Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold816
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: 56479
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:777 original size:13 final size:13
Alignment explanation
Indices: 735--781 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
725 TATTATATTT
735 TTTATAATATTATA
1 TTTAT-ATATTATA
749 TTT-TA-ATTAT-
1 TTTATATATTATA
759 TTTATATATTATA
1 TTTATATATTATA
772 TTTATATATT
1 TTTATATATT
782 GATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
12 6 0.20
13 11 0.37
14 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATATATTATA
Found at i:1574 original size:30 final size:29
Alignment explanation
Indices: 1534--1592 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1524 AATTATTTGA
*
1534 AAATTTA-TTTTATTATTTATAATAATTTT
1 AAATTTATTTTTA-TATTAATAATAATTTT
*
1563 AAATATTATTTTTATATTAATATTAATTTT
1 AAAT-TTATTTTTATATTAATAATAATTTT
1593 TATAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 17 0.65
31 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
AAATTTATTTTTATATTAATAATAATTTT
Found at i:1582 original size:18 final size:20
Alignment explanation
Indices: 1561--1607 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
1551 TATAATAATT
1561 TTAAATATT-ATTTTTAT-A
1 TTAAATATTAATTTTTATAA
1579 TT-AATATTAATTTTTATAA
1 TTAAATATTAATTTTTATAA
1598 TTAAAT-TTAA
1 TTAAATATTAA
1608 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.23
18 10 0.38
19 7 0.27
20 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAAATATTAATTTTTATAA
Found at i:1595 original size:24 final size:25
Alignment explanation
Indices: 1540--1595 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
1530 TTGAAAATTT
*
1540 ATTTTATTATTTATAATAATTTTAA
1 ATTTTATTATTTATAATAATATTAA
* *
1565 ATATTATT-TTTATATTAATATTAA
1 ATTTTATTATTTATAATAATATTAA
*
1589 TTTTTAT
1 ATTTTAT
1596 AATTAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTATTATTTATAATAATATTAA
Found at i:2103 original size:9 final size:9
Alignment explanation
Indices: 2078--2109 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
2068 TATCATATTC
2078 ATATTTAAT
1 ATATTTAAT
2087 AT-TTTAAT
1 ATATTTAAT
2095 ATATTTAAT
1 ATATTTAAT
2104 A-ATTTA
1 ATATTTA
2110 TATTTATACG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 13 0.59
9 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTTAAT
Found at i:3033 original size:22 final size:22
Alignment explanation
Indices: 3008--3049 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2998 TTATGTAAGT
*
3008 ATATACAATTATGATATGAAAA
1 ATATACAAATATGATATGAAAA
*
3030 ATATATAAATATGATATGAA
1 ATATACAAATATGATATGAA
3050 TACACGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (22 bp):
ATATACAAATATGATATGAAAA
Found at i:4840 original size:11 final size:11
Alignment explanation
Indices: 4824--4887 Score: 62
Period size: 11 Copynumber: 5.8 Consensus size: 11
4814 ATATATAGTA
4824 ATATTTATATT
1 ATATTTATATT
4835 ATATTTATATT
1 ATATTTATATT
*
4846 ATTTTTTATATT
1 A-TATTTATATT
*
4858 ATAATTAT-TT
1 ATATTTATATT
4868 AATATGTTATA-T
1 -ATAT-TTATATT
4880 AT-TTTATA
1 ATATTTATA
4888 AATTTTGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
9 5 0.11
10 3 0.07
11 22 0.49
12 15 0.33
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
ATATTTATATT
Found at i:4856 original size:18 final size:18
Alignment explanation
Indices: 4833--4867 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4823 AATATTTATA
4833 TTATATT-TATATTATTTT
1 TTATATTATA-ATTATTTT
4851 TTATATTATAATTATTT
1 TTATATTATAATTATTT
4868 AATATGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTATAATTATTTT
Found at i:4877 original size:23 final size:23
Alignment explanation
Indices: 4809--4879 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
4799 AATCTTGAGA
*
4809 ATATTAT-A-TATAGTAATATTT
1 ATATTATAATTATATTAATATTT
* * *
4830 ATATTATATTTATATTATTTTTT
1 ATATTATAATTATATTAATATTT
4853 ATATTATAATTAT-TTAATATGTT
1 ATATTATAATTATATTAATAT-TT
4876 ATAT
1 ATAT
4880 ATTTTATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.17
22 5 0.12
23 28 0.70
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (23 bp):
ATATTATAATTATATTAATATTT
Found at i:4913 original size:32 final size:33
Alignment explanation
Indices: 4877--4949 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
4867 TAATATGTTA
* *
4877 TATATTTTATAAATTTTGATATA-CTAATAATT
1 TATATTATATAAATTTTAATATATCTAATAATT
* * *
4909 TATATCATATAAATTTTAATTTATTTAATAATT
1 TATATTATATAAATTTTAATATATCTAATAATT
4942 TATATTAT
1 TATATTAT
4950 CATATTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (33 bp):
TATATTATATAAATTTTAATATATCTAATAATT
Found at i:5360 original size:26 final size:26
Alignment explanation
Indices: 5331--5380 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5321 TAATGATAGT
5331 ATTTAAAATATTATAT-ATTTATATAA
1 ATTTAAAATATTA-ATGATTTATATAA
* *
5357 ATTTAATATGTTAATGATTTATAT
1 ATTTAAAATATTAATGATTTATAT
5381 TATATAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTTAAAATATTAATGATTTATATAA
Found at i:14984 original size:21 final size:21
Alignment explanation
Indices: 14955--14995 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
14945 AAAAATTAAT
* *
14955 TTTTTTATATTATTAGAAATA
1 TTTTATATATTATTACAAATA
*
14976 TTTTATATATTTTTACAAAT
1 TTTTATATATTATTACAAAT
14996 CTAATGAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATATATTATTACAAATA
Found at i:15516 original size:17 final size:17
Alignment explanation
Indices: 15477--15532 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
15467 AATTAAAAAT
* *
15477 ATTTTTTTTTTCTTTCA
1 ATTTTTCTTCTCTTTCA
* *
15494 ACTTTTCTTCTCTTTTA
1 ATTTTTCTTCTCTTTCA
* *
15511 ATTTTTCATAT-TTTCA
1 ATTTTTCTTCTCTTTCA
15527 ATTTTT
1 ATTTTT
15533 TTCACCCCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
16 10 0.32
17 21 0.68
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTCTTCTCTTTCA
Found at i:16409 original size:20 final size:19
Alignment explanation
Indices: 16356--16409 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
16346 AAATTTATAT
*
16356 AAATATAAAAATATTTTAAA
1 AAATATAATAATA-TTTAAA
* * *
16376 TAAGATTATAATATTTAAA
1 AAATATAATAATATTTAAA
16395 AAATATAATACATAT
1 AAATATAATA-ATAT
16410 ATATGAACAG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATATAATAATATTTAAA
Found at i:16904 original size:16 final size:16
Alignment explanation
Indices: 16885--16956 Score: 58
Period size: 16 Copynumber: 4.5 Consensus size: 16
16875 AACACAAATC
16885 CAAAATGACCTAAACT
1 CAAAATGACCTAAACT
*
16901 CAAAATGAACC-GAACT
1 CAAAATG-ACCTAAACT
* *
16917 CAAAAT-ATTCTGAACT
1 CAAAATGA-CCTAAACT
** *
16933 TGAAATGACCTAAACC
1 CAAAATGACCTAAACT
16949 CAAAATGA
1 CAAAATGA
16957 TTAAACTCGA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
14 1 0.02
15 1 0.02
16 37 0.86
17 4 0.09
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.19
Consensus pattern (16 bp):
CAAAATGACCTAAACT
Found at i:18834 original size:28 final size:26
Alignment explanation
Indices: 18792--18854 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
18782 ACGATTATAT
18792 AAATATA-ATA-TATATAAAATTATTA
1 AAATATATATAGTATAT-AAATTATTA
* *
18817 AAATATAATATAGTATATATATTTTTA
1 AAATAT-ATATAGTATATAAATTATTA
18844 AAATATATATA
1 AAATATATATA
18855 ATACGAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 6 0.18
26 6 0.18
27 16 0.48
28 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AAATATATATAGTATATAAATTATTA
Found at i:18868 original size:24 final size:25
Alignment explanation
Indices: 18792--18873 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 25
18782 ACGATTATAT
18792 AAATATAATATATATAAAATTATTA
1 AAATATAATATATATAAAATTATTA
* *
18817 AAATATAATATAGTATATATATTTTTA
1 AAATATAATATA-TATA-AAATTATTA
*
18844 AAATAT-ATATA-ATACGAATTATTA
1 AAATATAATATATATA-AAATTATTA
*
18868 ATATAT
1 AAATAT
18874 CAAAATTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
24 14 0.29
25 12 0.25
26 9 0.19
27 13 0.27
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATATAATATATATAAAATTATTA
Found at i:19830 original size:17 final size:18
Alignment explanation
Indices: 19795--19831 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
19785 ATGAATATTT
19795 TAAAATTTATATAATATA
1 TAAAATTTATATAATATA
19813 TCAAAATTTATATAATATA
1 T-AAAATTTATATAATATA
19832 AAATATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATTTATATAATATA
Found at i:20293 original size:28 final size:30
Alignment explanation
Indices: 20252--20307 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
20242 TATTCGAATA
*
20252 ATATTTTATATATT-TAAATTT-TATAATC
1 ATATTTAATATATTATAAATTTCTATAATC
* *
20280 ATATTTAATGTATTATATATTTCTATAA
1 ATATTTAATATATTATAAATTTCTATAA
20308 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.52
29 6 0.26
30 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (30 bp):
ATATTTAATATATTATAAATTTCTATAATC
Found at i:24723 original size:3 final size:3
Alignment explanation
Indices: 24688--24736 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
24678 TTAACCATCA
* * * * *
24688 ATG ACG ATG AAG ATA ATG ATA ATG ATG ACG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
24736 A
1 A
24737 AGTTGACTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.41, C:0.04, G:0.29, T:0.27
Consensus pattern (3 bp):
ATG
Found at i:27340 original size:18 final size:18
Alignment explanation
Indices: 27317--27352 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27307 ATTATGGCCA
27317 TGAGAGAAGAACTAAATT
1 TGAGAGAAGAACTAAATT
27335 TGAGAGAAGAACTAAATT
1 TGAGAGAAGAACTAAATT
27353 AAATTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
TGAGAGAAGAACTAAATT
Found at i:29208 original size:13 final size:13
Alignment explanation
Indices: 29190--29252 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
29180 GAGTTCTTAG
29190 TATCGATACATTA
1 TATCGATACATTA
*
29203 TATCGATAC-TCA
1 TATCGATACATTA
* *
29215 GTATCAATACATTT
1 -TATCGATACATTA
*
29229 TATCGATAC-TAAA
1 TATCGATACAT-TA
29242 TATCGATACAT
1 TATCGATACAT
29253 GGGTACTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.08
13 34 0.87
14 2 0.05
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:29224 original size:26 final size:26
Alignment explanation
Indices: 29162--29252 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
29152 TTTCTAGAGT
* * *
29162 GTATCGATATATTATA-CTGAGTTCTTA
1 GTATCGATACATTATATC-GA-TACTAA
*
29189 GTATCGATACATTATATCGATACTCA
1 GTATCGATACATTATATCGATACTAA
* *
29215 GTATCAATACATTTTATCGATACTAA
1 GTATCGATACATTATATCGATACTAA
*
29241 ATATCGATACAT
1 GTATCGATACAT
29253 GGGTACTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 37 0.67
27 17 0.31
28 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (26 bp):
GTATCGATACATTATATCGATACTAA
Found at i:31979 original size:32 final size:33
Alignment explanation
Indices: 31923--31986 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
31913 CACACTCAGA
*
31923 TGTATCAATACATATTACTTAGTATCGATACAT
1 TGTATCAATACATATTACATAGTATCGATACAT
* * *
31956 TGTATCGATACGTATT-CATAGTATTGATACA
1 TGTATCAATACATATTACATAGTATCGATACA
31987 CCTTGAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (33 bp):
TGTATCAATACATATTACATAGTATCGATACAT
Found at i:33189 original size:40 final size:40
Alignment explanation
Indices: 33141--33220 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
33131 TTGTATTCTT
33141 TATAATTCTATGATTAAAATCCTTAAACACTTAGCCCTTC
1 TATAATTCTATGATTAAAATCCTTAAACACTTAGCCCTTC
33181 TATAATTCTATGATTAAAATCCTTAAACACTTAGCCCTTC
1 TATAATTCTATGATTAAAATCCTTAAACACTTAGCCCTTC
33221 AAAGTCTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (40 bp):
TATAATTCTATGATTAAAATCCTTAAACACTTAGCCCTTC
Found at i:33912 original size:24 final size:24
Alignment explanation
Indices: 33876--33926 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
33866 CATTTGGTTC
* *
33876 ATAAACAAGTCCAATAATTAGGTG
1 ATAAACAAATCCAATAATTAAGTG
33900 ATAAACAAATCCAATAATTAAGTG
1 ATAAACAAATCCAATAATTAAGTG
33924 ATA
1 ATA
33927 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (24 bp):
ATAAACAAATCCAATAATTAAGTG
Found at i:34222 original size:26 final size:27
Alignment explanation
Indices: 34184--34246 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
34174 ATGAACAACT
* *
34184 TAATA-TATTTTTAATATTA-ACACTA
1 TAATATTATATTTAATATTATACAATA
*
34209 TAATATTATATTTAATTTTATACAATA
1 TAATATTATATTTAATATTATACAATA
34236 TAA-ATTATATT
1 TAATATTATATT
34247 ATATATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.15
26 20 0.61
27 8 0.24
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATATTATATTTAATATTATACAATA
Found at i:34283 original size:16 final size:16
Alignment explanation
Indices: 34271--34302 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
34261 GATATATTAT
34271 AAATAATATATATAAA
1 AAATAATATATATAAA
34287 AAATAATATATTATAA
1 AAATAATATA-TATAA
34303 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAATATATATAAA
Found at i:37118 original size:11 final size:11
Alignment explanation
Indices: 37104--37128 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
37094 TTTTTTATAT
37104 TATTTTAAAGC
1 TATTTTAAAGC
37115 TATTTTAAAGC
1 TATTTTAAAGC
37126 TAT
1 TAT
37129 GATGCTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
TATTTTAAAGC
Found at i:39711 original size:22 final size:22
Alignment explanation
Indices: 39667--39707 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
39657 TAAATTTATT
39667 TAAATTTAATCATAAAAATATA
1 TAAATTTAATCATAAAAATATA
39689 TAAATATTAAT-A-AAAAATA
1 TAAAT-TTAATCATAAAAATA
39708 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATTTAATCATAAAAATATA
Found at i:45075 original size:174 final size:174
Alignment explanation
Indices: 44766--45079 Score: 425
Period size: 174 Copynumber: 1.8 Consensus size: 174
44756 AAGAACCTAT
* * *
44766 AACCCGAAAAACTCGCTCCATTCAATTGGTGGAAAGCACAAAATGTAGAATTAAACAAATGATGA
1 AACCCAAAAAACTCGCTCCATTCAATTGGTGGAAAACACAAAATGTACAATTAAACAAATGATGA
* ** * * * * ** *
44831 TTACAAGTTAGCAGTTCAGAAAAGGTAATACTTTCCATTTTGGAGACAGAAAACCTGGCAACATG
66 TTACAAGTTAGCACTTCAGAAAAGAAAACACTTTACATTTTGGAAACAGAAAACCCGAAAACACG
44896 AACAAAACTTTTATAGATCAAATACTTGAAAGCAATGAAAAAGA
131 AACAAAACTTTTATAGATCAAATACTTGAAAGCAATGAAAAAGA
* * **
44940 AACCCAAAAAACTTGCTTCATTTC-ATTGGTGGAAAATGCAAAATGTACAATTAAACAAATGATG
1 AACCCAAAAAACTCGCTCCA-TTCAATTGGTGGAAAACACAAAATGTACAATTAAACAAATGATG
**
45004 ATTACAAGTTAGCACTTCATG-AAAGAAAACACTTTACATTTTGGAAATGGAAAACCCGAAAACA
65 ATTACAAGTTAGCACTTCA-GAAAAGAAAACACTTTACATTTTGGAAACAGAAAACCCGAAAACA
45068 CGAACAAAACTT
129 CGAACAAAACTT
45080 AGATAAAGCA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
174 115 0.97
175 4 0.03
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.24
Consensus pattern (174 bp):
AACCCAAAAAACTCGCTCCATTCAATTGGTGGAAAACACAAAATGTACAATTAAACAAATGATGA
TTACAAGTTAGCACTTCAGAAAAGAAAACACTTTACATTTTGGAAACAGAAAACCCGAAAACACG
AACAAAACTTTTATAGATCAAATACTTGAAAGCAATGAAAAAGA
Found at i:45289 original size:149 final size:149
Alignment explanation
Indices: 44966--45411 Score: 840
Period size: 149 Copynumber: 3.0 Consensus size: 149
44956 TTCATTTCAT
*
44966 TGGTGGAAAATGCAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
1 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
45031 AACACTTTACATTTTGGAAATGGAAAA-CCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
66 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
45095 TTCAAAGCAATAAAATGGA
131 TTCAAAGCAATAAAATGGA
*
45114 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATTATTACAAGTTAGCACTTCATGAAAGAA
1 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
*
45179 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGACAC
66 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
*
45244 TTCAAAGCAATGAAATGGA
131 TTCAAAGCAATAAAATGGA
45263 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
1 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
45328 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
66 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
*
45393 TTGAAAGCAATAAAATGGA
131 TTCAAAGCAATAAAATGGA
45412 AAAATTTGTT
Statistics
Matches: 289, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
148 90 0.31
149 199 0.69
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (149 bp):
TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
TTCAAAGCAATAAAATGGA
Found at i:46292 original size:26 final size:25
Alignment explanation
Indices: 46246--46300 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
46236 TAAATGAAAT
*
46246 ATAAAATAAAACAAAACAAACCCAA
1 ATAAAATAAAACAAAACAAACACAA
* *
46271 CATAAAATAAAGCCTAAA-AAACACAA
1 -ATAAAATAAA-ACAAAACAAACACAA
46297 ATAA
1 ATAA
46301 GAAGGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.16
26 17 0.68
27 4 0.16
ACGTcount: A:0.69, C:0.18, G:0.02, T:0.11
Consensus pattern (25 bp):
ATAAAATAAAACAAAACAAACACAA
Found at i:47221 original size:22 final size:22
Alignment explanation
Indices: 47196--47250 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
47186 AATATAATAA
47196 AATATTAAAAATATTTTA-AATT
1 AATATT-AAAATATTTTATAATT
* *
47218 AATATTTATATATTTTATAATT
1 AATATTAAAATATTTTATAATT
*
47240 AA-ATTTAAATA
1 AATATTAAAATA
47251 AAAAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATTAAAATATTTTATAATT
Found at i:47232 original size:21 final size:21
Alignment explanation
Indices: 47206--47246 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
47196 AATATTAAAA
47206 ATATTTTA-AATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
47227 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
47247 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:53227 original size:21 final size:20
Alignment explanation
Indices: 53203--53259 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
53193 TTTTAAATAG
*
53203 ATAAAAATTAAATATATTTA
1 ATAAAAATTAAAAATATTTA
*
53223 TATAAAAAATAAAAATATTTA
1 -ATAAAAATTAAAAATATTTA
* *
53244 ATAAATATTACAAATA
1 ATAAAAATTAAAAATA
53260 ATGTTCTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAAAATTAAAAATATTTA
Found at i:54676 original size:20 final size:20
Alignment explanation
Indices: 54651--54695 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
54641 GTAAAATTTG
54651 AAATTTCA-ATATTTGGATGA
1 AAATTTCAGAT-TTTGGATGA
* *
54671 AAATTTTAGATTTTGGGTGA
1 AAATTTCAGATTTTGGATGA
54691 AAATT
1 AAATT
54696 ATGTTGACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (20 bp):
AAATTTCAGATTTTGGATGA
Found at i:55441 original size:16 final size:15
Alignment explanation
Indices: 55416--55447 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
55406 TTTTTTTTAT
55416 TCTTAAATTATAATC
1 TCTTAAATTATAATC
55431 TCTTCAAATTATAATC
1 TCTT-AAATTATAATC
55447 T
1 T
55448 TTTTTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTTAAATTATAATC
Found at i:55611 original size:24 final size:24
Alignment explanation
Indices: 55567--55640 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 24
55557 GAGCTTACTT
*
55567 AAATTATTATTT-AATAATAATAATA
1 AAATT-TTATTTAAATATTAAT-ATA
55592 AAATTTTATTTAAAT-TTAATTATA
1 AAATTTTATTTAAATATTAA-TATA
*
55616 AAA--TTATATAAATATTAATATA
1 AAATTTTATTTAAATATTAATATA
55638 AAA
1 AAA
55641 ATCTTTTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
22 16 0.36
23 4 0.09
24 15 0.34
25 9 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATTTTATTTAAATATTAATATA
Found at i:56423 original size:17 final size:16
Alignment explanation
Indices: 56392--56435 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
56382 TATATAAAAT
*
56392 AAATTATTAATATATC
1 AAATTTTTAATATATC
56408 AAATTTTTATATATATC
1 AAATTTTTA-ATATATC
56425 AAATATTTTAA
1 AAAT-TTTTAA
56436 AATGAGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 8 0.32
17 12 0.48
18 5 0.20
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTTTAATATATC
Done.