Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1150
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: 73425
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:807 original size:18 final size:18
Alignment explanation
Indices: 786--824 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
776 CAAATAACAG
*
786 AAAAT-ATTACATTTTCCA
1 AAAATAATTA-ATTTTACA
804 AAAATAATTAATTTTACA
1 AAAATAATTAATTTTACA
822 AAA
1 AAA
825 CTTATAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATAATTAATTTTACA
Found at i:2577 original size:19 final size:19
Alignment explanation
Indices: 2553--2591 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2543 TTAATATATG
* *
2553 TATTTTTAATTTTTTTAAA
1 TATTTTTAATATATTTAAA
2572 TATTTTTAATATATTTAAA
1 TATTTTTAATATATTTAAA
2591 T
1 T
2592 GATTGTACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTTAATATATTTAAA
Found at i:2850 original size:12 final size:13
Alignment explanation
Indices: 2822--2851 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2812 GAATGCACTG
*
2822 AAAATAATAATCA
1 AAAACAATAATCA
2835 AAAACAATAATCA
1 AAAACAATAATCA
2848 AAAA
1 AAAA
2852 AAAAATCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAACAATAATCA
Found at i:4172 original size:13 final size:14
Alignment explanation
Indices: 4138--4174 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
4128 AATGAAATCA
4138 AAAAAATAAAGAGAG
1 AAAAAA-AAAGAGAG
4153 AAGAAAAAAAGAGAG
1 AA-AAAAAAAGAGAG
4168 AAAAAAA
1 AAAAAAA
4175 GCAAGCTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 12 0.57
16 4 0.19
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAGAG
Found at i:6385 original size:20 final size:19
Alignment explanation
Indices: 6342--6397 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
6332 TTTCATTTTT
6342 AAAATTAAAAAGTGAAAAACA
1 AAAATTAAAAA-TG-AAAACA
*
6363 AAAATTAAAAATGAAATCGA
1 AAAATTAAAAATGAAAAC-A
*
6383 AAAAATAAAAA-GAAA
1 AAAATTAAAAATGAAA
6398 GATGAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.25
20 13 0.41
21 11 0.34
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.14
Consensus pattern (19 bp):
AAAATTAAAAATGAAAACA
Found at i:6449 original size:42 final size:44
Alignment explanation
Indices: 6401--6488 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
6391 AAAGAAAGAT
6401 GAAAAAA-AGAGAAAAAAAGCAAGCTAACCATAATGAGAGAGAA
1 GAAAAAAGAGAGAAAAAAAGCAAGCTAACCATAATGAGAGAGAA
* *
6444 GAAAAAAGAGAGAAAAAAAGCAAGCTAACCATAGTGGGAGAGAA
1 GAAAAAAGAGAGAAAAAAAGCAAGCTAACCATAATGAGAGAGAA
6488 G
1 G
6489 GGAAAGAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 7 0.17
44 35 0.83
ACGTcount: A:0.59, C:0.09, G:0.25, T:0.07
Consensus pattern (44 bp):
GAAAAAAGAGAGAAAAAAAGCAAGCTAACCATAATGAGAGAGAA
Found at i:8864 original size:24 final size:26
Alignment explanation
Indices: 8813--8865 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
8803 CTCTTCTTTT
* **
8813 ATTTTTTCTTAAATTTCATTTTTCAA
1 ATTTTTTCTAAAATTTCATTTTGAAA
8839 ATTTTTT-TAAAATTT-ATTTTGAAA
1 ATTTTTTCTAAAATTTCATTTTGAAA
8863 ATT
1 ATT
8866 CAAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.42
25 7 0.29
26 7 0.29
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTTTTTCTAAAATTTCATTTTGAAA
Found at i:9975 original size:20 final size:21
Alignment explanation
Indices: 9950--9990 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
9940 TAAAATCTAA
9950 TAAAATAAA-TAATTTAATTC
1 TAAAATAAATTAATTTAATTC
9970 TAAAATAAATTTAATTTAATT
1 TAAAATAAA-TTAATTTAATT
9991 ATCTAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATAAATTAATTTAATTC
Found at i:10663 original size:11 final size:11
Alignment explanation
Indices: 10649--10679 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
10639 TAAAAAAATT
10649 AAAAAAAAGAG
1 AAAAAAAAGAG
10660 AAAAAAAAGAG
1 AAAAAAAAGAG
10671 AAATAAAAA
1 AAA-AAAAA
10680 CGGTAAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:11009 original size:24 final size:24
Alignment explanation
Indices: 10944--10993 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
10934 TTTAGATTTC
*
10944 TTTTTGAAATATTTAAAAAATAAAA
1 TTTTT-AAATCTTTAAAAAATAAAA
10969 TTTTTAAATCTTTAAAAAATAAAA
1 TTTTTAAATCTTTAAAAAATAAAA
10993 T
1 T
10994 ATTATTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TTTTTAAATCTTTAAAAAATAAAA
Found at i:11734 original size:2 final size:2
Alignment explanation
Indices: 11727--11759 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11717 CTTTGGTGTT
11727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11760 TATTGATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18575 original size:109 final size:107
Alignment explanation
Indices: 18381--18720 Score: 375
Period size: 109 Copynumber: 3.1 Consensus size: 107
18371 TGAAAATCGA
* *
18381 GGTTGGAGTATCCCCTCGAAAATGGTGGCGTTGGAGTAT-CCTAGAGATGAAGAAATTCAATGTT
1 GGTTGGAGTAT-CCCTCGAAAATGATGGGGTTGGAGTATCCCTAGAGATGAAGAAATTCAATGTT
* *
18445 TTAAAAGTAAAAACAGGGTTGAAGTATCCTCTCAGAATTGGTGG
65 TTAGAAGTAAAAAC-GGGTTGAAGTATCCTCTCAGAATTGATGG
* * *
18489 GGTTGGAGTATCCCTTTGGAAACGATGGGGTTGGAGTATCCCTAGAGATGAAGAAATTCAATGTT
1 GGTTGGAGTATCCC-TCGAAAATGATGGGGTTGGAGTATCCCTAGAGATGAAGAAATTCAATGTT
** *
18554 TTAGAAGTAAAAACGGTGTTGAAGTAT-CTCTTTGGAATTGATGA
65 TTAGAAGTAAAAACGG-GTTGAAGTATCCTC-TCAGAATTGATGG
* **
18598 GGTTAGAGTATCCACTCGAAAATGATGGGGTTGGAGTATCCCCT-GAGAT-AA-AAATTTTGATG
1 GGTTGGAGTATCC-CTCGAAAATGATGGGGTTGGAGTAT-CCCTAGAGATGAAGAAA-TTCAATG
* * * * * **
18660 TTTTGGAAAATAAAAATGGAGTTGGAGTATCCTTTCAGAAACGATGG
63 TTTTAG-AAGTAAAAACGG-GTTGAAGTATCCTCTCAGAATTGATGG
18707 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
18721 CAAAGACGAA
Statistics
Matches: 195, Mismatches: 28, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
107 6 0.03
108 48 0.25
109 134 0.69
110 7 0.04
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (107 bp):
GGTTGGAGTATCCCTCGAAAATGATGGGGTTGGAGTATCCCTAGAGATGAAGAAATTCAATGTTT
TAGAAGTAAAAACGGGTTGAAGTATCCTCTCAGAATTGATGG
Found at i:18862 original size:80 final size:80
Alignment explanation
Indices: 18620--18933 Score: 360
Period size: 80 Copynumber: 3.9 Consensus size: 80
18610 CACTCGAAAA
* * * * * * * *
18620 TGATGGGGTTGGAGTATCCCCTGAGATAAAAATTTTGATGTTTTGGAAAATAAAAATGGAGTTGG
1 TGATAGGGTTGGAGTATCCCCTAAGATGAAAATTTTGATGTTTTAG-AAGTAAAGACGGGGTTGG
* *
18685 AGTATCCTTTCAGAAA
65 AGTATCCCTTCAGAAT
* * * * * ** *
18701 CGATGGGGTTGGAGTATCCCCAAAGACGAAGAAATTCAATGTTTTAAAAGT-AAGAACGGGGTTG
1 TGATAGGGTTGGAGTATCCCCTAAGATGAA-AATTTTGATGTTTTAGAAGTAAAG-ACGGGGTTG
* *
18765 GAGTATCCTTTCGGAAT
64 GAGTATCCCTTCAGAAT
* * *
18782 TGATAGGGTTGGAGTATCCCCTAAGATGAAAATTTTGGTGTTTTAGAAGTAACGATGGGGTTGGA
1 TGATAGGGTTGGAGTATCCCCTAAGATGAAAATTTTGATGTTTTAGAAGTAAAGACGGGGTTGGA
18847 GTATCCCTTCAGAAT
66 GTATCCCTTCAGAAT
* * *
18862 TGATAGGGTTGGAGTATCTCCTAAGATGAAAATTTTGGTGTTTTAGAAGTAAAGACGGGGTTGAA
1 TGATAGGGTTGGAGTATCCCCTAAGATGAAAATTTTGATGTTTTAGAAGTAAAGACGGGGTTGGA
18927 GTATCCC
66 GTATCCC
18934 CGATGGTGAA
Statistics
Matches: 197, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
80 108 0.55
81 78 0.40
82 11 0.06
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (80 bp):
TGATAGGGTTGGAGTATCCCCTAAGATGAAAATTTTGATGTTTTAGAAGTAAAGACGGGGTTGGA
GTATCCCTTCAGAAT
Found at i:21357 original size:51 final size:52
Alignment explanation
Indices: 21247--21385 Score: 181
Period size: 51 Copynumber: 2.7 Consensus size: 52
21237 AATAGCTTAC
* * * * * *
21247 ATGTATTGATACATTGAAGAATGTATCGATATATTTGGGTCAAAAATCTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAACCTAGA
* *
21299 ATGTATCGATACAATGAAAAATGTATTGATACATTTAGGT-TAAAACCTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAACCTAGA
* *
21350 ATGTATCGATACAATGAAAAATTTATCAATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
21386 TCTTTCCAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 42 0.55
52 34 0.45
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAACCTAGA
Found at i:22054 original size:29 final size:26
Alignment explanation
Indices: 22010--22066 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 26
22000 AATATTATTT
22010 TATTTTTATATTAATATTAATATTAAAA
1 TATTTTTATATTAATATTAA-A-TAAAA
22038 TATTTTTATAATTAATATTAAATAAAA
1 TATTTTTAT-ATTAATATTAAATAAAA
22065 TA
1 TA
22067 ATAATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 7 0.25
28 10 0.36
29 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTTTTATATTAATATTAAATAAAA
Found at i:28385 original size:20 final size:20
Alignment explanation
Indices: 28360--28397 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28350 GAAAAAAGAT
28360 AGAATGTATCAATACATTGA
1 AGAATGTATCAATACATTGA
*
28380 AGAATGTATCGATACATT
1 AGAATGTATCAATACATT
28398 CATACATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCAATACATTGA
Found at i:28424 original size:16 final size:16
Alignment explanation
Indices: 28382--28500 Score: 78
Period size: 16 Copynumber: 7.0 Consensus size: 16
28372 TACATTGAAG
28382 AATGTATCGATACATTC
1 AATGTATCGATACA-TC
28399 ATACATGTATCGATACATC
1 --A-ATGTATCGATACATC
*
28418 AATGTATCGATATATC
1 AATGTATCGATACATC
* * *** * *
28434 TAGGTAAAAAGACA-G
1 AATGTATCGATACATC
*
28449 AATATATCGATACATTC
1 AATGTATCGATACA-TC
28466 ATACATGTATCGATACATC
1 --A-ATGTATCGATACATC
28485 AATGTATCGATACATC
1 AATGTATCGATACATC
28501 TGGGTAAAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 15
0.70 0.17 0.14
Matches are distributed among these distances:
15 7 0.09
16 36 0.47
17 2 0.03
19 6 0.08
20 25 0.33
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (16 bp):
AATGTATCGATACATC
Found at i:28462 original size:67 final size:67
Alignment explanation
Indices: 28380--28550 Score: 315
Period size: 67 Copynumber: 2.6 Consensus size: 67
28370 AATACATTGA
* *
28380 AGAATGTATCGATACATTCATACATGTATCGATACATCAATGTATCGATATATCTAGGTAAAAAG
1 AGAATATATCGATACATTCATACATGTATCGATACATCAATGTATCGATACATCTAGGTAAAAAG
28445 AC
66 AC
*
28447 AGAATATATCGATACATTCATACATGTATCGATACATCAATGTATCGATACATCTGGGTAAAAAG
1 AGAATATATCGATACATTCATACATGTATCGATACATCAATGTATCGATACATCTAGGTAAAAAG
28512 AC
66 AC
28514 AGAATATATCGATACATTCATACATGTATCGATACAT
1 AGAATATATCGATACATTCATACATGTATCGATACAT
28551 TTAGTTAAAA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 101 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (67 bp):
AGAATATATCGATACATTCATACATGTATCGATACATCAATGTATCGATACATCTAGGTAAAAAG
AC
Found at i:28477 original size:87 final size:83
Alignment explanation
Indices: 28331--28500 Score: 216
Period size: 87 Copynumber: 2.0 Consensus size: 83
28321 TAACTAAAAA
* * * *
28331 AATGTATCGATACATCTGGGAAAAAAGATAGAATGTATCAATACATTGAAGAATGTATCGATACA
1 AATGTATCGATACATCTAGGAAAAAAGACAGAATATATCAATACATTCAAGAATGTATCGATACA
28396 TTCATACATGTATCGATACATC
66 -TC--A-ATGTATCGATACATC
* * * *
28418 AATGTATCGATATATCTAGGTAAAAAGACAGAATATATCGATACATTCATA-CATGTATCGATAC
1 AATGTATCGATACATCTAGGAAAAAAGACAGAATATATCAATACATTCA-AGAATGTATCGATAC
28482 ATCAATGTATCGATACATC
65 ATCAATGTATCGATACATC
28501 TGGGTAAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
83 15 0.20
84 1 0.01
86 2 0.03
87 55 0.74
88 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (83 bp):
AATGTATCGATACATCTAGGAAAAAAGACAGAATATATCAATACATTCAAGAATGTATCGATACA
TCAATGTATCGATACATC
Found at i:29837 original size:117 final size:117
Alignment explanation
Indices: 29631--29865 Score: 452
Period size: 117 Copynumber: 2.0 Consensus size: 117
29621 TTGTGATGAC
*
29631 TTCTTTTGTTTTTAATATTATTTTGGATTCGTCCAAGCTTGAAGGCCTATTCGATATTTATGAGA
1 TTCTTTTGTTTTTAAAATTATTTTGGATTCGTCCAAGCTTGAAGGCCTATTCGATATTTATGAGA
*
29696 GTTTAGACAAAAATGTTATACTAAAAAAATGGGTTTAGACAAAAAGGTTAAG
66 GTTTAGACAAAAATATTATACTAAAAAAATGGGTTTAGACAAAAAGGTTAAG
29748 TTCTTTTGTTTTTAAAATTATTTTGGATTCGTCCAAGCTTGAAGGCCTATTCGATATTTATGAGA
1 TTCTTTTGTTTTTAAAATTATTTTGGATTCGTCCAAGCTTGAAGGCCTATTCGATATTTATGAGA
29813 GTTTAGACAAAAATATTATACTAAAAAAATGGGTTTAGACAAAAAGGTTAAG
66 GTTTAGACAAAAATATTATACTAAAAAAATGGGTTTAGACAAAAAGGTTAAG
29865 T
1 T
29866 CCATTTAAAA
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (117 bp):
TTCTTTTGTTTTTAAAATTATTTTGGATTCGTCCAAGCTTGAAGGCCTATTCGATATTTATGAGA
GTTTAGACAAAAATATTATACTAAAAAAATGGGTTTAGACAAAAAGGTTAAG
Found at i:32676 original size:28 final size:28
Alignment explanation
Indices: 32644--32709 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
32634 ATTTTATTTC
* *
32644 AGTTATATATGGTATTCAATTTGA-TTTT
1 AGTTATATATGGTATT-AAGTTCAGTTTT
* *
32672 GGTTATATACGGTATTAAGTTCAGTTTT
1 AGTTATATATGGTATTAAGTTCAGTTTT
32700 AGTTATATAT
1 AGTTATATAT
32710 ATACATATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.50
Consensus pattern (28 bp):
AGTTATATATGGTATTAAGTTCAGTTTT
Found at i:32710 original size:2 final size:2
Alignment explanation
Indices: 32703--32735 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
32693 CAGTTTTAGT
*
32703 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32736 GATTCATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38074 original size:19 final size:21
Alignment explanation
Indices: 38050--38089 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
38040 AATTAAATAT
38050 ATAAAAAAT-TTTA-ATAAAA
1 ATAAAAAATATTTATATAAAA
*
38069 ATAAAATATATTTATATAAAA
1 ATAAAAAATATTTATATAAAA
38090 TACATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAAAATATTTATATAAAA
Found at i:38692 original size:22 final size:22
Alignment explanation
Indices: 38646--38700 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
38636 TTTTATTTTT
*
38646 AAAATTAAAAAAGTGAAAAATA
1 AAAATTAAAAAAGTGAAAAAAA
*
38668 AAAATT-AAAAA-TGAAATCAAA
1 AAAATTAAAAAAGTGAAA-AAAA
*
38689 AAAATAAAAAAA
1 AAAATTAAAAAA
38701 AAAAAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.18
21 12 0.43
22 11 0.39
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAATTAAAAAAGTGAAAAAAA
Found at i:38712 original size:11 final size:11
Alignment explanation
Indices: 38698--38736 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
38688 AAAAATAAAA
38698 AAAAAAAAGAG
1 AAAAAAAAGAG
38709 AAAAAAAAGAG
1 AAAAAAAAGAG
*
38720 AGAGAAAAAGCAG
1 A-AAAAAAAG-AG
38733 AAAA
1 AAAA
38737 GCATACTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 12 0.50
12 9 0.38
13 3 0.12
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:38721 original size:13 final size:13
Alignment explanation
Indices: 38686--38728 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
38676 AAATGAAATC
* *
38686 AAAAAAATAAAAA
1 AAAAAAAGAGAAA
38699 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
38712 AAAAAGAGAGAGAAA
1 AAAAA-A-AGAGAAA
38727 AA
1 AA
38729 GCAGAAAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 16 0.62
14 1 0.04
15 9 0.35
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:38723 original size:15 final size:15
Alignment explanation
Indices: 38694--38728 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38684 TCAAAAAAAT
38694 AAAAAAAAAAAAGAG
1 AAAAAAAAAAAAGAG
* *
38709 AAAAAAAAGAGAGAG
1 AAAAAAAAAAAAGAG
38724 AAAAA
1 AAAAA
38729 GCAGAAAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAG
Found at i:39585 original size:18 final size:18
Alignment explanation
Indices: 39550--39583 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39540 GTTGTTTATC
39550 ATAAAATAAAGACTTTTA
1 ATAAAATAAAGACTTTTA
*
39568 ATAAAATTAA-ACTTTT
1 ATAAAATAAAGACTTTT
39584 TACTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAAAATAAAGACTTTTA
Found at i:40898 original size:12 final size:14
Alignment explanation
Indices: 40868--40905 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
40858 TTTAAAATCA
*
40868 AAAAGTAAAAAATT
1 AAAATTAAAAAATT
40882 AAAATTAAAAAA-T
1 AAAATTAAAAAATT
40895 -AAATTAAAAAA
1 AAAATTAAAAAA
40906 GAGACAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 1 0.04
14 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAATTAAAAAATT
Found at i:46345 original size:79 final size:78
Alignment explanation
Indices: 46201--46661 Score: 332
Period size: 79 Copynumber: 5.8 Consensus size: 78
46191 TGAGGATAAA
* * * * *
46201 AACGGGGTTGGAGTAT-CTCCGA-GATGAAAATTTCAATATTTTAGAAACAAAAATGAGATTAGA
1 AACGAGGTTGGAGTATCCT-CGAGGATAAAAATTT-AATATTTTAGAAA-TAAAATGAGGTTGGA
*
46264 GTACCCCCTCAAAAAT
63 GTATCCCCTCAAAAAT
* *
46280 AACGAGATTAGAGTATCCTCGA-GATAAGAAATTTAATATTTTAGAAATAAAATCGAGGTTGGAG
1 AACGAGGTTGGAGTATCCTCGAGGATAA-AAATTTAATATTTTAGAAATAAAAT-GAGGTTGGAG
* *
46344 TATTCCCTAAAAAAT
64 TATCCCCTCAAAAAT
* * * * * * * *
46359 AACAAGGTTGGTGCATCCTCGAGGGTAAAAAATTGATATTTTGGAAATAAAACTGGGGTTGGAGT
1 AACGAGGTTGGAGTATCCTCGAGGATAAAAATTTAATATTTTAGAAATAAAA-TGAGGTTGGAGT
**
46424 ATCCCCTCGGAAAT
65 ATCCCCTCAAAAAT
* * * * **
46438 AACGGGGTTGGATTATCC-CTGATGATGAAAAACTCGATATTTTAGAAATAAAAATGAGGTTGGA
1 AACGAGGTTGGAGTATCCTC-GAGGAT-AAAAATTTAATATTTTAGAAAT-AAAATGAGGTTGGA
** * *
46502 GTATCCGTTCGAAAGT
63 GTATCCCCTCAAAAAT
* * * ** **
46518 AAC-AGGGTTGGAGTATCCCCAATGGAGAAAAA-TCGATATTTGGGAAATAAAAATGAGGTTGGA
1 AACGA-GGTTGGAGTATCCTCGA-GGATAAAAATTTAATATTTTAGAAAT-AAAATGAGGTTGGA
*
46581 GTATCCCCTCGAAAAT
63 GTATCCCCTCAAAAAT
* * *
46597 AAC-AGGGTTGGAGTATCCCCGATGG-TGAAAAA-TTGATATTTT-GAAAATAAAA-GGGGTTGG
1 AACGA-GGTTGGAGTATCCTCGA-GGAT-AAAAATTTAATATTTTAG-AAATAAAATGAGGTTGG
46657 AGTAT
62 AGTAT
46662 TGCCTCGGAA
Statistics
Matches: 315, Mismatches: 54, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
77 12 0.04
78 11 0.03
79 211 0.67
80 74 0.23
81 7 0.02
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.27
Consensus pattern (78 bp):
AACGAGGTTGGAGTATCCTCGAGGATAAAAATTTAATATTTTAGAAATAAAATGAGGTTGGAGTA
TCCCCTCAAAAAT
Found at i:46527 original size:159 final size:157
Alignment explanation
Indices: 46244--46661 Score: 420
Period size: 159 Copynumber: 2.7 Consensus size: 157
46234 CAATATTTTA
* * * * * * * *
46244 GAAACAAAAATGAGATTAGAGTACCCCCTCAAAAATAAC-GAGATTAGAGTATCCTCGA-GAT-A
1 GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCCCGATGATGA
**
46306 AGAAATTTAATATTTTAGAAAT-AAAATCGAGGTTGGAGTATTCCCTAAAAAATAACAAGGTTGG
65 A-AAA-TCGATATTTTAGAAATAAAAAT-GAGGTTGGAGTA-TCCCTAAAAAATAACAAGGTTGG
* * * * *
46370 TGCATCCTCGAGGGTA-AAAAATTGATATTTTG
126 AGCATCCCCAAGGG-AGAAAAATCGATATTTGG
* * * * * *
46402 GAAATAAAACTGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGATTATCCCTGATGATGAA
1 GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGATGAA
* ** * * *
46467 AAACTCGATATTTTAGAAATAAAAATGAGGTTGGAGTATCCGTTCGAAAGTAACAGGGTTGGAGT
66 AAA-TCGATATTTTAGAAATAAAAATGAGGTTGGAGTATCC-CTAAAAAATAACAAGGTTGGAGC
*
46532 ATCCCCAATGGAGAAAAATCGATATTTGG
129 ATCCCCAAGGGAGAAAAATCGATATTTGG
*
46561 GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGGTGAA
1 GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGATGAA
* *
46626 AAATTGATATTTT-GAAA-ATAAAA-GGGGTTGGAGTAT
66 AAATCGATATTTTAGAAATA-AAAATGAGGTTGGAGTAT
46662 TGCCTCGGAA
Statistics
Matches: 216, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
156 13 0.06
157 8 0.04
158 56 0.26
159 132 0.61
160 7 0.03
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (157 bp):
GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGATGAA
AAATCGATATTTTAGAAATAAAAATGAGGTTGGAGTATCCCTAAAAAATAACAAGGTTGGAGCAT
CCCCAAGGGAGAAAAATCGATATTTGG
Found at i:46786 original size:79 final size:78
Alignment explanation
Indices: 46698--46892 Score: 239
Period size: 79 Copynumber: 2.5 Consensus size: 78
46688 ATCCCCTTGG
* * ** * *
46698 TTTTATTTCTAAAATATTAAATTTCTCGTCTCGGGGATACTCCAACCCTATTATTTTTTAGGGGG
1 TTTTATTTCTAAAATATTAAATTT-TCGTCTCAGGGATACTCCAACCCCATTATTTTCGAGAGGA
* *
46763 TGCTCCAATCCCCT
65 TACTCCAATCCCAT
*
46777 TTTTATTTCTAAAATATTTAAATTTTCGTCTCAGGGATACTCCAACCCCGTTATTTTCGAGAGGA
1 TTTTATTTCTAAAATA-TTAAATTTTCGTCTCAGGGATACTCCAACCCCATTATTTTCGAGAGGA
46842 TACTCCAATCCCAT
65 TACTCCAATCCCAT
* * * *
46856 TTTTATCTCCAAAGTATTAAAGTTTTCATCT-AGGGAT
1 TTTTATTTCTAAAATATTAAA-TTTTCGTCTCAGGGAT
46893 GTGCTCCAAC
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
78 11 0.11
79 82 0.81
80 8 0.08
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (78 bp):
TTTTATTTCTAAAATATTAAATTTTCGTCTCAGGGATACTCCAACCCCATTATTTTCGAGAGGAT
ACTCCAATCCCAT
Found at i:56014 original size:4 final size:4
Alignment explanation
Indices: 55999--56028 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
55989 AAACAAAACA
*
55999 AAAT ATAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
56029 GCACCTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:58213 original size:79 final size:78
Alignment explanation
Indices: 58086--58344 Score: 317
Period size: 79 Copynumber: 3.3 Consensus size: 78
58076 TACTTTGGAG
* * * *
58086 ATAAAAACGGGGTTGGAGTATTCCCTTGAAAATAACG-GAGTT-AGAGTATCCCCGATGGTAAAA
1 ATAAAAACGGGGTTGGAGTA-TCCCTCGGAAACAACGAG-GTTGA-AGTATCCCCGATGGT-GAA
*
58149 AAATTGATATTTTGGAA
62 AAATTGATATTTTGAAA
* *
58166 ATAAAAA-GGGGTTGAAGTATCCTCTCGGAAACAACGAGGTTGAAGTATCCCCGATAGTGAAAAA
1 ATAAAAACGGGGTTGGAGTATCC-CTCGGAAACAACGAGGTTGAAGTATCCCCGATGGTGAAAAA
58230 TTGATATTTTGAAA
65 TTGATATTTTGAAA
* * ** *
58244 ATAAAAAAGGGGTTGGAGTATCCCTTCGGAAACAACAAGGTTGGTGTATCCCTGATGGTGAAAAA
1 ATAAAAACGGGGTTGGAGTATCCC-TCGGAAACAACGAGGTTGAAGTATCCCCGATGGTGAAAAA
*
58309 TCGATATTTTGAAA
65 TTGATATTTTGAAA
*
58323 ATAAAAACGGGATTGGAGTATC
1 ATAAAAACGGGGTTGGAGTATC
58345 TCTAATAGTG
Statistics
Matches: 158, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
78 29 0.18
79 120 0.76
80 9 0.06
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.26
Consensus pattern (78 bp):
ATAAAAACGGGGTTGGAGTATCCCTCGGAAACAACGAGGTTGAAGTATCCCCGATGGTGAAAAAT
TGATATTTTGAAA
Found at i:58406 original size:50 final size:51
Alignment explanation
Indices: 58281--58448 Score: 225
Period size: 51 Copynumber: 3.3 Consensus size: 51
58271 GGAAACAACA
*
58281 AGGTTGGTGTATCCCTGATGGTGAAAAATCGATATTTTGAAAATAAAAACG
1 AGGTTGGAGTATCCCTGATGGTGAAAAATCGATATTTTGAAAATAAAAACG
* * * *
58332 -GGATTGGAGTATCTCTAATAGTGAAAAATCGATATTTTGGAAAT-AAAACG
1 AGG-TTGGAGTATCCCTGATGGTGAAAAATCGATATTTTGAAAATAAAAACG
* * *
58382 AGGTTGGAGCATCCCGGATGGTGAAAAAGT-AATATTTTGAAAATAAAAACG
1 AGGTTGGAGTATCCCTGATGGTGAAAAA-TCGATATTTTGAAAATAAAAACG
58433 AGGTTGGAGTATCCCT
1 AGGTTGGAGTATCCCT
58449 CAAAAATAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
50 40 0.40
51 59 0.60
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (51 bp):
AGGTTGGAGTATCCCTGATGGTGAAAAATCGATATTTTGAAAATAAAAACG
Found at i:58608 original size:79 final size:78
Alignment explanation
Indices: 58378--58683 Score: 364
Period size: 79 Copynumber: 3.9 Consensus size: 78
58368 TTGGAAATAA
* * * * * *
58378 AACGAGGTTGGAGCATCCCGGATGGTGAAAAAGTAATATTTTGAAAATAAAAACGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAATGAGGTTGGAGT
*** *
58443 ATCCCTCAAAAAT
66 ATCCCTTGGAAAC
* * * *
58456 AATGGGGTTGGAGTATCCCCGATGGTG-AAAATTGATAGTTTGGAAATAAAAATGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAATGAGGTTGGAG-
*
58520 TTTCCCTTGGAAAC
65 TATCCCTTGGAAAC
* * *
58534 AACGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGGAAATAAAAATGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAATGAGGTTGGAGT
58599 ATCCTCTTGGAAAC
66 ATCC-CTTGGAAAC
* * * * *
58613 AACAGGGTTGGAGTATCCTCGATGGAGAAAAATTGATATTTTGGAAAT-AAAATCGAGGTTAGAG
1 AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAAT-GAGGTTGGAG
58677 TATCCCT
65 TATCCCT
58684 GAGATAAGGA
Statistics
Matches: 195, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
77 30 0.15
78 68 0.35
79 97 0.50
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAATGAGGTTGGAGT
ATCCCTTGGAAAC
Found at i:58609 original size:31 final size:28
Alignment explanation
Indices: 58574--58632 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
58564 AATCAATATT
58574 TTGGAAATAAAAATGGGGTTGGAGTATCCTC
1 TTGGAAA-AAAAA--GGGTTGGAGTATCCTC
* *
58605 TTGGAAACAACAGGGTTGGAGTATCCTC
1 TTGGAAAAAAAAGGGTTGGAGTATCCTC
58633 GATGGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
30 3 0.12
31 7 0.27
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (28 bp):
TTGGAAAAAAAAGGGTTGGAGTATCCTC
Found at i:58782 original size:130 final size:130
Alignment explanation
Indices: 58568--58813 Score: 298
Period size: 130 Copynumber: 1.9 Consensus size: 130
58558 GTGAAAAATC
* * * *** ** *
58568 AATATTTTGGAAATAAAAATGGGGTTGGAGTATCCTCTTGGAAACAACAGGGTTGGAGTATCCTC
1 AATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAACAACAGGGTTAAAGTATCCTA
* * * * *
58633 GATGGAGAAAAATTGATATTTTGGAAATAAAATCGAGGTTAGAGTATCCCTGAGATAAGGAATTT
66 GATGGAGAAAAATTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCTGAGATAAGGAATTT
* *
58698 AATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAAAGTATCCCT
1 AATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAACAACAGGGTTAAAGTAT-CCT
* *
58763 GAGAT-GAG-GAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCT
65 -AGATGGAGAAAAATTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCT
58814 TTAAAATTAA
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
130 87 0.91
131 6 0.06
132 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (130 bp):
AATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAACAACAGGGTTAAAGTATCCTA
GATGGAGAAAAATTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCTGAGATAAGGAATTT
Found at i:58809 original size:79 final size:79
Alignment explanation
Indices: 58669--58875 Score: 245
Period size: 79 Copynumber: 2.6 Consensus size: 79
58659 ATAAAATCGA
* ** **
58669 GGTTAGAGTATCCCTGAGATAAGGAATTTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTAGAGTATCCCTGAGATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCC
58734 CTCAAAAATAACAG
66 CTCAAAAATAACAG
*
58748 GGTTAAAGTATCCCTGAGATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCC
1 GGTTAGAGTATCCCTGAGATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCC
* * * *
58813 TTTAAAATTAACGG
66 CTCAAAAATAACAG
* * * * * * *
58827 GGTTGGTGTATCCCCGATGGTGA-AAAATTGATATTTTAGAAATAAAACC
1 GGTTAGAGTATCCCTGA-GATGAGGAATTTAATATTTTAGAAATAAAACC
58876 GAGATTGTAG
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 105 0.96
80 4 0.04
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (79 bp):
GGTTAGAGTATCCCTGAGATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCC
CTCAAAAATAACAG
Found at i:58888 original size:79 final size:78
Alignment explanation
Indices: 58696--58998 Score: 270
Period size: 79 Copynumber: 3.8 Consensus size: 78
58686 GATAAGGAAT
* * * * **
58696 TTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAAAGTATCC
1 TTAATATTTTAGAAATAAAACCGAGATTGGAGTATCCCTTC-AAAATAACGGGGTTGGAGTATCC
* * * *
58761 CTGA-GATGAGGAAT
65 CCGATGGTGA-AAAA
* * ** * *
58775 TTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCTTTAAAATTAACGGGGTTGGTGTATCC
1 TTAATATTTTAGAAATAAAACCGAGATTGGAGTATCCCTTCAAAA-TAACGGGGTTGGAGTATCC
58840 CCGATGGTGAAAAA
65 CCGATGGTGAAAAA
* * * * *
58854 TTGATATTTTAGAAATAAAACCGAGATTGTAGTATTCCTTCAGAAATAATGGGATTGGAGTATCC
1 TTAATATTTTAGAAATAAAACCGAGATTGGAGTATCCCTTCA-AAATAACGGGGTTGGAGTATCC
*
58919 TCGATGGTGAAAAA
65 CCGATGGTGAAAAA
* * * * * *
58933 TCAATATTTT-GAAAATAAAACTGGGATTGGAGTAT-CTTCTCGGAAATAACGGGGTTTGAGTAT
1 TTAATATTTTAG-AAATAAAACCGAGATTGGAGTATCCCT-TC-AAAATAACGGGGTTGGAGTAT
58996 CCC
63 CCC
58999 TAATGGTAAA
Statistics
Matches: 182, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
78 7 0.04
79 168 0.92
80 7 0.04
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (78 bp):
TTAATATTTTAGAAATAAAACCGAGATTGGAGTATCCCTTCAAAATAACGGGGTTGGAGTATCCC
CGATGGTGAAAAA
Found at i:61561 original size:20 final size:21
Alignment explanation
Indices: 61536--61589 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
61526 CATTTTAGGC
61536 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTGT
*
61556 ATGTATCGATACATTTACTGT
1 ATGTATCGATACATTCACTGT
* *
61577 TTCTATCGATACA
1 ATGTATCGATACA
61590 AATTATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTGT
Found at i:64258 original size:28 final size:29
Alignment explanation
Indices: 64237--64293 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
64227 AATATTATTT
64237 TATTTTTAT-ATTAATATTAATATTAAAA
1 TATTTTTATAATTAATATTAATATTAAAA
64265 TATTTTTATAATTAATATTAA-A-TAAAA
1 TATTTTTATAATTAATATTAATATTAAAA
64292 TA
1 TA
64294 ATAATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 7 0.25
28 10 0.36
29 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTTTTATAATTAATATTAATATTAAAA
Found at i:64301 original size:29 final size:29
Alignment explanation
Indices: 64241--64311 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
64231 TTATTTTATT
*
64241 TTTAT-ATTAATATTAATATTAAAATATT
1 TTTATAATTAATATTAATATTAAAATATA
64269 TTTATAATTAATATTAA-A-TAAAATAATAA
1 TTTATAATTAATATTAATATTAAAAT-AT-A
*
64298 TTTATTAATAAATA
1 TTTA-TAATTAATA
64312 AAAATTTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 6 0.16
28 8 0.22
29 15 0.41
30 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTATAATTAATATTAATATTAAAATATA
Found at i:65993 original size:23 final size:23
Alignment explanation
Indices: 65967--66010 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
65957 TTATGTATTT
65967 TATTATATCATAATTATATTTAA
1 TATTATATCATAATTATATTTAA
* * *
65990 TATTATTTTATATTTATATTT
1 TATTATATCATAATTATATTT
66011 TTAATACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATATCATAATTATATTTAA
Found at i:66831 original size:23 final size:24
Alignment explanation
Indices: 66789--66865 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 24
66779 CTAAAATGTT
* *
66789 ATATATATATATATATTATATATA
1 ATATAAATATATATAATATATATA
*
66813 ATGTAAAT-TATATAATATATA-A
1 ATATAAATATATATAATATATATA
* * *
66835 ATATAAATATAAAAAATATATATT
1 ATATAAATATATATAATATATATA
66859 ATA-AAAT
1 ATATAAAT
66866 TCGAATTGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 8 0.18
23 27 0.61
24 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (24 bp):
ATATAAATATATATAATATATATA
Found at i:66851 original size:15 final size:16
Alignment explanation
Indices: 66821--66864 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
66811 TAATGTAAAT
*
66821 TATATAATAT-ATAAA
1 TATATAATATAAAAAA
66836 TATA-AATATAAAAAA
1 TATATAATATAAAAAA
*
66851 TATATATTATAAAA
1 TATATAATATAAAA
66865 TTCGAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 12 0.48
16 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TATATAATATAAAAAA
Found at i:66857 original size:2 final size:2
Alignment explanation
Indices: 66788--66845 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
66778 ACTAAAATGT
* *
66788 TA TA TA TA TA TA TA TA T- TA TA TA TA -A TG TA AA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
66827 -A TA TA TA AA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA
66846 AAAAATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:67883 original size:16 final size:18
Alignment explanation
Indices: 67842--67885 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
67832 GTTTTAAAAA
*
67842 TATATAATGTATATTAAT
1 TATATAATTTATATTAAT
*
67860 TTTATAATTTATA-T-AT
1 TATATAATTTATATTAAT
67876 TATATAATTT
1 TATATAATTT
67886 TTACCATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 11 0.48
17 1 0.04
18 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATATAATTTATATTAAT
Found at i:71074 original size:2 final size:2
Alignment explanation
Indices: 71067--71129 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
71057 CAAGATTCTA
71067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
71109 AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
71130 AACAAATGGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72253 original size:125 final size:122
Alignment explanation
Indices: 72005--72253 Score: 403
Period size: 124 Copynumber: 2.0 Consensus size: 122
71995 TGCTGATAAA
*
72005 ATATTGATGTGTCATGTGATGTAAAATTTAAATTTTATATAAAAAAAGATTTAAGTTATGTGTCG
1 ATATTGATGTGTCATGTGATGTAAAATTTAAATTTTATACAAAAAAAGATTTAAGTTATGTGTCG
*
72070 AGTTTTAGGTAATTTTTCTTATAAAATTTTAAATCCCATATGATATAGCATATTAGC
66 AGTTTTAGGTAATCTTTCTTATAAAATTTTAAATCCCATATGATATAGCATATTAGC
72127 ATATTGATGTGTCATGTGATGTAATAATTTTAAATTTTATACAAAAAAAGGATTTAAGTTATGTG
1 ATATTGATGTGTCATGTGATGTAA-AA-TTTAAATTTTATACAAAAAAA-GATTTAAGTTATGTG
* *
72192 TCGAG-TTTAGGTAATCTTTCTTAT-AAATTTTAAATCCTCATCTGCTATAAGCATATTAGC
63 TCGAGTTTTAGGTAATCTTTCTTATAAAATTTTAAATCC-CATATGATAT-AGCATATTAGC
72252 AT
1 AT
72254 TTTATCAGCA
Statistics
Matches: 118, Mismatches: 4, Indels: 7
0.91 0.03 0.05
Matches are distributed among these distances:
122 24 0.20
123 15 0.13
124 46 0.39
125 33 0.28
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (122 bp):
ATATTGATGTGTCATGTGATGTAAAATTTAAATTTTATACAAAAAAAGATTTAAGTTATGTGTCG
AGTTTTAGGTAATCTTTCTTATAAAATTTTAAATCCCATATGATATAGCATATTAGC
Found at i:72683 original size:14 final size:14
Alignment explanation
Indices: 72664--72698 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
72654 TCGTAATGTA
72664 ATTTTATAATCATT
1 ATTTTATAATCATT
*
72678 ATTTTATAATCGTT
1 ATTTTATAATCATT
72692 ATTTTAT
1 ATTTTAT
72699 GATTTCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (14 bp):
ATTTTATAATCATT
Done.