Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold873
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: 42462
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:480 original size:1 final size:1
Alignment explanation
Indices: 476--539 Score: 119
Period size: 1 Copynumber: 64.0 Consensus size: 1
466 TGGGGGTGTT
*
476 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
540 AGAGTTAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.00, G:0.98, T:0.02
Consensus pattern (1 bp):
G
Found at i:516 original size:36 final size:36
Alignment explanation
Indices: 467--539 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
457 ATGGGGCGGT
* *
467 GGGGGTGTTGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGG
503 GGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGG
539 G
1 G
540 AGAGTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.95, T:0.05
Consensus pattern (36 bp):
GGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGG
Found at i:518 original size:38 final size:38
Alignment explanation
Indices: 467--539 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
457 ATGGGGCGGT
**
467 GGGGGTGTTGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
505 GGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
540 AGAGTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.95, T:0.05
Consensus pattern (38 bp):
GGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
Found at i:814 original size:13 final size:13
Alignment explanation
Indices: 771--814 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
761 TATTTAATGA
771 ATATAATTTTAAAT
1 ATATAA-TTTAAAT
*
785 ATAATATTTTAAA-
1 AT-ATAATTTAAAT
798 ATATAATTTAAAT
1 ATATAATTTAAAT
811 ATAT
1 ATAT
815 TAAATACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.35
13 6 0.23
14 8 0.31
15 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATAATTTAAAT
Found at i:8704 original size:19 final size:20
Alignment explanation
Indices: 8680--8720 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
8670 AATTTACATT
*
8680 AAAATAAAT-TTTATTTTTA
1 AAAATAAATATTTAATTTTA
8699 AAAATAAATATTTAATTTTA
1 AAAATAAATATTTAATTTTA
8719 AA
1 AA
8721 TTTATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATAAATATTTAATTTTA
Found at i:10218 original size:7 final size:7
Alignment explanation
Indices: 10206--10233 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
10196 AAAATAAAAT
10206 AAAATAA
1 AAAATAA
10213 AAAATAA
1 AAAATAA
10220 AAAATAA
1 AAAATAA
10227 AAAATAA
1 AAAATAA
10234 TATAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:10238 original size:5 final size:5
Alignment explanation
Indices: 10230--10338 Score: 50
Period size: 5 Copynumber: 21.8 Consensus size: 5
10220 AAAATAAAAA
*
10230 ATAAT ATAAT ATAAT AT--T ATAAT AATAAT ATGAGT ATAAT ATAAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT AT-AAT ATAAT AT-AAT
* * * * ** *
10276 ATATT A-AAA ATTAT ATAA- ATTAA- ATTAT -TAAT ATAAT ATCTT AAAAT
1 ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT
10323 AATAAT AATAAT ATAA
1 -ATAAT -ATAAT ATAA
10339 AAATATGAAG
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
3 3 0.04
4 8 0.10
5 43 0.55
6 24 0.31
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:10278 original size:11 final size:11
Alignment explanation
Indices: 10187--10314 Score: 58
Period size: 10 Copynumber: 12.0 Consensus size: 11
10177 TGATGCCGTA
*
10187 AAATAT-ATAA
1 AAATATAATAT
*
10197 AAATAAAATA-
1 AAATATAATAT
* *
10207 AAATAAAAAAT
1 AAATATAATAT
10218 AAA-A-AATA-
1 AAATATAATAT
*
10226 AAAAATAATAT
1 AAATATAATAT
10237 -AATATAATATT
1 AAATATAATA-T
10248 ATAATAATAATAT
1 A-AAT-ATAATAT
* *
10261 GAGTATAATAT
1 AAATATAATAT
10272 AAATAT-AT-T
1 AAATATAATAT
* *
10281 AAAAATTATAT
1 AAATATAATAT
10292 AAAT-TAAATTAT
1 AAATAT-AA-TAT
*
10304 TAATATAATAT
1 AAATATAATAT
10315 CTTAAAATAA
Statistics
Matches: 92, Mismatches: 12, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
8 3 0.03
9 10 0.11
10 32 0.35
11 26 0.28
12 10 0.11
13 5 0.05
14 6 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AAATATAATAT
Found at i:10333 original size:22 final size:21
Alignment explanation
Indices: 10295--10336 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10285 ATTATATAAA
* *
10295 TTAAATTATTAATATAATATC
1 TTAAAATAATAATATAATATC
10316 TTAAAATAATAATAATAATAT
1 TTAAAATAATAAT-ATAATAT
10337 AAAAATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAATAATAATATAATATC
Found at i:10343 original size:11 final size:11
Alignment explanation
Indices: 10186--10294 Score: 59
Period size: 11 Copynumber: 10.2 Consensus size: 11
10176 ATGATGCCGT
10186 AAAAT-ATATA
1 AAAATAATATA
*
10196 AAAATAAAAT-
1 AAAATAATATA
*
10206 AAAATAA-AAA
1 AAAATAATATA
*
10216 ATAAAAAATA-A
1 A-AAATAATATA
10227 AAAATAATATA
1 AAAATAATATA
*
10238 ATATAATATTATA
1 A-A-AATAATATA
* *
10251 ATAATAATATG
1 AAAATAATATA
**
10262 AGTATAATATA
1 AAAATAATATA
*
10273 AATAT-AT-TA
1 AAAATAATATA
*
10282 AAAATTATATA
1 AAAATAATATA
10293 AA
1 AA
10295 TTAAATTATT
Statistics
Matches: 77, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
9 7 0.09
10 24 0.31
11 35 0.45
12 2 0.03
13 9 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AAAATAATATA
Found at i:13173 original size:2 final size:2
Alignment explanation
Indices: 13166--13199 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13156 AAGATGAATG
13166 TA TA TA TA TA TA TA TA TA TA 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
13200 GAAGCTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13585 original size:20 final size:22
Alignment explanation
Indices: 13560--13602 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
13550 TTTAATGAGG
13560 TAAAAT-GATAAGATTTT-GAA
1 TAAAATCGATAAGATTTTAGAA
*
13580 TAAAATCGATAATATTTTAGAA
1 TAAAATCGATAAGATTTTAGAA
13602 T
1 T
13603 TATAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (22 bp):
TAAAATCGATAAGATTTTAGAA
Found at i:14294 original size:16 final size:18
Alignment explanation
Indices: 14273--14334 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 18
14263 TATATAAAAA
14273 ATATAAT-TAAA-ATATG
1 ATATAATATAAATATATG
14289 ATATAATATAAATATAT-
1 ATATAATATAAATATATG
* * * *
14306 AAATATTTTAAA-ATA-A
1 ATATAATATAAATATATG
14322 ATATAATATAAAT
1 ATATAATATAAAT
14335 TATTATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
16 19 0.53
17 13 0.36
18 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATAATATAAATATATG
Found at i:14352 original size:29 final size:31
Alignment explanation
Indices: 14257--14352 Score: 85
Period size: 33 Copynumber: 3.1 Consensus size: 31
14247 TGACACGATG
* *
14257 AATATATATATAAA-AAATATA-ATTAAAATA
1 AATATA-ATATAAATATATATATTTTAAAATA
*
14287 TGATATAATATAAATATATAAATATTTTAAAATA
1 -AATATAATATAAATATAT--ATATTTTAAAATA
14321 AATATAATATAAAT-TAT-TATTTTATAAA-A
1 AATATAATATAAATATATATATTTTA-AAATA
14350 AAT
1 AAT
14353 TAAATCAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
29 11 0.20
30 10 0.18
31 8 0.14
32 3 0.05
33 16 0.29
34 8 0.14
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
AATATAATATAAATATATATATTTTAAAATA
Found at i:14465 original size:3 final size:3
Alignment explanation
Indices: 14457--14490 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
14447 ATCCCTTTTC
14457 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
14491 AGAAATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:15518 original size:22 final size:22
Alignment explanation
Indices: 15483--15565 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 22
15473 CAATTAGAGG
*
15483 ATAAAATGTAATATAAA-A-ATA
1 ATAAAAT-TTATATAAATATATA
15504 ATTAAAATATTATATTAAATATATA
1 A-TAAAAT-TTATA-TAAATATATA
*
15529 ATAAAATTTATAT-AATATAAA
1 ATAAAATTTATATAAATATATA
*
15550 ATATTAATTTAT-TAAA
1 ATA-AAATTTATATAAA
15566 ATTTATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
21 12 0.23
22 20 0.38
23 9 0.17
24 7 0.13
25 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (22 bp):
ATAAAATTTATATAAATATATA
Found at i:15540 original size:14 final size:14
Alignment explanation
Indices: 15523--15575 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 14
15513 TTATATTAAA
15523 TATATAATAAAATT
1 TATATAATAAAATT
15537 TATATAATATAAAATAT
1 TATAT-A-ATAAAAT-T
* *
15554 TAATTTATTAAAATT
1 T-ATATAATAAAATT
15569 TATATAA
1 TATATAA
15576 ATATATAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.29
15 3 0.10
16 13 0.42
17 3 0.10
18 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAATAAAATT
Found at i:15548 original size:16 final size:16
Alignment explanation
Indices: 15529--15580 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
15519 TAAATATATA
15529 ATAAAATTTATATAAT
1 ATAAAATTTATATAAT
*
15545 ATAAAATATTA-AT-TT
1 ATAAAAT-TTATATAAT
15560 ATTAAAATTTATATAAAT
1 A-TAAAATTTATAT-AAT
15578 ATA
1 ATA
15581 TAAGATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 5 0.17
16 17 0.59
17 5 0.17
18 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAATTTATATAAT
Found at i:15553 original size:12 final size:12
Alignment explanation
Indices: 15483--15553 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 12
15473 CAATTAGAGG
*
15483 ATAAAATGTAAT
1 ATAAAATATAAT
15495 ATAAAA-ATAAT
1 ATAAAATATAAT
*
15506 -TAAAATATTAT
1 ATAAAATATAAT
15517 ATTAAATATATAAT
1 A-TAAA-ATATAAT
15531 A-AAATTTATATAAT
1 ATAAA---ATATAAT
15545 ATAAAATAT
1 ATAAAATAT
15554 TAATTTATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
10 5 0.10
11 8 0.16
12 13 0.27
13 4 0.08
14 16 0.33
15 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:21198 original size:2 final size:2
Alignment explanation
Indices: 21191--21224 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21181 TATTACTAAT
21191 TA TA TA TA TA TA TA TA TA TA 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
21225 AACTTGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22925 original size:2 final size:2
Alignment explanation
Indices: 22918--22946 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22908 CTAGAAGCCC
22918 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
22947 AATGGCTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:23958 original size:18 final size:18
Alignment explanation
Indices: 23931--23972 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
23921 TATCAGCAAT
*
23931 AGCCAAAGCCAAAGCCAC
1 AGCCACAGCCAAAGCCAC
* *
23949 AGCCACAGCCATAGCCAT
1 AGCCACAGCCAAAGCCAC
23967 AGCCAC
1 AGCCAC
23973 CAGCATCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.40, G:0.17, T:0.05
Consensus pattern (18 bp):
AGCCACAGCCAAAGCCAC
Found at i:25276 original size:127 final size:127
Alignment explanation
Indices: 25102--25367 Score: 462
Period size: 127 Copynumber: 2.1 Consensus size: 127
25092 TAAATATATA
* ** *
25102 AATAATTAATACCATCCAAATGGATAAAAGAGGTTAATTTTATTATATATTGAACATTAAATATA
1 AATATTTAATACCATCCAAAAAGATAAAAGAGGTTAATTCTATTATATATTGAACATTAAATATA
25167 TATATATTT-GTAATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
66 TATATATTTGGT-ATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
* *
25229 AATATTTAATACCATCCAAAAAGATAAGAGAGGTTAATTCTATTATATATTGAACATTATATATA
1 AATATTTAATACCATCCAAAAAGATAAAAGAGGTTAATTCTATTATATATTGAACATTAAATATA
25294 TATATATTTGGTATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
66 TATATATTTGGTATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
25356 AATATTTAATAC
1 AATATTTAATAC
25368 TCCTTTATCG
Statistics
Matches: 132, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
127 130 0.98
128 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (127 bp):
AATATTTAATACCATCCAAAAAGATAAAAGAGGTTAATTCTATTATATATTGAACATTAAATATA
TATATATTTGGTATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
Found at i:26977 original size:17 final size:17
Alignment explanation
Indices: 26955--26987 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
26945 TTCTTGAACA
26955 AATTTAGTATCATATTC
1 AATTTAGTATCATATTC
26972 AATTTAGTATCATATT
1 AATTTAGTATCATATT
26988 AATCCCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (17 bp):
AATTTAGTATCATATTC
Found at i:38414 original size:3 final size:3
Alignment explanation
Indices: 38408--38445 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
38398 AAAAAGTGTT
38408 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38446 TTGCATGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40002 original size:19 final size:18
Alignment explanation
Indices: 39969--40009 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
39959 AAATTGAATT
39969 ATTTAATATATTTAATAA
1 ATTTAATATATTTAATAA
* *
39987 ATTTAATTTGATTTAATTA
1 ATTTAATAT-ATTTAATAA
40006 ATTT
1 ATTT
40010 TAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTAATATATTTAATAA
Found at i:40013 original size:26 final size:25
Alignment explanation
Indices: 39942--40026 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 25
39932 TATTGTATTT
* * * *
39942 TTTATATATTTAATTATAAATTGAA
1 TTTATTTAATTAATTTTAAATTTAA
39967 -TTATTTAA-TATATTTAATAAATTTAA
1 TTTATTTAATTA-ATTT--TAAATTTAA
*
39993 TTTGATTTAATTAATTTTAAATATAA
1 TTT-ATTTAATTAATTTTAAATTTAA
40019 TTTTATTT
1 -TTTATTT
40027 TATTTTAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
23 2 0.04
24 9 0.19
26 20 0.42
27 5 0.10
28 10 0.21
29 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTATTTAATTAATTTTAAATTTAA
Found at i:40078 original size:15 final size:15
Alignment explanation
Indices: 40058--40100 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
40048 ATTATTAAGT
*
40058 AATAATTTTTAAAAA
1 AATAATTATTAAAAA
40073 AATAATTATTAAAATATA
1 AATAATTATT-AAA-A-A
40091 AATAATTATT
1 AATAATTATT
40101 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 3 0.12
17 1 0.04
18 11 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAATTATTAAAAA
Found at i:41524 original size:27 final size:27
Alignment explanation
Indices: 41473--41525 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
41463 AAAACTATTA
**
41473 TTGCATGTAGAGTAGTAAATTTTTTTT
1 TTGCATGTAGAGTAGTAAAAGTTTTTT
*
41500 TTGCATGTAGAGTGGTAAAAGTTTTT
1 TTGCATGTAGAGTAGTAAAAGTTTTT
41526 ATAACTACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (27 bp):
TTGCATGTAGAGTAGTAAAAGTTTTTT
Done.