Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold736
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: 33232
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Found at i:6482 original size:52 final size:52
Alignment explanation
Indices: 6334--6462 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
6324 TGAAATATGA
6334 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
* * *
6386 AAATTTGCTTGTATGTATCGATACATTTTATAGTGTATCGATACATCTAGG-C
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCT-GGAC
6438 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
6463 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
52 69 0.97
53 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
Found at i:6489 original size:13 final size:13
Alignment explanation
Indices: 6471--6495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6461 CAAAGATCAG
6471 TGTATCGATACAA
1 TGTATCGATACAA
6484 TGTATCGATACA
1 TGTATCGATACA
6496 TTTGGGTAAT
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):
TGTATCGATACAA
Found at i:6558 original size:13 final size:13
Alignment explanation
Indices: 6540--6590 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 13
6530 AGCTTCGTAG
6540 CGATACATTGTAT
1 CGATACATTGTAT
6553 CGATACAAACTTATGTAT
1 CGATAC--A--T-TGTAT
6571 CGATACATTGTAT
1 CGATACATTGTAT
6584 CGATACA
1 CGATACA
6591 ACATTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 18 0.55
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.33
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:6578 original size:31 final size:32
Alignment explanation
Indices: 6540--6609 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
6530 AGCTTCGTAG
6540 CGATACATTGTATCGATACAA-ACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
6571 CGATACATTGTATCGATACAACATTTTTGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
6603 CGATACA
1 CGATACA
6610 AATCGTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 21 0.58
32 15 0.42
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:6765 original size:20 final size:20
Alignment explanation
Indices: 6740--6780 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6730 TCTCGACTAG
6740 GGACGATGAGAAATGGATTC
1 GGACGATGAGAAATGGATTC
6760 GGACGATGAGAAATGGATTC
1 GGACGATGAGAAATGGATTC
6780 G
1 G
6781 TCCCCACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.37, T:0.20
Consensus pattern (20 bp):
GGACGATGAGAAATGGATTC
Found at i:12307 original size:3 final size:3
Alignment explanation
Indices: 12299--12346 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
12289 CAACTTCTTT
* * *
12299 ATC ATC ATC ATC ATT ATC ATC ATC TTC ATC ATC ATC TTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
12347 TTTGATGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (3 bp):
ATC
Found at i:12319 original size:12 final size:12
Alignment explanation
Indices: 12300--12348 Score: 82
Period size: 12 Copynumber: 4.1 Consensus size: 12
12290 AACTTCTTTA
12300 TCATCATCATCAT
1 TCATCATCATC-T
12313 T-ATCATCATCT
1 TCATCATCATCT
12324 TCATCATCATCT
1 TCATCATCATCT
12336 TCATCATCATCT
1 TCATCATCATCT
12348 T
1 T
12349 TGATGGTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.91
13 1 0.03
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.43
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:14082 original size:33 final size:33
Alignment explanation
Indices: 13995--14082 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 33
13985 TTCATGTATT
*
13995 GATACAAAGCAATATGTATCAATACAATATATC
1 GATACAAAGCAATATGTATCGATACAATATATC
* *
14028 GATACAAAGCAATATGCATCGATATAATATATC
1 GATACAAAGCAATATGTATCGATACAATATATC
*
14061 GATACAAAGTAATATGTATCGA
1 GATACAAAGCAATATGTATCGA
14083 AACATCTGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (33 bp):
GATACAAAGCAATATGTATCGATACAATATATC
Found at i:15520 original size:65 final size:66
Alignment explanation
Indices: 15408--15615 Score: 217
Period size: 65 Copynumber: 3.1 Consensus size: 66
15398 TCAAATCGAC
* *
15408 CCTTTTCGATTTAGGTTTCATCCTAGTCAAC-TTTAATTGACTATACTAGTTTAGCCCTGGTCAA
1 CCTTTTCGATATAGGTTTCATCCTAGTCAACTTTTAATTGACTATACTAGTTTAGCCATGGTCAA
15472 -
66 T
* * * *
15472 CTTTTCTCGATATAGGTTTCATCCTAGTC-ACTTTTAGTTGACTGTACTAGTTTAGCCATGTTCA
1 CCTTT-TCGATATAGGTTTCATCCTAGTCAACTTTTAATTGACTATACTAGTTTAGCCATGGTCA
15536 AT
65 AT
* * * *
15538 CCTTTTCGACTA-ATGTTTCACCCTAGTCAACTTTTCTAACTTGTTGACTATACTGGTTTAGCCT
1 CCTTTTCGA-TATAGGTTTCATCCTAGTCAAC-TTT-TAA----TTGACTATACTAGTTTAGCCA
*
15602 TGGTCAAC
59 TGGTCAAT
15610 CCTTTT
1 CCTTTT
15616 AATTTGTTAA
Statistics
Matches: 118, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
64 6 0.05
65 69 0.58
66 8 0.07
67 3 0.03
68 2 0.02
72 30 0.25
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (66 bp):
CCTTTTCGATATAGGTTTCATCCTAGTCAACTTTTAATTGACTATACTAGTTTAGCCATGGTCAA
T
Found at i:15608 original size:41 final size:40
Alignment explanation
Indices: 15563--15656 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 40
15553 TTTCACCCTA
* * * *
15563 GTCAACTTTTCTAACTTGTTGACTATACTGGTTTAGCCTTG
1 GTCAACCTTT-TAACTTGTTAACTATAATAGTTTAGCCTTG
* * *
15604 GTCAACCCTTTTAATTTGTTAACTGTAATAGTTTAGCTTTG
1 GTCAA-CCTTTTAACTTGTTAACTATAATAGTTTAGCCTTG
15645 GTCAACCCTTTT
1 GTCAA-CCTTTT
15657 TTACTTAGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 41 0.91
42 4 0.09
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (40 bp):
GTCAACCTTTTAACTTGTTAACTATAATAGTTTAGCCTTG
Found at i:15775 original size:105 final size:106
Alignment explanation
Indices: 15578--15827 Score: 265
Period size: 105 Copynumber: 2.4 Consensus size: 106
15568 CTTTTCTAAC
* * * * * * * **
15578 TTGTTGACTATACTGGTTTAGCCTTGGTCAACCCTTTTAATTTGTTAACTGTAATAGTTTAGCTT
1 TTGTTGACTATAATGGTTTAGCCCTGGTCAACCCCTCTAACTTATTAACTATAATAGTTTAGCCC
* * * * *
15643 TGGTCAACCCTTTTTTACTTAGGTTTCATCGTAGTTA-CCT
66 TAGTCAACCCTTTTTAACTTAAGTTTCATCATAGTCATCCT
** *
15683 TTAGTTGACTATAAT-GTTTAGCCCTGGTCAACCCCTCTAACTTATTGGCTATAATGGTTTAGCC
1 TT-GTTGACTATAATGGTTTAGCCCTGGTCAACCCCTCTAACTTATTAACTATAATAGTTTAGCC
15747 CTAGTCAA-CCTTTTTCAACTTAAGTTTCATCATAGTCATCCT
65 CTAGTCAACCCTTTTT-AACTTAAGTTTCATCATAGTCATCCT
* * * *
15789 TTGTTGATTGTAATGGTTTA-CCCTAGTCAACCACTCTAA
1 TTGTTGACTATAATGGTTTAGCCCTGGTCAACCCCTCTAA
15828 TTGGCTAAAT
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
104 7 0.06
105 92 0.77
106 21 0.17
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (106 bp):
TTGTTGACTATAATGGTTTAGCCCTGGTCAACCCCTCTAACTTATTAACTATAATAGTTTAGCCC
TAGTCAACCCTTTTTAACTTAAGTTTCATCATAGTCATCCT
Found at i:15880 original size:40 final size:41
Alignment explanation
Indices: 15792--15895 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 41
15782 TCATCCTTTG
* *
15792 TTGATTGTAATGGTTTA-CCCTAGTCAACCACTCTAATTGGC
1 TTGA-TGTAATGGTTTAGCCCTAGCCAACCACTCTAATTGGA
** * *
15833 TAAATGTAATGGTTTAGCCCTAGCCAACCTCTCTAATT-TA
1 TTGATGTAATGGTTTAGCCCTAGCCAACCACTCTAATTGGA
**
15873 TTGATGTAACAGTTTAGCCCTAG
1 TTGATGTAATGGTTTAGCCCTAG
15896 TTAACCCTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
40 31 0.60
41 21 0.40
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (41 bp):
TTGATGTAATGGTTTAGCCCTAGCCAACCACTCTAATTGGA
Found at i:15945 original size:40 final size:41
Alignment explanation
Indices: 15840--15946 Score: 112
Period size: 40 Copynumber: 2.6 Consensus size: 41
15830 GGCTAAATGT
* * *
15840 AATGGTTTAGCCCTAGCCAACCTCTCTAATTTATTGATGTAA
1 AATGGTTTAGCCCTAGTCAACCT-TTTAATTTATTGATCTAA
* * *
15882 CA--GTTTAGCCCTAGTTAACCCTTTTAATTTGTTGA-CTAA
1 AATGGTTTAGCCCTAGTCAA-CCTTTTAATTTATTGATCTAA
*
15921 AATGGTTTAGCTCTAGTCAACCTTTT
1 AATGGTTTAGCCCTAGTCAACCTTTT
15947 TTACTTAGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
39 4 0.08
40 31 0.58
41 17 0.32
42 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (41 bp):
AATGGTTTAGCCCTAGTCAACCTTTTAATTTATTGATCTAA
Found at i:16402 original size:41 final size:41
Alignment explanation
Indices: 16345--16458 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
16335 TTGGTTATTC
* * * ** *
16345 TTTGTTGACTCATATGGTTTCATCTCGGTCAACTTTTC-CTT
1 TTTGTTGACTCGTATGGTTTCATCCCGATCAACACTTCTC-A
* *
16386 TTTGTTAACTCGTATGGTTTTATCCCGATCAACACTTCTCA
1 TTTGTTGACTCGTATGGTTTCATCCCGATCAACACTTCTCA
* *
16427 TATGTTGACTCGTATGGTTTCATCCCAATCAA
1 TTTGTTGACTCGTATGGTTTCATCCCGATCAA
16459 TAGTTTTCCC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 59 0.98
42 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (41 bp):
TTTGTTGACTCGTATGGTTTCATCCCGATCAACACTTCTCA
Found at i:16816 original size:41 final size:41
Alignment explanation
Indices: 16770--16848 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
16760 TTGGTCACCC
* * *
16770 TTCATTGACTTTTATGGTTTTGT-CTAGATCAATTTTTTTCA
1 TTCATTGACTCTTATGGTTTTATCCTA-ATCAATCTTTTTCA
16811 TTCATTGACTCTTATGGTTTTATCCTAATCAATCTTTT
1 TTCATTGACTCTTATGGTTTTATCCTAATCAATCTTTT
16849 AAGTTTCTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 31 0.91
42 3 0.09
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.54
Consensus pattern (41 bp):
TTCATTGACTCTTATGGTTTTATCCTAATCAATCTTTTTCA
Found at i:18089 original size:6 final size:6
Alignment explanation
Indices: 18080--18105 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
18070 TTTATGATTA
18080 TTAATT TTAATT TTAATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TT
18106 GGGTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTAATT
Found at i:23171 original size:36 final size:35
Alignment explanation
Indices: 23116--23193 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
23106 ATTAGATCTA
*
23116 ATAATTTATGTAATCATATTGTGTATTTATTATATT
1 ATAATTTATGTAATCATATTGTATATTTA-TATATT
* * *
23152 ATAATTTTATTTAAT-ATATTTTATATTTATATATG
1 ATAA-TTTATGTAATCATATTGTATATTTATATATT
23187 AT-ATTTA
1 ATAATTTA
23194 AATAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 1 0.03
35 7 0.19
36 16 0.43
37 9 0.24
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (35 bp):
ATAATTTATGTAATCATATTGTATATTTATATATT
Found at i:23245 original size:27 final size:28
Alignment explanation
Indices: 23159--23284 Score: 100
Period size: 28 Copynumber: 4.5 Consensus size: 28
23149 ATTATAATTT
*
23159 TATTTAATATATTTTATATTTATATATGA
1 TATTTAAAATATTTTATATTTATATAT-A
* *
23188 TATTT-AAATAATTTATA-TTATATAAA
1 TATTTAAAATATTTTATATTTATATATA
*
23214 TTTTTAAAATATTTATATATTTATAT-TA
1 TATTTAAAATATTT-TATATTTATATATA
* **
23242 TTTTGTATTATCATTTTAT-TTTATAT-TA
1 TATT-TAAAAT-ATTTTATATTTATATATA
* *
23270 TATTTTAATTATTTT
1 TATTTAAAATATTTT
23285 TTTATATAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
26 10 0.13
27 16 0.20
28 31 0.39
29 18 0.23
30 4 0.05
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.61
Consensus pattern (28 bp):
TATTTAAAATATTTTATATTTATATATA
Found at i:23262 original size:18 final size:17
Alignment explanation
Indices: 23223--23305 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 17
23213 ATTTTTAAAA
*
23223 TATTTATATATT-TATAT
1 TATTT-TATATTATATTT
*
23240 TATTTTGTATTATCATTT
1 TATTTTATATTAT-ATTT
23258 TATTTTATATTATATTT
1 TATTTTATATTATATTT
* * *
23275 TAATTATTTTTTTATATAAT
1 T-ATT-TTATATTATAT-TT
23295 TATTTTATATT
1 TATTTTATATT
23306 TAATATTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
16 5 0.09
17 11 0.21
18 23 0.43
19 12 0.23
20 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (17 bp):
TATTTTATATTATATTT
Found at i:23273 original size:23 final size:22
Alignment explanation
Indices: 23226--23314 Score: 58
Period size: 23 Copynumber: 4.0 Consensus size: 22
23216 TTTAAAATAT
* * *
23226 TTATATATTTATATTATTTTGTA
1 TTATAT-TTTATTTTATATTATA
23249 TTATCATTTTATTTTATATTATA
1 TTAT-ATTTTATTTTATATTATA
* *
23272 TTTTAATTATTTTTTTATA-TA-A
1 TTAT-ATT-TTATTTTATATTATA
*
23294 TTAT-TTTATATTTAATATTAT
1 TTATATTT-TATTTTATATTAT
23315 CAAATCTAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
19 1 0.02
20 9 0.17
21 2 0.04
22 4 0.08
23 25 0.48
24 11 0.21
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (22 bp):
TTATATTTTATTTTATATTATA
Found at i:23280 original size:11 final size:12
Alignment explanation
Indices: 23145--23305 Score: 54
Period size: 13 Copynumber: 13.6 Consensus size: 12
23135 TGTGTATTTA
23145 TTATATTATAATT
1 TTATATTAT-ATT
23158 TTAT-TTA-A-T
1 TTATATTATATT
* *
23167 ATATTTTATATT
1 TTATATTATATT
*
23179 TATATATGATATT
1 T-TATATTATATT
* *
23192 TAAATAATT-TATA
1 T-TAT-ATTATATT
*
23205 TTATA-TAAATT
1 TTATATTATATT
**
23216 TT-TAAAATATT
1 TTATATTATATT
*
23227 TATATATT-TATA
1 T-TATATTATATT
* *
23239 TTAT-TT-TGTA
1 TTATATTATATT
*
23249 TTATCATTTTATT
1 TTAT-ATTATATT
23262 TTATATTATATT
1 TTATATTATATT
*
23274 TTA-ATTATTTTT
1 TTATATTA-TATT
*
23286 TTATATAATTATT
1 TTATATTA-TATT
23299 TTATATT
1 TTATATT
23306 TAATATTATC
Statistics
Matches: 111, Mismatches: 23, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
9 4 0.04
10 16 0.14
11 18 0.16
12 29 0.26
13 42 0.38
14 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (12 bp):
TTATATTATATT
Found at i:23312 original size:39 final size:41
Alignment explanation
Indices: 23222--23312 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 41
23212 AATTTTTAAA
*
23222 ATATTTATATATTTATATTATTTTGTATTATCATTTTATTTT
1 ATATTTATAT-TTTATATTATTTTGTATTATCATATTATTTT
23264 ATA-TTATATTTTA-ATTATTTT-T-TTAT-ATAATTATTTT
1 ATATTTATATTTTATATTATTTTGTATTATCAT-ATTATTTT
23301 ATATTTAATATT
1 ATATTT-ATATT
23313 ATCAAATCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
36 2 0.04
37 14 0.31
38 3 0.07
39 13 0.29
40 4 0.09
41 6 0.13
42 3 0.07
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (41 bp):
ATATTTATATTTTATATTATTTTGTATTATCATATTATTTT
Found at i:28987 original size:29 final size:29
Alignment explanation
Indices: 28944--29000 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
28934 AATACCTTAT
* *
28944 TTATTATTTATATATTATTATT-ATTTAAA
1 TTATCATTTAAATATTATT-TTAATTTAAA
28973 TTATCATTTAAATATTATTTTAATTTAA
1 TTATCATTTAAATATTATTTTAATTTAA
29001 GTTTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATCATTTAAATATTATTTTAATTTAAA
Found at i:28994 original size:12 final size:12
Alignment explanation
Indices: 28960--28997 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28950 TTTATATATT
28960 ATTATTATTTAA
1 ATTATTATTTAA
*
28972 ATTATCATTTAA
1 ATTATTATTTAA
*
28984 A-TATTATTTTA
1 ATTATTATTTAA
28995 ATT
1 ATT
28998 TAAGTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATTATTTAA
Found at i:29005 original size:23 final size:23
Alignment explanation
Indices: 28962--29006 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28952 TATATATTAT
*
28962 TATTATTTAAATTATCATTTAAA
1 TATTATTTAAATTATAATTTAAA
*
28985 TATTATTTTAATT-TAAGTTTAA
1 TATTATTTAAATTATAA-TTTAA
29007 TTAATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTATTTAAATTATAATTTAAA
Found at i:29142 original size:15 final size:15
Alignment explanation
Indices: 29122--29151 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29112 CCTTCCTCTA
*
29122 ATTTATTTTTTATTT
1 ATTTATTTTTCATTT
29137 ATTTATTTTTCATTT
1 ATTTATTTTTCATTT
29152 TGATCTATAC
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:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTATTTTTCATTT
Found at i:29465 original size:40 final size:40
Alignment explanation
Indices: 29418--29514 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 40
29408 TTAAGTTTTG
* * *
29418 ATTATTTTTTACACTTTCACATCAAAATCAAGCTTTTAAA
1 ATTATTTTTTACATTTTCACATCAAAATAAAACTTTTAAA
* * * *
29458 ATTA-TTTTAATATTTTTACATCAAAATAAAACTTTTAAG
1 ATTATTTTTTACATTTTCACATCAAAATAAAACTTTTAAA
*
29497 ATT-TATTTTACATTTTCA
1 ATTATTTTTTACATTTTCA
29515 TCAAAACTAA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
39 41 0.91
40 4 0.09
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.47
Consensus pattern (40 bp):
ATTATTTTTTACATTTTCACATCAAAATAAAACTTTTAAA
Found at i:31107 original size:21 final size:23
Alignment explanation
Indices: 31076--31137 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
31066 TGAATAAAAG
31076 AAATAATTATATAATATA-AATT
1 AAATAATTATATAATATATAATT
*
31098 AAAT-ATTATATCATATATAATT
1 AAATAATTATATAATATATAATT
31120 -AATAATTA-ATAAATATAT
1 AAATAATTATAT-AATATAT
31138 GTAAGTCAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATAATTATATAATATATAATT
Found at i:31243 original size:12 final size:13
Alignment explanation
Indices: 31213--31250 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
31203 TTGTTCATAC
31213 TTATTTTTTAAAT
1 TTATTTTTTAAAT
* *
31226 TAATTTTTT-TAT
1 TTATTTTTTAAAT
31238 TTATTTTTTAAAT
1 TTATTTTTTAAAT
31251 ATTAAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTTTTAAAT
Found at i:31267 original size:19 final size:19
Alignment explanation
Indices: 31243--31296 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
31233 TTTATTTATT
31243 TTTTAAATATTAAATAA-AA
1 TTTTAAAT-TTAAATAATAA
31262 TTTTAAATTTAAATAAATAA
1 TTTTAAATTTAAAT-AATAA
31282 TTTTAAATTTAAATA
1 TTTTAAATTTAAATA
31297 GATCTACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.18
19 11 0.33
20 16 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTAAATTTAAATAATAA
Found at i:33112 original size:20 final size:19
Alignment explanation
Indices: 33086--33212 Score: 84
Period size: 20 Copynumber: 6.7 Consensus size: 19
33076 TTACATGTAA
33086 TACAT-AAACATTACTAAT
1 TACATAAAACATTACTAAT
* * * *
33104 TATATATAAACGTTATTAGT
1 TACATA-AAACATTACTAAT
* * *
33124 TATA-AAAATATTGC-AAGT
1 TACATAAAACATTACTAA-T
*
33142 TACATAAAATATTACTAAT
1 TACATAAAACATTACTAAT
33161 TACATACAAACATTA-TCAAT
1 TACATA-AAACATTACT-AAT
* * *
33181 TAAAAAAAATATTAC-AAT
1 TACATAAAACATTACTAAT
33199 TACATAAAACATTA
1 TACATAAAACATTA
33213 GCTTTCATAT
Statistics
Matches: 83, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
17 1 0.01
18 27 0.33
19 25 0.30
20 30 0.36
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (19 bp):
TACATAAAACATTACTAAT
Found at i:33152 original size:19 final size:18
Alignment explanation
Indices: 33128--33212 Score: 89
Period size: 19 Copynumber: 4.5 Consensus size: 18
33118 ATTAGTTATA
*
33128 AAAATATTGCAAGTTACAT
1 AAAATATTACAA-TTACAT
33147 AAAATATTACTAATTACAT
1 AAAATATTAC-AATTACAT
* * *
33166 ACAAACATTATCAATTAAAA
1 A-AAATATTA-CAATTACAT
33186 AAAATATTACAATTACAT
1 AAAATATTACAATTACAT
*
33204 AAAACATTA
1 AAAATATTA
33213 GCTTTCATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
18 15 0.27
19 23 0.42
20 16 0.29
21 1 0.02
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATATTACAATTACAT
Found at i:33161 original size:57 final size:57
Alignment explanation
Indices: 33086--33212 Score: 159
Period size: 57 Copynumber: 2.2 Consensus size: 57
33076 TTACATGTAA
* * * * * * *
33086 TACAT-AAACATTACTAATTATATATAAACGTTATTAGTT-ATAAAAATATTGCAAGT
1 TACATAAAACATTACTAATTACATACAAACATTATCAATTAAAAAAAATATTACAA-T
*
33142 TACATAAAATATTACTAATTACATACAAACATTATCAATTAAAAAAAATATTACAAT
1 TACATAAAACATTACTAATTACATACAAACATTATCAATTAAAAAAAATATTACAAT
33199 TACATAAAACATTA
1 TACATAAAACATTA
33213 GCTTTCATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
56 5 0.08
57 42 0.70
58 13 0.22
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (57 bp):
TACATAAAACATTACTAATTACATACAAACATTATCAATTAAAAAAAATATTACAAT
Done.