0.05
79 65 0.76
80 16 0.19
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAAGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCTGGAT
ATAGTAACTAGCAC
Found at i:35791 original size:46 final size:45
Alignment explanation
Indices: 35731--35905 Score: 167
Period size: 46 Copynumber: 3.8 Consensus size: 45
35721 TGGTTGAGCA
*
35731 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * * *
35777 TTCAAACTCATTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G
*
35822 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * *
35870 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTAGG
35906 GGCGGGTTAC
Statistics
Matches: 104, Mismatches: 16, Indels: 19
0.75 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 56 0.54
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (45 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATG
Found at i:35887 original size:93 final size:93
Alignment explanation
Indices: 35728--35898 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
35718 GGATGGTTGA
* * **
35728 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCAAACTCATTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCAAACTCATTGAGT
35793 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
35821 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCAAACTCATTGAGT
*
35886 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
35899 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCAAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40604 original size:37 final size:37
Alignment explanation
Indices: 40554--40632 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40544 TTATTACGAA
* * *
40554 GTCTTACCCGGACATAATCTTCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCTCACACGAAGTCATCGG
*
40591 GTCTTACCCGGACAAAATCCTCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCTCACACGAAGTCATCGG
40628 GTCTT
1 GTCTT
40633 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCTCACACGAAGTCATCGG
Found at i:40877 original size:47 final size:47
Alignment explanation
Indices: 40751--41354 Score: 965
Period size: 47 Copynumber: 12.6 Consensus size: 47
40741 CCCTTCGGGA
* * * * * *
40751 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
40798 CCTGTCACATATATATACACTTCCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40847 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40894 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40941 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40990 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41039 CCTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41090 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41137 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41184 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41231 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41278 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
*
41327 CTTATCACATATATACACTTTCATATTC
1 CTTATCACATATATACACTTTCACATTC
41355 GAATACTCAT
Statistics
Matches: 529, Mismatches: 20, Indels: 16
0.94 0.04 0.03
Matches are distributed among these distances:
47 302 0.57
49 180 0.34
51 47 0.09
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.