Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1255
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: 65327
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1999 original size:32 final size:32
Alignment explanation
Indices: 1956--2016 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1946 AGCTTTTGGT
1956 TTTTTCATGTTGTCAAAGAGTTGAACAATAGG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATAGG
*
1988 TTTTTCGTGTTGTCAAAGAGTTGAACAAT
1 TTTTTCATGTTGTCAAAGAGTTGAACAAT
2017 GAAAATAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATAGG
Found at i:10219 original size:27 final size:27
Alignment explanation
Indices: 10181--10233 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
10171 TCACTAACTA
10181 ATACTAATCTAATACTAATAGAATAGT
1 ATACTAATCTAATACTAATAGAATAGT
10208 ATACTAATCTAATACTAATAGAATAG
1 ATACTAATCTAATACTAATAGAATAG
10234 AAAAAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (27 bp):
ATACTAATCTAATACTAATAGAATAGT
Found at i:10220 original size:5 final size:6
Alignment explanation
Indices: 10177--10227 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
10167 GGGATCACTA
* *
10177 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT AGT-AT ACTAAT -CTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
10221 ACTAAT A
1 ACTAAT A
10228 GAATAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 18 0.47
6 20 0.53
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (6 bp):
ACTAAT
Found at i:10243 original size:14 final size:14
Alignment explanation
Indices: 10224--10251 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10214 ATCTAATACT
10224 AATAGAATAGAAAA
1 AATAGAATAGAAAA
10238 AATAGAATAGAAAA
1 AATAGAATAGAAAA
10252 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:15524 original size:22 final size:24
Alignment explanation
Indices: 15498--15543 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
15488 TGTCCATCTT
15498 TTTAATAGAATC-T-ATATATATA
1 TTTAATAGAATCTTAATATATATA
*
15520 TTTAATATAATCTTAATATATATA
1 TTTAATAGAATCTTAATATATATA
15544 AGACATCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 9 0.43
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTAATAGAATCTTAATATATATA
Found at i:18538 original size:18 final size:18
Alignment explanation
Indices: 18509--18586 Score: 120
Period size: 18 Copynumber: 4.3 Consensus size: 18
18499 GTCACGATCG
*
18509 ATATCGTCACTATCATCA
1 ATATCGTCACTAGCATCA
* *
18527 ATAGCTTCACTAGCATCA
1 ATATCGTCACTAGCATCA
18545 ATATCGTCACTAGCATCA
1 ATATCGTCACTAGCATCA
*
18563 ATATCGTCACTATCATCA
1 ATATCGTCACTAGCATCA
18581 ATATCG
1 ATATCG
18587 ATATCATCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (18 bp):
ATATCGTCACTAGCATCA
Found at i:18556 original size:36 final size:36
Alignment explanation
Indices: 18509--18598 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
18499 GTCACGATCG
*
18509 ATATCGTCACTATCATCAATAGCTTCACTAGCATCA
1 ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
* * *
18545 ATATCGTCACTAGCATCAATATCGTCACTATCATCA
1 ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
18581 ATATCG--A-TATCATCAATA
1 ATATCGTCACTATCATCAATA
18599 AGAAAACCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 10 0.20
34 1 0.02
36 38 0.78
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (36 bp):
ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
Found at i:18585 original size:9 final size:9
Alignment explanation
Indices: 18509--18585 Score: 55
Period size: 9 Copynumber: 8.6 Consensus size: 9
18499 GTCACGATCG
*
18509 ATATCGTCA
1 ATATCATCA
*
18518 CTATCATCA
1 ATATCATCA
* *
18527 ATAGCTTCA
1 ATATCATCA
* *
18536 CTAGCATCA
1 ATATCATCA
*
18545 ATATCGTCA
1 ATATCATCA
* *
18554 CTAGCATCA
1 ATATCATCA
*
18563 ATATCGTCA
1 ATATCATCA
*
18572 CTATCATCA
1 ATATCATCA
18581 ATATC
1 ATATC
18586 GATATCATCA
Statistics
Matches: 49, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (9 bp):
ATATCATCA
Found at i:18591 original size:15 final size:17
Alignment explanation
Indices: 18509--18598 Score: 94
Period size: 18 Copynumber: 5.2 Consensus size: 17
18499 GTCACGATCG
18509 ATATCGTCACTATCATCA
1 ATATCG-CACTATCATCA
* * *
18527 ATAGCTTCACTAGCATCA
1 ATATC-GCACTATCATCA
*
18545 ATATCGTCACTAGCATCA
1 ATATCG-CACTATCATCA
18563 ATATCGTCACTATCATCA
1 ATATCG-CACTATCATCA
18581 ATATCG-A-TATCATCA
1 ATATCGCACTATCATCA
18596 ATA
1 ATA
18599 AGAAAACCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
15 11 0.17
16 1 0.02
18 52 0.81
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (17 bp):
ATATCGCACTATCATCA
Found at i:20994 original size:21 final size:21
Alignment explanation
Indices: 20964--21052 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
20954 CTCACAAAGA
* *
20964 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
20984 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
21005 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
21026 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
21050 AAA
1 AAA
21053 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:21045 original size:24 final size:21
Alignment explanation
Indices: 20964--21032 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
20954 CTCACAAAGA
* * *
20964 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
20984 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
21005 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
21026 AAAAAGA
1 AAAAAGA
21033 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:25226 original size:14 final size:14
Alignment explanation
Indices: 25207--25237 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
25197 TACAATATAT
25207 ATAAGAATTATACG
1 ATAAGAATTATACG
25221 ATAAGAATTATACG
1 ATAAGAATTATACG
25235 ATA
1 ATA
25238 TATATCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:25867 original size:14 final size:14
Alignment explanation
Indices: 25850--25902 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
25840 ATATTTATAT
25850 TAAATATTATTAAA
1 TAAATATTATTAAA
25864 TAAATATTATTAAA
1 TAAATATTATTAAA
* *
25878 TTATTATTATTAAAA
1 TAAATATTATT-AAA
25893 TGAAATATTA
1 T-AAATATTA
25903 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 23 0.70
15 4 0.12
16 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATATTATTAAA
Found at i:30878 original size:3 final size:3
Alignment explanation
Indices: 30866--30975 Score: 61
Period size: 3 Copynumber: 37.7 Consensus size: 3
30856 CAATTTTTTT
* * *
30866 TTA TTAA TTA TTA TT- TTC TT- TTT TTT TTA TTA TT- TT- TTA TTAA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * * *
30909 TTA TTA TTA ATA TT- TTA TTAA TTA TTA TTA ATA TT- TTT TTA ATA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * *
30953 TTA ATA TTT TTA TTA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
30976 TCCTATTTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
2 12 0.14
3 64 0.75
4 9 0.11
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30901 original size:10 final size:10
Alignment explanation
Indices: 30858--30938 Score: 58
Period size: 10 Copynumber: 8.1 Consensus size: 10
30848 AATTTAGTCA
*
30858 ATTTTTTTTT
1 ATTTTTTATT
**
30868 ATTAATTATT
1 ATTTTTTATT
30878 ATTTTCTT-TT
1 ATTTT-TTATT
30888 -TTTTTTATT
1 ATTTTTTATT
30897 ATTTTTTATT
1 ATTTTTTATT
* *
30907 AATTATTATT
1 ATTTTTTATT
*
30917 AATATTTTATT
1 -ATTTTTTATT
* *
30928 AATTATTATT
1 ATTTTTTATT
30938 A
1 A
30939 ATATTTTTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
8 2 0.04
9 6 0.11
10 37 0.69
11 9 0.17
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:30926 original size:21 final size:20
Alignment explanation
Indices: 30864--30967 Score: 103
Period size: 21 Copynumber: 5.4 Consensus size: 20
30854 GTCAATTTTT
* *
30864 TTTTATTAATTATTATTTTC
1 TTTTATTAATTATTATTATA
*
30884 TTTT-TT--TT-TTATTATT
1 TTTTATTAATTATTATTATA
30900 TTTTATTAATTATTATTAATA
1 TTTTATTAATTATTATT-ATA
30921 TTTTATTAATTATTATTAATA
1 TTTTATTAATTATTATT-ATA
* *
30942 TTTTTTTAA-TATTAATAT-
1 TTTTATTAATTATTATTATA
30960 TTTTATTA
1 TTTTATTA
30968 TTAATATTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.14
17 4 0.05
18 7 0.10
19 6 0.08
20 15 0.21
21 31 0.42
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATTAATTATTATTATA
Found at i:30939 original size:10 final size:10
Alignment explanation
Indices: 30892--30940 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
30882 TCTTTTTTTT
* *
30892 TTATTATTTT
1 TTATTAATTA
30902 TTATTAATTA
1 TTATTAATTA
*
30912 TTATTAATATT
1 TTATTAAT-TA
30923 TTATTAATTA
1 TTATTAATTA
30933 TTATTAAT
1 TTATTAAT
30941 ATTTTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATTAATTA
Found at i:30971 original size:21 final size:21
Alignment explanation
Indices: 30900--30975 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
30890 TTTTATTATT
*
30900 TTTTATTAATTATTATTAATA
1 TTTTATTAATTAATATTAATA
*
30921 TTTTATTAATTATTATTAATA
1 TTTTATTAATTAATATTAATA
30942 -TTT-TT--TTAATATTAATA
1 TTTTATTAATTAATATTAATA
30959 TTTTTATT-ATTAATATT
1 -TTTTATTAATTAATATT
30976 TCCTATTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
17 11 0.22
19 5 0.10
20 5 0.10
21 29 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATTAATTAATATTAATA
Found at i:31631 original size:15 final size:15
Alignment explanation
Indices: 31611--31640 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31601 ATGTCTATGC
*
31611 ATGGAATTATAATGT
1 ATGGAATTAGAATGT
31626 ATGGAATTAGAATGT
1 ATGGAATTAGAATGT
31641 CAAAAAGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (15 bp):
ATGGAATTAGAATGT
Found at i:32674 original size:19 final size:19
Alignment explanation
Indices: 32658--32712 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
32648 TTTTATTATC
32658 CTTTTCTATTCTAATTAGA
1 CTTTTCTATTCTAATTAGA
32677 CTTTTCTATTCTAATTAGA
1 CTTTTCTATTCTAATTAGA
32696 CTTTTCTATTCTAATTA
1 CTTTTCTATTCTAATTA
32713 ATAAGAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (19 bp):
CTTTTCTATTCTAATTAGA
Found at i:32824 original size:17 final size:17
Alignment explanation
Indices: 32802--32835 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
32792 CCTTGCATCT
32802 TCAAATAACCCGATAGA
1 TCAAATAACCCGATAGA
*
32819 TCAAATAACTCGATAGA
1 TCAAATAACCCGATAGA
32836 ATAGATCCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (17 bp):
TCAAATAACCCGATAGA
Found at i:33897 original size:13 final size:13
Alignment explanation
Indices: 33879--33905 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33869 TCAACTCTTA
33879 TTACAAGTTAATT
1 TTACAAGTTAATT
33892 TTACAAGTTAATT
1 TTACAAGTTAATT
33905 T
1 T
33906 CTGAAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTACAAGTTAATT
Found at i:34435 original size:13 final size:13
Alignment explanation
Indices: 34417--34442 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34407 GATTCTTAAT
34417 TTTATTATATAGA
1 TTTATTATATAGA
34430 TTTATTATATAGA
1 TTTATTATATAGA
34443 AGATAGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTATTATATAGA
Found at i:34471 original size:21 final size:21
Alignment explanation
Indices: 34445--34484 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
34435 TATATAGAAG
34445 ATAGATATATACAACTTTTCT
1 ATAGATATATACAACTTTTCT
*
34466 ATAGATATATAGAACTTTT
1 ATAGATATATACAACTTTT
34485 ATCAGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (21 bp):
ATAGATATATACAACTTTTCT
Found at i:34516 original size:21 final size:21
Alignment explanation
Indices: 34492--34531 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
34482 TTTATCAGTA
*
34492 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATTTATATTAT
* *
34513 ATTCTATATCATTTCTATT
1 ATTCCATATCATTTATATT
34532 CTATAGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTCCATATCATTTATATTAT
Found at i:35805 original size:24 final size:22
Alignment explanation
Indices: 35761--35805 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
35751 CTTATTTATA
*
35761 TTTTTTATATTTTCGATTTCCT
1 TTTTTTATATTTTCCATTTCCT
*
35783 TTTTTTTTATTTATCCATCTTCC
1 TTTTTTATATTT-TCCAT-TTCC
35806 ATTGAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.13, C:0.18, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTATATTTTCCATTTCCT
Found at i:36319 original size:20 final size:20
Alignment explanation
Indices: 36273--36312 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
36263 TCTATATAGA
*
36273 ATAATATTCTAAATTCTAAT
1 ATAATATTCTAAATTCGAAT
36293 ATAATATTCTAAATTCGAAT
1 ATAATATTCTAAATTCGAAT
36313 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (20 bp):
ATAATATTCTAAATTCGAAT
Found at i:36348 original size:12 final size:12
Alignment explanation
Indices: 36333--36357 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36323 TATCTATATA
36333 TAATTAGATAAT
1 TAATTAGATAAT
36345 TAATTAGATAAT
1 TAATTAGATAAT
36357 T
1 T
36358 TTTCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TAATTAGATAAT
Found at i:36404 original size:19 final size:19
Alignment explanation
Indices: 36354--36404 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
36344 TTAATTAGAT
36354 AATTTTTCTATTTTTATTA
1 AATTTTTCTATTTTTATTA
* *
36373 AA-ATTTCTAATTTTATTTA
1 AATTTTTCTATTTTTA-TTA
36392 AATTTTTCTATTT
1 AATTTTTCTATTT
36405 AAATTTAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 11 0.42
19 7 0.27
20 8 0.31
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTTCTATTTTTATTA
Found at i:36405 original size:18 final size:19
Alignment explanation
Indices: 36354--36405 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
36344 TTAATTAGAT
*
36354 AATTTTTCTATTTTTATTA
1 AATTTTTCTATTTATATTA
*
36373 AA-ATTTCTAATTT-TATTTA
1 AATTTTTCT-ATTTATA-TTA
36392 AATTTTTCTATTTA
1 AATTTTTCTATTTA
36406 AATTTAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 7 0.26
19 15 0.56
20 5 0.19
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTCTATTTATATTA
Found at i:39511 original size:19 final size:18
Alignment explanation
Indices: 39487--39523 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
39477 TTTTTTTTAA
39487 TAAATTATTAATTTATTAT
1 TAAATTATTAA-TTATTAT
*
39506 TAAATTATTCATTATTAT
1 TAAATTATTAATTATTAT
39524 GAATTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAATTATTAATTATTAT
Found at i:43231 original size:8 final size:8
Alignment explanation
Indices: 43218--43243 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
43208 CTTTATTACT
43218 ATTAACAA
1 ATTAACAA
43226 ATTAACAA
1 ATTAACAA
43234 ATTAACAA
1 ATTAACAA
43242 AT
1 AT
43244 CAAATGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (8 bp):
ATTAACAA
Found at i:57250 original size:13 final size:12
Alignment explanation
Indices: 57232--57264 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
57222 TAATTTATGG
57232 GAACAAATAAATA
1 GAACAAATAAA-A
57245 GAACAAATAAAA
1 GAACAAATAAAA
57257 -AACAAATA
1 GAACAAATA
57265 GCGGTAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 1 0.05
13 11 0.55
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (12 bp):
GAACAAATAAAA
Found at i:59763 original size:15 final size:15
Alignment explanation
Indices: 59743--59776 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
59733 ATACAATATC
59743 AATATTAAATTAAAT
1 AATATTAAATTAAAT
59758 AATATTAAATTAAAT
1 AATATTAAATTAAAT
59773 AATA
1 AATA
59777 GGTAATAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATTAAATTAAAT
Found at i:61828 original size:13 final size:12
Alignment explanation
Indices: 61801--61833 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
61791 TCCCTACCGC
61801 TATTTGTT-TTT
1 TATTTGTTCTTT
61812 TATTTGTTCTATT
1 TATTTGTTCT-TT
61825 TATTTGTTC
1 TATTTGTTC
61834 CCATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 1 0.05
13 11 0.55
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73
Consensus pattern (12 bp):
TATTTGTTCTTT
Done.