Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024903.1 Corchorus olitorius cultivar O-4 contig24936, whole genome shotgun sequence
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: 97206
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1723 original size:17 final size:17
Alignment explanation
Indices: 1701--1734 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1691 CGAATATCAC
1701 CATCATCCAGAAAGAAT
1 CATCATCCAGAAAGAAT
1718 CATCATCCAGAAAGAAT
1 CATCATCCAGAAAGAAT
1735 TATAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (17 bp):
CATCATCCAGAAAGAAT
Found at i:2169 original size:18 final size:19
Alignment explanation
Indices: 2146--2188 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2136 AAACAATTAC
2146 AAAAAC-AAAATAG-GAAAA
1 AAAAACGAAAA-AGCGAAAA
*
2164 AAAAACGCAAAAGCGAAAA
1 AAAAACGAAAAAGCGAAAA
2183 AAAAAC
1 AAAAAC
2189 TTGTTCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.74, C:0.12, G:0.12, T:0.02
Consensus pattern (19 bp):
AAAAACGAAAAAGCGAAAA
Found at i:6250 original size:82 final size:82
Alignment explanation
Indices: 6113--6276 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
6103 CATTATGAGT
6113 GTGCATAAGGTAACAAAAGACAGCAAAGCTTGCAAATGTAACAGTGAAGAAAATCAAAACCAAGC
1 GTGCATAAGGTAACAAAAGACAGCAAAGCTTGCAAATGTAACAGTGAAGAAAATCAAAACCAAGC
6178 ACTTCAGTAAGCAATAG
66 ACTTCAGTAAGCAATAG
6195 GTGCATAAGGTAACAAAAGACAGCAAAGCTTGCAAATGTAACAGTGAAGAAAATCAAAACCAAGC
1 GTGCATAAGGTAACAAAAGACAGCAAAGCTTGCAAATGTAACAGTGAAGAAAATCAAAACCAAGC
*
6260 ATTTCAGTAAGCAATAG
66 ACTTCAGTAAGCAATAG
6277 CCGATATCCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (82 bp):
GTGCATAAGGTAACAAAAGACAGCAAAGCTTGCAAATGTAACAGTGAAGAAAATCAAAACCAAGC
ACTTCAGTAAGCAATAG
Found at i:9115 original size:31 final size:31
Alignment explanation
Indices: 9044--9115 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
9034 GTCTATCAGC
*
9044 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
9075 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
9105 GTTTTAATTTG
1 -TTTTAATTTG
9116 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:9966 original size:13 final size:13
Alignment explanation
Indices: 9948--9973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9938 AAATTAATAA
9948 TGTTATATTATAT
1 TGTTATATTATAT
9961 TGTTATATTATAT
1 TGTTATATTATAT
9974 ATTATCAATA
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TGTTATATTATAT
Found at i:10138 original size:23 final size:23
Alignment explanation
Indices: 10112--10162 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
10102 AAACCCGAGA
* *
10112 CCGAGCCCGACCC-AGGCCCGAAC
1 CCGAACCCGACCCGA-GACCGAAC
*
10135 CCGAACCCTACCCGAGACCGAAC
1 CCGAACCCGACCCGAGACCGAAC
10158 CCGAA
1 CCGAA
10163 AATACCCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.27, C:0.49, G:0.22, T:0.02
Consensus pattern (23 bp):
CCGAACCCGACCCGAGACCGAAC
Found at i:10173 original size:16 final size:16
Alignment explanation
Indices: 10152--10242 Score: 105
Period size: 16 Copynumber: 5.7 Consensus size: 16
10142 CTACCCGAGA
10152 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
10168 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
* *
10184 CCGAGCCCGAAGATAC
1 CCGAACCCGAAAATAC
**
10200 CCGAACCC-AACTTAAC
1 CCGAACCCGAAAAT-AC
10216 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
10232 CCGAACCCGAA
1 CCGAACCCGAA
10243 CCCGTCCGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.10
16 51 0.81
17 6 0.10
ACGTcount: A:0.38, C:0.41, G:0.14, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:10200 original size:32 final size:32
Alignment explanation
Indices: 10152--10241 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
10142 CTACCCGAGA
10152 CCGAACCCGAAAATACCCGAACCCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* * * *
10184 CCGAGCCCGAAGATACCCGAACCCAACTTAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
10216 CCGAACCCGAAAATACCCGAACCCGA
1 CCGAACCCGAAAATACCCGAACCCGA
10242 ACCCGTCCGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.38, C:0.41, G:0.14, T:0.07
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:10662 original size:12 final size:12
Alignment explanation
Indices: 10645--10669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10635 TTATGGGGTG
10645 AAATAATGGAGA
1 AAATAATGGAGA
10657 AAATAATGGAGA
1 AAATAATGGAGA
10669 A
1 A
10670 TCATTTGACC
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:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AAATAATGGAGA
Found at i:15330 original size:12 final size:12
Alignment explanation
Indices: 15313--15337 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15303 TTATGGGGTG
15313 AAATAATGGAGA
1 AAATAATGGAGA
15325 AAATAATGGAGA
1 AAATAATGGAGA
15337 A
1 A
15338 TTTTTGACCT
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:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AAATAATGGAGA
Found at i:15657 original size:15 final size:16
Alignment explanation
Indices: 15639--15671 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
15629 TATTAAATAA
15639 ATAATAATTATT-TTT
1 ATAATAATTATTATTT
15654 ATAATAATTATTATTT
1 ATAATAATTATTATTT
15670 AT
1 AT
15672 CCCATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAATAATTATTATTT
Found at i:27371 original size:47 final size:46
Alignment explanation
Indices: 27317--27413 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 46
27307 TGCTTAGAAA
27317 TTATCCTTCCCTTTTGTAATTGATAGTCGATACTTTGTTATTCAACT
1 TTATCCTTCCCTTTTGTAATTGATAGTCGATACTTTGTTATTC-ACT
27364 TTATCCTTCCCTTTTGTAATTGATAGTCGATACTTTGTTATTCACT
1 TTATCCTTCCCTTTTGTAATTGATAGTCGATACTTTGTTATTCACT
27410 TTAT
1 TTAT
27414 ACTGATTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 7 0.14
47 43 0.86
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.51
Consensus pattern (46 bp):
TTATCCTTCCCTTTTGTAATTGATAGTCGATACTTTGTTATTCACT
Found at i:30402 original size:63 final size:63
Alignment explanation
Indices: 30303--30444 Score: 266
Period size: 63 Copynumber: 2.3 Consensus size: 63
30293 TGGGGACCCT
*
30303 CAACATAGCTTCGTGTGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
1 CAACATAGCTTCGTGCGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
30366 CAACATAGCTTCGTGCGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
1 CAACATAGCTTCGTGCGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
*
30429 CAACATAGCTTGGTGC
1 CAACATAGCTTCGTGC
30445 TGCTTCTCAG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 77 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (63 bp):
CAACATAGCTTCGTGCGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
Found at i:30638 original size:17 final size:17
Alignment explanation
Indices: 30601--30647 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
30591 TCTAATTAAT
* *
30601 AATATTCATTATTATTTA
1 AATATTTATT-TTAATTA
30619 AATATTTATTTTAATTA
1 AATATTTATTTTAATTA
*
30636 AATATTTGTTTT
1 AATATTTATTTT
30648 GATAATATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
AATATTTATTTTAATTA
Found at i:30691 original size:79 final size:75
Alignment explanation
Indices: 30560--30717 Score: 228
Period size: 79 Copynumber: 2.1 Consensus size: 75
30550 TTATTTAGAA
*
30560 ATTTGTTTGGATAATATACTAAGCTTTCGCTTCTAATTAATAATATTCATTATTATTTAAATATT
1 ATTTGTTTGGATAATATACTAAGCTTTCACTTCTAATTAAT-A-A-TCATTATTATTTAAATATT
*
30625 TATTTTAATTAAAT
63 T-GTTTAATTAAAT
*
30639 ATTTGTTTTGATAATATACTAAGCTTTCACTTCTAATTAAT-ATCTATTATTATTTAAATATTTG
1 ATTTGTTTGGATAATATACTAAGCTTTCACTTCTAATTAATAATC-ATTATTATTTAAATATTTG
*
30703 TTTAATTGAAT
65 TTTAATTAAAT
30714 ATTT
1 ATTT
30718 TGATTTCTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
75 16 0.22
76 19 0.26
79 39 0.53
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (75 bp):
ATTTGTTTGGATAATATACTAAGCTTTCACTTCTAATTAATAATCATTATTATTTAAATATTTGT
TTAATTAAAT
Found at i:32450 original size:28 final size:27
Alignment explanation
Indices: 32416--32490 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 27
32406 GTAAATCAAG
32416 TTAAAAATAAAATAAATTACACTAGAGA
1 TTAAAAA-AAAATAAATTACACTAGAGA
*
32444 TTAAAAAGAAAATAAATTAAACTAGAGA
1 TTAAAAA-AAAATAAATTACACTAGAGA
32472 TT-AAAAAAAATAAATTACA
1 TTAAAAAAAAATAAATTACA
32491 AAAACAACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 12 0.27
27 4 0.09
28 28 0.64
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (27 bp):
TTAAAAAAAAATAAATTACACTAGAGA
Found at i:32526 original size:38 final size:38
Alignment explanation
Indices: 32484--32564 Score: 132
Period size: 35 Copynumber: 2.2 Consensus size: 38
32474 AAAAAAAATA
*
32484 AATTACAAAAACAACTAAACATGATAATACTAGTAGAC
1 AATTACAAAAACAACTAAACATGAGAATACTAGTAGAC
32522 AATT---AAAACAACTAAACATGAGAATACTAGTAGAC
1 AATTACAAAAACAACTAAACATGAGAATACTAGTAGAC
32557 AATTACAA
1 AATTACAA
32565 TTTAAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
35 34 0.87
38 5 0.13
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.21
Consensus pattern (38 bp):
AATTACAAAAACAACTAAACATGAGAATACTAGTAGAC
Found at i:32535 original size:35 final size:35
Alignment explanation
Indices: 32491--32561 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
32481 ATAAATTACA
*
32491 AAAACAACTAAACATGATAATACTAGTAGACAATT
1 AAAACAACTAAACATGAGAATACTAGTAGACAATT
32526 AAAACAACTAAACATGAGAATACTAGTAGACAATT
1 AAAACAACTAAACATGAGAATACTAGTAGACAATT
32561 A
1 A
32562 CAATTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (35 bp):
AAAACAACTAAACATGAGAATACTAGTAGACAATT
Found at i:32855 original size:57 final size:55
Alignment explanation
Indices: 32792--32930 Score: 136
Period size: 56 Copynumber: 2.5 Consensus size: 55
32782 AACTTTAAGG
*
32792 TTGACTATCAATATTTGGGGTTTGACCAAGCATATACAATGAAATG-TTTTTTGTGGT
1 TTGACTATCAA-ATTTGGGGTTTGACCAAGCATATACAATG--ATGTTTTTTTGTGGC
* * * * * *
32849 TTGACTATTGAACTTTGGGGTTTGACTATGCTTGTACAATGATGTTTTTTTGTGGC
1 TTGACTA-TCAAATTTGGGGTTTGACCAAGCATATACAATGATGTTTTTTTGTGGC
* * *
32905 TTGACCATTAAAATTTGTGGTTTGAC
1 TTGACTA-TCAAATTTGGGGTTTGAC
32931 TATCGAACTT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
55 3 0.04
56 32 0.46
57 31 0.45
58 3 0.04
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (55 bp):
TTGACTATCAAATTTGGGGTTTGACCAAGCATATACAATGATGTTTTTTTGTGGC
Found at i:33024 original size:53 final size:52
Alignment explanation
Indices: 32959--33095 Score: 202
Period size: 53 Copynumber: 2.6 Consensus size: 52
32949 GATCATCATC
*
32959 TTTTGGAGTTTGACTATGCATGTACAATGATATTTTGTGGTTTAACTATTGAA
1 TTTTGGGGTTTGAC-ATGCATGTACAATGATATTTTGTGGTTTAACTATTGAA
* * *
33012 TTTTGGGGTTTGACCATGCATGTACAATGATGTTTTGTGGTTTGATTATTGAA
1 TTTTGGGGTTTGA-CATGCATGTACAATGATATTTTGTGGTTTAACTATTGAA
*
33065 TTTTAGGGTTTGAACATGCATGTACAATGAT
1 TTTTGGGGTTTG-ACATGCATGTACAATGAT
33096 TTAATGTTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
53 75 0.97
54 2 0.03
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (52 bp):
TTTTGGGGTTTGACATGCATGTACAATGATATTTTGTGGTTTAACTATTGAA
Found at i:33225 original size:74 final size:73
Alignment explanation
Indices: 33104--33437 Score: 497
Period size: 74 Copynumber: 4.5 Consensus size: 73
33094 ATTTAATGTT
* *
33104 TTTTGTGGTTTTACTATCGAACTTTGGGGTTTGACCATCATCTTTTGGAGTTTGACTATGCATGT
1 TTTTGTGGTTTGACTATTGAA-TTTGGGGTTTGACCATCATCTTTTGGAGTTTGACTATGCATGT
33169 ACAATGCTA
65 ACAATGCTA
* *
33178 TTTTGTGGTTTGCCTATTGAATTTGGGGGTTTGACCATCATCTTTTGGAGTTTGACTGTGCATGT
1 TTTTGTGGTTTGACTATTGAATTT-GGGGTTTGACCATCATCTTTTGGAGTTTGACTATGCATGT
33243 ACAATGCTA
65 ACAATGCTA
*
33252 TTTTGTGGTTTGACTATCGAACTTTGGGGTTTGACCATCATCTTTTGGAGTTTGACTATGCATGT
1 TTTTGTGGTTTGACTATTGAA-TTTGGGGTTTGACCATCATCTTTTGGAGTTTGACTATGCATGT
* *
33317 AAAATACTA
65 ACAATGCTA
* * * * *
33326 TTTTGTGGTTTGACTATTGAATTTGAGGGTTTGACCATCTTCCTTTGGGGTTTGACCATGTATGT
1 TTTTGTGGTTTGACTATTGAATTTG-GGGTTTGACCATCATCTTTTGGAGTTTGACTATGCATGT
* *
33391 ACAATGATG
65 ACAATGCTA
33400 TTTTGTGGTTTGACTATTGAATTTTGGGGTTTGACCAT
1 TTTTGTGGTTTGACTATTGAA-TTTGGGGTTTGACCAT
33438 GCATATACAA
Statistics
Matches: 237, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
73 7 0.03
74 223 0.94
75 7 0.03
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44
Consensus pattern (73 bp):
TTTTGTGGTTTGACTATTGAATTTGGGGTTTGACCATCATCTTTTGGAGTTTGACTATGCATGTA
CAATGCTA
Found at i:33298 original size:21 final size:22
Alignment explanation
Indices: 33252--33307 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
33242 TACAATGCTA
* *
33252 TTTTGTGGTTTGACTATCGAAC
1 TTTTGGGGTTTGACCATCGAAC
*
33274 -TTTGGGGTTTGACCATC-ATC
1 TTTTGGGGTTTGACCATCGAAC
*
33294 TTTTGGAGTTTGAC
1 TTTTGGGGTTTGAC
33308 TATGCATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.45
Consensus pattern (22 bp):
TTTTGGGGTTTGACCATCGAAC
Found at i:34489 original size:31 final size:30
Alignment explanation
Indices: 34439--34515 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
34429 TAATTTAGCT
34439 AGTTGCTATTTC--TTTTTTTTTTACCAAA
1 AGTTGCTATTTCTTTTTTTTTTTTACCAAA
34467 AGTTGCTATTTCTTTTTTTTTTTTTACCAAA
1 AGTTGCTATTTC-TTTTTTTTTTTTACCAAA
** *
34498 AAATGCTATTTCCTTTTT
1 AGTTGCTATTTCTTTTTT
34516 AATAATTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 12 0.28
30 5 0.12
31 26 0.60
ACGTcount: A:0.21, C:0.14, G:0.06, T:0.58
Consensus pattern (30 bp):
AGTTGCTATTTCTTTTTTTTTTTTACCAAA
Found at i:35638 original size:1 final size:1
Alignment explanation
Indices: 35632--35661 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
35622 TCGTCGTTTT
35632 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35662 GCCTTAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38449 original size:18 final size:18
Alignment explanation
Indices: 38426--38461 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38416 AACTTTAATA
*
38426 GTAAAAAAATATATAGAT
1 GTAAAAAAAAATATAGAT
38444 GTAAAAAAAAATATAGAT
1 GTAAAAAAAAATATAGAT
38462 TGGATTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (18 bp):
GTAAAAAAAAATATAGAT
Found at i:39147 original size:16 final size:16
Alignment explanation
Indices: 39128--39171 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
39118 ACCCGCCCGA
*
39128 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
39144 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
39160 ACCCGAACCCGA
1 ACCCGAACCCGA
39172 GGCAGCCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.41, G:0.16, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:39198 original size:11 final size:11
Alignment explanation
Indices: 39175--39204 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
39165 AACCCGAGGC
39175 AGCCCGAACCCG
1 AGCCCG-ACCCG
39187 AGCCCGACCCG
1 AGCCCGACCCG
39198 AGCCCGA
1 AGCCCGA
39205 ACCTGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.23, C:0.50, G:0.27, T:0.00
Consensus pattern (11 bp):
AGCCCGACCCG
Found at i:39716 original size:31 final size:31
Alignment explanation
Indices: 39645--39716 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
39635 GTCTATCAGC
*
39645 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
39676 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
39706 GTTTTAATTTG
1 -TTTTAATTTG
39717 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:40012 original size:6 final size:6
Alignment explanation
Indices: 40003--40047 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
39993 CAAAATCAAA
* *
40003 CCCGAG CCCGAA CCCGA- CCCGAG -CCGAG CCCGAG CCCGAA CCCGA
1 CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGA
40048 AAATACTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.22, C:0.51, G:0.27, T:0.00
Consensus pattern (6 bp):
CCCGAG
Found at i:40029 original size:22 final size:23
Alignment explanation
Indices: 40004--40047 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
39994 AAAATCAAAC
40004 CCGAGCCCGAACCCG-ACCCGAG
1 CCGAGCCCGAACCCGAACCCGAG
*
40026 CCGAGCCCGAGCCCGAACCCGA
1 CCGAGCCCGAACCCGAACCCGA
40048 AAATACTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.23, C:0.50, G:0.27, T:0.00
Consensus pattern (23 bp):
CCGAGCCCGAACCCGAACCCGAG
Found at i:40060 original size:16 final size:16
Alignment explanation
Indices: 40037--40143 Score: 105
Period size: 16 Copynumber: 6.8 Consensus size: 16
40027 CGAGCCCGAG
40037 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
40053 CTCGAACCCGACATAAT-
1 CCCGAACCCGA-A-AATA
*
40070 -CCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
**
40085 CCCGAACCCG-ACTTAA
1 CCCGAACCCGAAAAT-A
*
40101 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
*
40117 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
40132 CCCGAACCCGAA
1 CCCGAACCCGAA
40144 CCCGCCCAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
14 3 0.04
15 17 0.23
16 47 0.64
17 3 0.04
18 3 0.04
ACGTcount: A:0.36, C:0.39, G:0.16, T:0.08
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:40080 original size:32 final size:32
Alignment explanation
Indices: 40037--40143 Score: 146
Period size: 32 Copynumber: 3.4 Consensus size: 32
40027 CGAGCCCGAG
* *
40037 CCCGAACCCGAAAATACTCGAACCCGACATAA
1 CCCGAGCCCGAAAATACCCGAACCCGACATAA
* *
40069 TCCGAGCCCGAAAATACCCGAACCCGACTTAA
1 CCCGAGCCCGAAAATACCCGAACCCGACATAA
40101 CCCGAGCCCGAAAATACCCGAACCCGA-AGT-A
1 CCCGAGCCCGAAAATACCCGAACCCGACA-TAA
*
40132 CCCGAACCCGAA
1 CCCGAGCCCGAA
40144 CCCGCCCAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
31 12 0.18
32 55 0.82
ACGTcount: A:0.36, C:0.39, G:0.16, T:0.08
Consensus pattern (32 bp):
CCCGAGCCCGAAAATACCCGAACCCGACATAA
Found at i:41387 original size:22 final size:22
Alignment explanation
Indices: 41359--41400 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41349 ACTAACAATA
*
41359 ACAAGG-ACCAAAATGAGAGTGC
1 ACAAGGAAACAAAA-GAGAGTGC
41381 ACAAGGAAACAAAAGAGAGT
1 ACAAGGAAACAAAAGAGAGT
41401 AAACAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.14, G:0.26, T:0.07
Consensus pattern (22 bp):
ACAAGGAAACAAAAGAGAGTGC
Found at i:41406 original size:22 final size:22
Alignment explanation
Indices: 41358--41406 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
41348 TACTAACAAT
* *
41358 AACAAGGACCAAAATGAGAGTG
1 AACAAGGAACAAAATGAGAGTA
*
41380 CACAAGGAAACAAAA-GAGAGTA
1 AACAAGG-AACAAAATGAGAGTA
41402 AACAA
1 AACAA
41407 TTCTGTATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.14, G:0.22, T:0.06
Consensus pattern (22 bp):
AACAAGGAACAAAATGAGAGTA
Found at i:48759 original size:54 final size:54
Alignment explanation
Indices: 48672--48779 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 54
48662 TAACACTTTC
* * * *
48672 TTTTTCCTTCCCATTCCCATTTCTATTGAAAAAATTCTTAATACAAAAATTTACA
1 TTTTTCCTTCCCATTCCCATCTCTATTGAAAAAA-TCCTAACACAAAAATGTACA
*
48727 TTTTT-CTTCCCATTCCCATCTCT-TTTACAAAAATCCTAACACAAAAATGTACA
1 TTTTTCCTTCCCATTCCCATCTCTATTGA-AAAAATCCTAACACAAAAATGTACA
48780 GTAGAGAGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 20 0.43
54 22 0.47
55 5 0.11
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (54 bp):
TTTTTCCTTCCCATTCCCATCTCTATTGAAAAAATCCTAACACAAAAATGTACA
Found at i:54596 original size:18 final size:18
Alignment explanation
Indices: 54551--54603 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
54541 ATGATTTCTT
*
54551 TTTTTTATTGGTTTTTTTAC
1 TTTTTTATT--TTTTTTTAA
**
54571 TTAATTATTTTTTTTTAA
1 TTTTTTATTTTTTTTTAA
54589 TTTTTTATATTTTTT
1 TTTTTTAT-TTTTTT
54604 ATTATTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 14 0.52
19 6 0.22
20 7 0.26
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTTTATTTTTTTTTAA
Found at i:54742 original size:31 final size:29
Alignment explanation
Indices: 54706--54774 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
54696 GTTGAAAAAG
* *
54706 TATCAAATTGAACTGATTTTGAAAGATTTAA
1 TATCAAATTGAAC-AACTTTG-AAGATTTAA
* * *
54737 TATCAATTTGAGCAACTTTGAAGGTTTAA
1 TATCAAATTGAACAACTTTGAAGATTTAA
54766 TATCAAATT
1 TATCAAATT
54775 AAGCCTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 16 0.50
30 5 0.16
31 11 0.34
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (29 bp):
TATCAAATTGAACAACTTTGAAGATTTAA
Found at i:61905 original size:350 final size:352
Alignment explanation
Indices: 61057--61973 Score: 1435
Period size: 355 Copynumber: 2.6 Consensus size: 352
61047 GTTGAACCCA
* * * *
61057 ATTTGATTAGAAAAAGTAAACGATT-CAAACCCGTCATATCCAGACCCGACTAACTCGTAACCCG
1 ATTTGACTAGAAAAAGTAAACG-TTCCAAACCTGTCATATCCAGACCTGACAAACTCGTAACCCG
* * *
61121 AATGACTCGAGAAATTAACCCGAGAGACGCAATAATATTATAAACTAAAATTATGTTTTATTCAG
65 AATGACTCGAGAAGTTAACCCGAAAGACGCAAAAATATTATAAACTAAAATTATGTTTTATTCAG
* * *
61186 TCAAATCCACATAGTTATAATTTTAACTATTATAAAATATCATTTATTCAATAAAATTTATGTTA
130 TCAAATCCACATTGTTATAATTTTAAC-ATT-TAAATTATCATTTATTCAATAAAATTTATATTA
*
61251 TTGTTATAATTTTACATATTATGATTAAATTTACTAAACTTCATTATATGAACAATAATTATATG
193 TTGTTATAATTTTACCTATTATGATTAAATTTACTAAACTTCATTATATGAACAATAATTATATG
* *
61316 AATAAATACTAAATCGGTTATATGAATAATTTATGATAAGTTTATAATTAGTAATTTGTTTTTTT
258 AATAAATACTAAATCAGTTATATGAATAATTTATGATAAGTTTATAATTAGTAATTTGTGTTTTT
61381 ACATAATGAATAAATATAAATAATAATTATT
323 ACATAATGAATAAATATAAATAATAA-TATT
* * * * **
61412 ATTTAACCAGAAAAAGTAAACGTTCCACACCTGTCATATCTAGACCTGACAAACTCGTAACTTGA
1 ATTTGACTAGAAAAAGTAAACGTTCCAAACCTGTCATATCCAGACCTGACAAACTCGTAACCCGA
* *
61477 ATGACCCGAGAAGTTAACCCGAAAGACGCAAGAATATTATAAACTAAAATTATGTTTTATTCAGT
66 ATGACTCGAGAAGTTAACCCGAAAGACGCAAAAATATTATAAACTAAAATTATGTTTTATTCAGT
*
61542 CAAATCAACATTGTTATAATTTTAACCATTCTAAATTATCATTTATTCAATAAAATTTATATTAT
131 CAAATCCACATTGTTATAATTTTAA-CATT-TAAATTATCATTTATTCAATAAAATTTATATTAT
61607 TGTTATAATTTTACCTATTATGATTAAATTTACTAAACTTCATTATATGAACAATAATATATATG
194 TGTTATAATTTTACCTATTATGATTAAATTTACTAAACTTCATTATATGAACAATAAT-TATATG
* *
61672 GATAAATACTAAATCATTTATATGAATAATTTATGATAAGTTTATAATTAGTAATTTGTGTTTTT
258 AATAAATACTAAATCAGTTATATGAATAATTTATGATAAGTTTATAATTAGTAATTTGTGTTTTT
*
61737 ACATAATGAAT-AA-AT-AATAGT-A-ATT
323 ACATAATGAATAAATATAAATAATAATATT
61762 ATTTGACTAGAAAAAGTAAACGTTCCAAACCTGTCATATCCAGACCTGACAAACTCGTAACCCGA
1 ATTTGACTAGAAAAAGTAAACGTTCCAAACCTGTCATATCCAGACCTGACAAACTCGTAACCCGA
*
61827 ATGACTCGATAAGTTAACCCGAAAGACGCAAAAATATTATAAACTAAAATTATGTTTTATTCAGT
66 ATGACTCGAGAAGTTAACCCGAAAGACGCAAAAATATTATAAACTAAAATTATGTTTTATTCAGT
* *
61892 CAAATCCACATTGTTATAATTTT---A---GAATTATCATTTATTCAATAAAATTTATATTATTA
131 CAAATCCACATTGTTATAATTTTAACATTTAAATTATCATTTATTCAATAAAATTTATATTATTG
61951 TTATAATTTTACCTATTATGATT
196 TTATAATTTTACCTATTATGATT
61974 TTTTTTTGAG
Statistics
Matches: 522, Mismatches: 37, Indels: 19
0.90 0.06 0.03
Matches are distributed among these distances:
342 56 0.11
346 1 0.00
350 146 0.28
352 1 0.00
353 5 0.01
354 4 0.01
355 230 0.44
356 79 0.15
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (352 bp):
ATTTGACTAGAAAAAGTAAACGTTCCAAACCTGTCATATCCAGACCTGACAAACTCGTAACCCGA
ATGACTCGAGAAGTTAACCCGAAAGACGCAAAAATATTATAAACTAAAATTATGTTTTATTCAGT
CAAATCCACATTGTTATAATTTTAACATTTAAATTATCATTTATTCAATAAAATTTATATTATTG
TTATAATTTTACCTATTATGATTAAATTTACTAAACTTCATTATATGAACAATAATTATATGAAT
AAATACTAAATCAGTTATATGAATAATTTATGATAAGTTTATAATTAGTAATTTGTGTTTTTACA
TAATGAATAAATATAAATAATAATATT
Found at i:62770 original size:6 final size:6
Alignment explanation
Indices: 62753--62785 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
62743 GTACTTTTTA
*
62753 ATATAG -TATAG ATATAG ATATAG ATATTG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
62786 GAGGATTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (6 bp):
ATATAG
Found at i:70393 original size:30 final size:30
Alignment explanation
Indices: 70319--70393 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
70309 TGGTGGTGGA
* *
70319 ATTGGAAAGGGTGGCTGGTTTGGAGGTCGC
1 ATTGGAAAGGGTGGTTGGTTTAGAGGTCGC
*
70349 ATTGGAAAGGGTGGTTGGTTTAGAGGTCGT
1 ATTGGAAAGGGTGGTTGGTTTAGAGGTCGC
*
70379 ATTGGGAAGGGTGGT
1 ATTGGAAAGGGTGGT
70394 CGATTTGGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.19, C:0.05, G:0.47, T:0.29
Consensus pattern (30 bp):
ATTGGAAAGGGTGGTTGGTTTAGAGGTCGC
Found at i:82041 original size:68 final size:68
Alignment explanation
Indices: 81930--82066 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 68
81920 TGTTATGAGA
* * * *
81930 TTTCAATTGTATTTGTTGAGGAAGGGGTTTGTTTGTTGGCTCATAGATTAGTGTTTCGGTAATGT
1 TTTCAATTGTATTTGTTGAGGAAGGGGTTTGTTTGTTGCCTCATAAATTAGCGTTTCAGTAATGT
81995 AGC
66 AGC
*
81998 TTTCAATTGTATTTGTTGGGGAAGGGGTTTGTTTGTTGCCTCATAAATTAGCGTTTCAGTAATGT
1 TTTCAATTGTATTTGTTGAGGAAGGGGTTTGTTTGTTGCCTCATAAATTAGCGTTTCAGTAATGT
82063 AGC
66 AGC
82066 T
1 T
82067 AATCATGTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.20, C:0.09, G:0.28, T:0.44
Consensus pattern (68 bp):
TTTCAATTGTATTTGTTGAGGAAGGGGTTTGTTTGTTGCCTCATAAATTAGCGTTTCAGTAATGT
AGC
Found at i:84493 original size:194 final size:194
Alignment explanation
Indices: 84164--84552 Score: 670
Period size: 194 Copynumber: 2.0 Consensus size: 194
84154 CGGGAGGAAT
* *
84164 AGTCCCGCATCACACGATTATCCAGCTCAATCTTGGCTAGAGAATGTGCAAATACATTGGCTTCC
1 AGTCCCGCAGCACACGATTATCCAGCTCAATCTTAGCTAGAGAATGTGCAAATACATTGGCTTCC
* * * * * *
84229 CTTTTTATAAATTGAGGCATACATAAATCAAATAGGATTTCCAAATCTCTAATTTCATCTATAAC
66 CTATTTACAAATTGAAGCACACATAAATCAAATAGAATTGCCAAATCTCTAATTTCATCTATAAC
* *
84294 TACCAAACATACCAAATGTATAAACAAATAAATTACAAACTAAACTCACATTCCGTGAGACTAG
131 TACCAAACATACCAAATATACAAACAAATAAATTACAAACTAAACTCACATTCCGTGAGACTAG
84358 AGTCCCGCAGCACACGATTATCCAGCTCAATCTTAGCTAGAGAATGTGCAAATACATTGGCTTCC
1 AGTCCCGCAGCACACGATTATCCAGCTCAATCTTAGCTAGAGAATGTGCAAATACATTGGCTTCC
* *
84423 CTATTTACAAATTGAAGCGCACATAAATCAAATAGAATTGCCAAATCTCTAATTTCATCTATATC
66 CTATTTACAAATTGAAGCACACATAAATCAAATAGAATTGCCAAATCTCTAATTTCATCTATAAC
84488 TACCAAACATACCAAATATACAAACAAATAAATTACAAACTAAACTCACATTCCGTGAGACTAG
131 TACCAAACATACCAAATATACAAACAAATAAATTACAAACTAAACTCACATTCCGTGAGACTAG
84552 A
1 A
84553 ATCCAAGACC
Statistics
Matches: 183, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
194 183 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (194 bp):
AGTCCCGCAGCACACGATTATCCAGCTCAATCTTAGCTAGAGAATGTGCAAATACATTGGCTTCC
CTATTTACAAATTGAAGCACACATAAATCAAATAGAATTGCCAAATCTCTAATTTCATCTATAAC
TACCAAACATACCAAATATACAAACAAATAAATTACAAACTAAACTCACATTCCGTGAGACTAG
Found at i:86121 original size:86 final size:86
Alignment explanation
Indices: 85956--86121 Score: 185
Period size: 86 Copynumber: 1.9 Consensus size: 86
85946 TATGCTTGGA
* * * *
85956 TTTTCTTAAAAATTGTGAGATTTGACTTAATACGTAATTGTTATATGAATTCATGACATGAGTAG
1 TTTTCTTAAAAATTGTAAAATTTGACTTAATACATAATTGTTATATGAATTCATGACATGAG-AA
* *
86021 ACATTTTTTTTAACCGATAACT
65 ACATATTTTGTAACCGATAACT
* * * *
86043 TTTTCTTAAAGATTG-AAAATTTGACTTAGTACATAATTTTTATTTGAATTCATGACA-GTA-AA
1 TTTTCTTAAAAATTGTAAAATTTGACTTAATACATAATTGTTATATGAATTCATGACATG-AGAA
86105 ACATCAATTTTGTAACC
65 ACAT--ATTTTGTAACC
86122 ATGCAAACCA
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
84 5 0.08
85 1 0.02
86 46 0.70
87 14 0.21
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (86 bp):
TTTTCTTAAAAATTGTAAAATTTGACTTAATACATAATTGTTATATGAATTCATGACATGAGAAA
CATATTTTGTAACCGATAACT
Found at i:87277 original size:31 final size:31
Alignment explanation
Indices: 87242--87302 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
87232 AAGATTGAAA
*
87242 TATGAAAACA-AGAAGAACAAATAAGAACTTG
1 TATGAAAA-AGAGAAGAACAAAGAAGAACTTG
* *
87273 TATGAAAAAGTGAAGAACAACGAAGAACTT
1 TATGAAAAAGAGAAGAACAAAGAAGAACTT
87303 TTAGAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.16
Consensus pattern (31 bp):
TATGAAAAAGAGAAGAACAAAGAAGAACTTG
Found at i:88924 original size:11 final size:11
Alignment explanation
Indices: 88890--88937 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
88880 TTGAAATAAT
88890 TCTTC-AATAG
1 TCTTCAAATAG
88900 TCTTC--A-AG
1 TCTTCAAATAG
88908 TCTTCAAATTA-
1 TCTTCAAA-TAG
88919 TCTTCAAATAG
1 TCTTCAAATAG
88930 TCTTCAAA
1 TCTTCAAA
88938 CATGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 8 0.24
11 16 0.48
12 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:90212 original size:33 final size:33
Alignment explanation
Indices: 90170--90232 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
90160 TTCGAAAAAT
90170 GCATTAATTAAGATTATGATCAATATGCATATG
1 GCATTAATTAAGATTATGATCAATATGCATATG
90203 GCATTAATTAAGATTATGATCAATATGCAT
1 GCATTAATTAAGATTATGATCAATATGCAT
90233 GAAAACTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (33 bp):
GCATTAATTAAGATTATGATCAATATGCATATG
Found at i:93899 original size:22 final size:22
Alignment explanation
Indices: 93842--94094 Score: 141
Period size: 22 Copynumber: 11.6 Consensus size: 22
93832 TTACTAACAA
* * *
93842 TTCATATGGAGGTTTTTAAATT
1 TTCATATGGAGGTTATCAAAAT
* * *
93864 TTCAT-TACGTGGTTATCAATAT
1 TTCATAT-GGAGGTTATCAAAAT
* *
93886 ATCATATGGAGGTTATCAACAT
1 TTCATATGGAGGTTATCAAAAT
* **
93908 CTCATAGTGTTGGTTATCAAAAT
1 TTCATA-TGGAGGTTATCAAAAT
*
93931 TTCAT-TGGGAAGTTATCAAAAT
1 TTCATAT-GGAGGTTATCAAAAT
93953 TTCATA-GTGAGGTCT-TCAAAAT
1 TTCATATG-GAGGT-TATCAAAAT
*
93975 TTCATATGGAGGTTAACAAAAT
1 TTCATATGGAGGTTATCAAAAT
**
93997 TTCATA---AGGTTAAAAAAAAT
1 TTCATATGGAGGTT-ATCAAAAT
*** *
94017 TT-ATAAAAAGGTTCTCAAAAT
1 TTCATATGGAGGTTATCAAAAT
* *
94038 TTCATAAT--ATCGTTATTAAAAT
1 TTCAT-ATGGA-GGTTATCAAAAT
94060 TTCATA-GGAAGGTTATCAAAAT
1 TTCATATGG-AGGTTATCAAAAT
* *
94082 TTCAAAAGGAGGT
1 TTCATATGGAGGT
94095 CATGAAAAAT
Statistics
Matches: 180, Mismatches: 31, Indels: 40
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.04
20 9 0.05
21 13 0.07
22 126 0.70
23 24 0.13
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
TTCATATGGAGGTTATCAAAAT
Found at i:93946 original size:45 final size:44
Alignment explanation
Indices: 93872--94002 Score: 140
Period size: 45 Copynumber: 3.0 Consensus size: 44
93862 TTTTCATTAC
* * * *
93872 GTGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGT
1 GTGGTTATCAAAATTTCATATGGAAGTTATCAAAATCTCATAGT
*
93916 GTTGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGT
1 G-TGGTTATCAAAATTTCATAT-GGAAGTTATCAAAATCTCATAGT
* * * *
93961 GAGGTCT-TCAAAATTTCATATGGAGGTTAACAAAATTTCATA
1 GTGGT-TATCAAAATTTCATATGGAAGTTATCAAAATCTCATA
94003 AGGTTAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
44 36 0.48
45 39 0.52
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (44 bp):
GTGGTTATCAAAATTTCATATGGAAGTTATCAAAATCTCATAGT
Found at i:93995 original size:44 final size:45
Alignment explanation
Indices: 93842--94085 Score: 170
Period size: 44 Copynumber: 5.6 Consensus size: 45
93832 TTACTAACAA
* * * * *
93842 TTCATATGGAGGTTTTTAAATTTTCATTA-CGT-GGTTATCAATAT
1 TTCATATGGAGGTTATCAAAATTTCA-TAGTGTAGGTTATCAAAAT
* * * *
93886 ATCATATGGAGGTTATCAACATCTCATAGTGTTGGTTATCAAAAT
1 TTCATATGGAGGTTATCAAAATTTCATAGTGTAGGTTATCAAAAT
*
93931 TTCAT-TGGGAAGTTATCAAAATTTCATAGTG-AGGTCT-TCAAAAT
1 TTCATAT-GGAGGTTATCAAAATTTCATAGTGTAGGT-TATCAAAAT
* **
93975 TTCATATGGAGGTTAACAAAATTTCATA----AGGTTAAAAAAAAT
1 TTCATATGGAGGTTATCAAAATTTCATAGTGTAGGTT-ATCAAAAT
*** * * * * *
94017 TT-ATAAAAAGGTTCTCAAAATTTCATAATAT-CGTTATTAAAAT
1 TTCATATGGAGGTTATCAAAATTTCATAGTGTAGGTTATCAAAAT
94060 TTCATA-GGAAGGTTATCAAAATTTCA
1 TTCATATGG-AGGTTATCAAAATTTCA
94086 AAAGGAGGTC
Statistics
Matches: 159, Mismatches: 28, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
40 1 0.01
41 24 0.15
42 7 0.04
43 10 0.06
44 79 0.50
45 38 0.24
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (45 bp):
TTCATATGGAGGTTATCAAAATTTCATAGTGTAGGTTATCAAAAT
Found at i:94014 original size:19 final size:20
Alignment explanation
Indices: 93970--94014 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
93960 TGAGGTCTTC
*
93970 AAAATTTCATATGGAGGTTAAC
1 AAAATTTCATA--GAGGTTAAA
93992 AAAATTTCATA-AGGTTAAA
1 AAAATTTCATAGAGGTTAAA
94011 AAAA
1 AAAA
94015 ATTTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
22 11 0.50
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAATTTCATAGAGGTTAAA
Found at i:94102 original size:22 final size:22
Alignment explanation
Indices: 94055--94102 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
94045 TATCGTTATT
* *
94055 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCAAAGGAAGGTCATC
*
94077 AAAATTTCAAAAGG-AGGTCATG
1 AAAATTTC-AAAGGAAGGTCATC
94099 AAAA
1 AAAA
94103 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (22 bp):
AAAATTTCAAAGGAAGGTCATC
Done.