Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017051.1 Corchorus olitorius cultivar O-4 contig17084, 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: 185084
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:305 original size:17 final size:17
Alignment explanation
Indices: 270--316 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
260 ATGTATAAAT
270 ATCTATACATCTA-CAC
1 ATCTATACATCTATCAC
*
286 ATCTACACATCTATCAC
1 ATCTATACATCTATCAC
303 ATCTATACATCTAT
1 ATCTATACATCTAT
317 ACAATACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (17 bp):
ATCTATACATCTATCAC
Found at i:316 original size:8 final size:8
Alignment explanation
Indices: 270--319 Score: 73
Period size: 8 Copynumber: 6.1 Consensus size: 8
260 ATGTATAAAT
270 ATCTATAC
1 ATCTATAC
*
278 ATCTACAC
1 ATCTATAC
*
286 ATCTACAC
1 ATCTATAC
294 ATCTATCAC
1 ATCTAT-AC
303 ATCTATAC
1 ATCTATAC
311 ATCTATAC
1 ATCTATAC
319 A
1 A
320 ATACTCTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
8 31 0.79
9 8 0.21
ACGTcount: A:0.38, C:0.30, G:0.00, T:0.32
Consensus pattern (8 bp):
ATCTATAC
Found at i:1454 original size:30 final size:30
Alignment explanation
Indices: 1420--1482 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1410 GTTTACCATT
* * *
1420 TTCATTTCAGCAGCCCTTTCCTTTACTTGG
1 TTCATTTCAGAAGCCCATTACTTTACTTGG
* *
1450 TTCATTTTAGAAGCCCATTACTTTGCTTGG
1 TTCATTTCAGAAGCCCATTACTTTACTTGG
1480 TTC
1 TTC
1483 GAAGCCCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.25, G:0.14, T:0.44
Consensus pattern (30 bp):
TTCATTTCAGAAGCCCATTACTTTACTTGG
Found at i:1488 original size:24 final size:24
Alignment explanation
Indices: 1459--1505 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1449 GTTCATTTTA
*
1459 GAAGCCCATTACTTTGCTTGGTTC
1 GAAGCCCATTACTTGGCTTGGTTC
*
1483 GAAGCCCATTTCTTGGCTTGGTT
1 GAAGCCCATTACTTGGCTTGGTT
1506 TCTTTGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (24 bp):
GAAGCCCATTACTTGGCTTGGTTC
Found at i:4419 original size:38 final size:40
Alignment explanation
Indices: 4377--4455 Score: 108
Period size: 38 Copynumber: 2.0 Consensus size: 40
4367 GGCTTTAGTT
* *
4377 TGTATGCTTGGGTCTTA-TCCTTT-TATGATGGTTTTTAA
1 TGTATGCTTGAGCCTTACTCCTTTATATGATGGTTTTTAA
*
4415 TGTATGCTTGAGCCTTACTTCTTTTATATGATGGTTTTTAA
1 TGTATGCTTGAGCCTTAC-TCCTTTATATGATGGTTTTTAA
4456 ATACATTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
38 15 0.43
40 5 0.14
41 15 0.43
ACGTcount: A:0.18, C:0.11, G:0.19, T:0.52
Consensus pattern (40 bp):
TGTATGCTTGAGCCTTACTCCTTTATATGATGGTTTTTAA
Found at i:5165 original size:25 final size:25
Alignment explanation
Indices: 5137--5184 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5127 CAATTTAGGG
5137 AAAGATCCCACCAAAGTATTTTTTC
1 AAAGATCCCACCAAAGTATTTTTTC
** *
5162 AAAGATTTCGCCAAAGTATTTTT
1 AAAGATCCCACCAAAGTATTTTT
5185 CGAAGTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (25 bp):
AAAGATCCCACCAAAGTATTTTTTC
Found at i:5458 original size:78 final size:75
Alignment explanation
Indices: 5181--5581 Score: 281
Period size: 78 Copynumber: 4.9 Consensus size: 75
5171 GCCAAAGTAT
* *
5181 TTTTCGAAGTTTTAATTCAGGGAAAGATCCCATCAAGTTTTTCAGAAGTTTT-AATTTAGGGAAA
1 TTTTC-AAGTTTTAATTTAGGGAAAGATCCCATCTAGTTTTTC--AAGTTTTCAATTTAGGGAAA
* *
5245 GATCCCATCTAGTCATT
63 GATCCCATC-CG--A-G
* *
5262 TTCTTCAAAGATTTCAAGATTAGGGAAAGATCCCA-CTAAAGTATTTTTTACAAAGATTTTC-AT
1 TT-TTC-AAG-TTTTAA-TTTAGGGAAAGATCCCATCT--AG---TTTTT-C-AAG-TTTTCAAT
* * **
5325 ATAGGGAAAGATCCCTTCAAATAG
54 TTAGGGAAAGATCCCATC--CGAG
** * *
5349 TTTTCAAAAACCTTTAATTTAGGGAAAGATCCCATCTAGTATTT-AAGCTCTTCAATTTAGGGAA
1 TTTTC---AAGTTTTAATTTAGGGAAAGATCCCATCTAGTTTTTCAAG-TTTTCAATTTAGGGAA
**
5413 AGATCCCATCCTGTCT
62 AGATCCCATCC-G-AG
*
5429 TTTTCAGAGTTTTAATTTAGGGAAAGATCCCATCTAGTCTTCTTCAAAATTTTCAATTTAGGGAA
1 TTTTCA-AGTTTTAATTTAGGGAAAGATCCCATCTAGT-TT-TTC-AAGTTTTCAATTTAGGGAA
*
5494 AGATCCCGT-CGAG
62 AGATCCCATCCGAG
*
5507 TTTTCAAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTTTTTCGAAGTTTTCAATTAAGGGAA
1 TTTTCAAGTTTT-AATTTAGGGAAAGATCCCATCTAG--TTTTTC-AAGTTTTCAATTTAGGGAA
5572 AGATCCCATC
62 AGATCCCATC
5582 AAAGATTTTA
Statistics
Matches: 257, Mismatches: 36, Indels: 56
0.74 0.10 0.16
Matches are distributed among these distances:
77 7 0.03
78 87 0.34
79 11 0.04
80 27 0.11
81 25 0.10
82 12 0.05
83 6 0.02
84 15 0.06
85 4 0.02
86 19 0.07
87 8 0.03
88 12 0.05
89 23 0.09
90 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (75 bp):
TTTTCAAGTTTTAATTTAGGGAAAGATCCCATCTAGTTTTTCAAGTTTTCAATTTAGGGAAAGAT
CCCATCCGAG
Found at i:5499 original size:41 final size:40
Alignment explanation
Indices: 5181--5581 Score: 299
Period size: 41 Copynumber: 9.9 Consensus size: 40
5171 GCCAAAGTAT
* * * *
5181 TTTTCGAAGTTTT-AATTCAGGGAAAGATCCCATCAAGT-
1 TTTTCAAAATTTTCAATTTAGGGAAAGATCCCATCTAGTC
*
5219 TTTTCAGAAGTTTT-AATTTAGGGAAAGATCCCATCTAGTC
1 TTTTCA-AAATTTTCAATTTAGGGAAAGATCCCATCTAGTC
* *
5259 ATTTTCTTCAAAGA-TTTCAAGATTAGGGAAAGATCCCA-CTAAAGTATT
1 ---TT-TTCAAA-ATTTTCAA-TTTAGGGAAAGATCCCATCT--AG--TC
* * * * *
5307 TTTTACAAAGATTTTC-ATATAGGGAAAGATCCCTTCAAATAG
1 TTTT-CAAA-ATTTTCAATTTAGGGAAAGATCCCATCTAGT-C
*
5349 TTTTCAAAAACCTTT-AATTTAGGGAAAGATCCCATCTAGT-
1 TTTTC-AAAA-TTTTCAATTTAGGGAAAGATCCCATCTAGTC
* ** *
5389 ATTT-AAGCTCTTCAATTTAGGGAAAGATCCCATCCT-GTC
1 TTTTCAAAATTTTCAATTTAGGGAAAGATCCCAT-CTAGTC
* *
5428 TTTTTCAGAGTTTT-AATTTAGGGAAAGATCCCATCTAGTC
1 -TTTTCAAAATTTTCAATTTAGGGAAAGATCCCATCTAGTC
* *
5468 TTCTTCAAAATTTTCAATTTAGGGAAAGATCCCGTCGAG--
1 TT-TTCAAAATTTTCAATTTAGGGAAAGATCCCATCTAGTC
*
5507 TTTTC-AAGTTTTCAATTTAGGGAAAGATCCCATCTAGTC
1 TTTTCAAAATTTTCAATTTAGGGAAAGATCCCATCTAGTC
* * *
5546 TTTTTCGAAGTTTTCAATTAAGGGAAAGATCCCATC
1 -TTTTCAAAATTTTCAATTTAGGGAAAGATCCCATC
5582 AAAGATTTTA
Statistics
Matches: 296, Mismatches: 35, Indels: 61
0.76 0.09 0.16
Matches are distributed among these distances:
37 31 0.10
38 32 0.11
39 38 0.13
40 43 0.15
41 57 0.19
42 30 0.10
43 8 0.03
44 24 0.08
45 26 0.09
46 6 0.02
48 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (40 bp):
TTTTCAAAATTTTCAATTTAGGGAAAGATCCCATCTAGTC
Found at i:6793 original size:93 final size:93
Alignment explanation
Indices: 6685--6861 Score: 302
Period size: 93 Copynumber: 1.9 Consensus size: 93
6675 TCATAGAAAT
* * * *
6685 AAAAAGTCATTGGATGTGTGATCATATATCGAA-ATATTTGATTGTGATGAGATTTTTGATTATT
1 AAAAAGTCATTGGATGTATGATCATACAT-AAAGATATTTGATTGTGATGAGATTTCTGATTATT
6749 GTATATCCCTAAAAAAAATTTGAGAGATA
65 GTATATCCCTAAAAAAAATTTGAGAGATA
6778 AAAAAGTCATTGGATGTATGATCATACATAAAGATATTTGATTGTGATGAGATTTCTGATTATTG
1 AAAAAGTCATTGGATGTATGATCATACATAAAGATATTTGATTGTGATGAGATTTCTGATTATTG
6843 TATATCCCTAAAAAAAATT
66 TATATCCCTAAAAAAAATT
6862 CAGAATTCAC
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 2 0.03
93 77 0.97
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.37
Consensus pattern (93 bp):
AAAAAGTCATTGGATGTATGATCATACATAAAGATATTTGATTGTGATGAGATTTCTGATTATTG
TATATCCCTAAAAAAAATTTGAGAGATA
Found at i:7525 original size:21 final size:21
Alignment explanation
Indices: 7501--7548 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
7491 TGAGATTATG
7501 AGATTAAACACTGTACAGATC
1 AGATTAAACACTGTACAGATC
*** *
7522 AGATTAGGTACTGTACAGATG
1 AGATTAAACACTGTACAGATC
7543 AGATTA
1 AGATTA
7549 TAATCAGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (21 bp):
AGATTAAACACTGTACAGATC
Found at i:7882 original size:13 final size:12
Alignment explanation
Indices: 7851--7892 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
7841 ACTCCATTAC
*
7851 AAAAATCCAAAA
1 AAAAATACAAAA
7863 AAAAATACAAAA
1 AAAAATACAAAA
7875 GAAAAATA-AAGAA
1 -AAAAATACAA-AA
7888 AAAAA
1 AAAAA
7893 GTTTCACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.81, C:0.07, G:0.05, T:0.07
Consensus pattern (12 bp):
AAAAATACAAAA
Found at i:11010 original size:21 final size:20
Alignment explanation
Indices: 10957--11014 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
10947 TGAATAAGAA
10957 GAGAGGAAGAAGAGAGAAGTG
1 GAGAGGAAG-AGAGAGAAGTG
*
10978 GAGAAGAGAGAGAGAGAA-TCGG
1 GAGAGGA-AGAGAGAGAAGT--G
11000 GAGAGGAAGAGAGAG
1 GAGAGGAAGAGAGAG
11015 GAAGATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 22 0.69
22 9 0.28
ACGTcount: A:0.47, C:0.02, G:0.48, T:0.03
Consensus pattern (20 bp):
GAGAGGAAGAGAGAGAAGTG
Found at i:11300 original size:42 final size:43
Alignment explanation
Indices: 11249--11342 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
11239 AGTAAATTAC
*
11249 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
11290 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAT
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
11335 CTAATATT
1 CTAATATT
11343 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:12580 original size:20 final size:20
Alignment explanation
Indices: 12555--12592 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12545 TTTAGAAATT
12555 GAAAAAATTGTTCTTAATGC
1 GAAAAAATTGTTCTTAATGC
12575 GAAAAAATTGTTCTTAAT
1 GAAAAAATTGTTCTTAAT
12593 TTGCCACTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
GAAAAAATTGTTCTTAATGC
Found at i:13886 original size:27 final size:27
Alignment explanation
Indices: 13856--13908 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
13846 TTTTTCAAAT
13856 ATATTTCAAATT-TGCCATTATTAAAAA
1 ATATTT-AAATTATGCCATTATTAAAAA
*
13883 ATATTTTAATTATGCCATTATTAAAA
1 ATATTTAAATTATGCCATTATTAAAA
13909 TATAATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (27 bp):
ATATTTAAATTATGCCATTATTAAAAA
Found at i:14390 original size:17 final size:18
Alignment explanation
Indices: 14368--14401 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
14358 GGTTATAAAA
14368 AATCATAGGAA-GTTTAC
1 AATCATAGGAAGGTTTAC
14385 AATCATAGGAAGGTTTA
1 AATCATAGGAAGGTTTA
14402 TTGAAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (18 bp):
AATCATAGGAAGGTTTAC
Found at i:14433 original size:22 final size:21
Alignment explanation
Indices: 14405--14480 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
14395 AGGTTTATTG
*
14405 AAATTTCATAGTTAGCTTATC
1 AAATTTCATAGTTAGATTATC
* *
14426 AAAGTTTCATA-TGGAGTTTATC
1 AAA-TTTCATAGT-TAGATTATC
* *
14448 ACAATTTCATAGGTAAATTATC
1 A-AATTTCATAGTTAGATTATC
14470 AAAATTTCATA
1 -AAATTTCATA
14481 ACGTGGTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 4 0.09
22 37 0.84
23 3 0.07
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (21 bp):
AAATTTCATAGTTAGATTATC
Found at i:14490 original size:22 final size:23
Alignment explanation
Indices: 14465--14525 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
14455 CATAGGTAAA
*
14465 TTATCAAAATTTCATAACG-TGG
1 TTATCAAAATTTCATAACGATAG
* * **
14487 TTATCAAATTTTAAT-TGGATAG
1 TTATCAAAATTTCATAACGATAG
14509 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
14526 AAATATTCAA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTCATAACGATAG
Found at i:14491 original size:44 final size:43
Alignment explanation
Indices: 14405--14525 Score: 109
Period size: 44 Copynumber: 2.8 Consensus size: 43
14395 AGGTTTATTG
* ** * ** *
14405 AAATTTCATAGTTAGCTTATCAAAGTTTCATATGGAGTTTATC
1 AAATTTCATAGGTAAATTATCAAAATTTCATAACGAGGTTATC
*
14448 ACAATTTCATAGGTAAATTATCAAAATTTCATAACGTGGTTATC
1 A-AATTTCATAGGTAAATTATCAAAATTTCATAACGAGGTTATC
* * *
14492 AAATTTTAATTGG-ATAGTTATCAAAATTTCATAA
1 AAA-TTTCATAGGTA-AATTATCAAAATTTCATAA
14526 AAATATTCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
43 4 0.06
44 60 0.94
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (43 bp):
AAATTTCATAGGTAAATTATCAAAATTTCATAACGAGGTTATC
Found at i:16319 original size:22 final size:22
Alignment explanation
Indices: 16275--16408 Score: 127
Period size: 22 Copynumber: 6.2 Consensus size: 22
16265 TTGCCAAAAA
*
16275 TCATAGGAAGGTTA-CAAAATT
1 TCATAGGTAGGTTATCAAAATT
* *
16296 TCATAGTTAGGTTATCAAAGTT
1 TCATAGGTAGGTTATCAAAATT
*
16318 TCATATGG-A-GTT-TCACAATT
1 TCATA-GGTAGGTTATCAAAATT
**
16338 TCATAGGTAAATTATCAAAATT
1 TCATAGGTAGGTTATCAAAATT
*
16360 TCATA-ATATGGTTATCAAAATT
1 TCATAGGTA-GGTTATCAAAATT
*
16382 TAATAGGGTA-GTTATCAAAATT
1 TCATA-GGTAGGTTATCAAAATT
16404 TCATA
1 TCATA
16409 AAAATATTCA
Statistics
Matches: 91, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.02
20 12 0.13
21 19 0.21
22 55 0.60
23 1 0.01
24 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TCATAGGTAGGTTATCAAAATT
Found at i:16541 original size:32 final size:32
Alignment explanation
Indices: 16490--16555 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
16480 CTGATCAGTT
16490 TTTCGATCGATATCATTTCACTAACTAGTGAA
1 TTTCGATCGATATCATTTCACTAACTAGTGAA
* * *
16522 TTTCGATCGGTGTCGTTTCACTAACTAGTGAA
1 TTTCGATCGATATCATTTCACTAACTAGTGAA
16554 TT
1 TT
16556 GCCACCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (32 bp):
TTTCGATCGATATCATTTCACTAACTAGTGAA
Found at i:24511 original size:31 final size:31
Alignment explanation
Indices: 24468--24546 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
24458 ATTTTTAGCC
*
24468 ACCAATTGGAGTCTAAACCTTTCAAAAGTTG
1 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
** *
24499 TTCAATTTGAGTCTAAACCTTTCAAAGGTTG
1 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
*
24530 ACCAATTTGATTCTAAA
1 ACCAATTTGAGTCTAAA
24547 AACAGAAACG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (31 bp):
ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
Found at i:45396 original size:16 final size:15
Alignment explanation
Indices: 45370--45416 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
45360 ACCGACCATT
45370 TATTAAATATATATTA
1 TATT-AATATATATTA
* *
45386 TTTTTAATATATAATA
1 -TATTAATATATATTA
45402 TATTAATATATATTA
1 TATTAATATATATTA
45417 ATCTGAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 10 0.38
17 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTAATATATATTA
Found at i:45875 original size:33 final size:33
Alignment explanation
Indices: 45833--45907 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 33
45823 AATTACATAT
**
45833 TATTTCTAATAATATTTATTGCATATTAAATAAA
1 TATTTCTAATAATATTTATCACATATT-AATAAA
45867 TA-TTC---TAATATTTATCACATATTAATAAA
1 TATTTCTAATAATATTTATCACATATTAATAAA
45896 TATTTCTAATAA
1 TATTTCTAATAA
45908 AATCAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
29 8 0.23
30 19 0.54
33 6 0.17
34 2 0.06
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (33 bp):
TATTTCTAATAATATTTATCACATATTAATAAA
Found at i:45878 original size:30 final size:30
Alignment explanation
Indices: 45842--45906 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
45832 TTATTTCTAA
**
45842 TAATATTTATTGCATATTAAATAAATA-TTC
1 TAATATTTATCACATATT-AATAAATATTTC
45872 TAATATTTATCACATATTAATAAATATTTC
1 TAATATTTATCACATATTAATAAATATTTC
45902 TAATA
1 TAATA
45907 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (30 bp):
TAATATTTATCACATATTAATAAATATTTC
Found at i:45919 original size:30 final size:30
Alignment explanation
Indices: 45855--45919 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
45845 TATTTATTGC
** *
45855 ATATTAAATAAATATTCTAATATTTATCAC
1 ATATTAAATAAATATTCTAATATAAATCAA
45885 ATATT-AATAAATATTTCTAATA-AAATCAAA
1 ATATTAAATAAATA-TTCTAATATAAATC-AA
45915 ATATT
1 ATATT
45920 TTTTGAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATTAAATAAATATTCTAATATAAATCAA
Found at i:49486 original size:31 final size:29
Alignment explanation
Indices: 49451--49525 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
49441 GAAAAAGGTT
* *
49451 AAAAGTTCAAATAGGGGTCTGAACTTCAAGG
1 AAAAGGTCAAATAGGGGTCTAAACTTC-A-G
** *
49482 AAAAGGTCATTTAAGGGTCTAAACTTCAG
1 AAAAGGTCAAATAGGGGTCTAAACTTCAG
49511 AAAAGGTCAAATAGG
1 AAAAGGTCAAATAGG
49526 TGCCCAACCT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
29 13 0.36
30 1 0.03
31 22 0.61
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (29 bp):
AAAAGGTCAAATAGGGGTCTAAACTTCAG
Found at i:50456 original size:76 final size:76
Alignment explanation
Indices: 50364--50511 Score: 269
Period size: 76 Copynumber: 1.9 Consensus size: 76
50354 TATTATATCC
* *
50364 ATAAATTAATACTCGATAAATTAATAACCTCTCTAAATTAATAATTTTTCATAGTCCCAACATTA
1 ATAAATTAACAATCGATAAATTAATAACCTCTCTAAATTAATAATTTTTCATAGTCCCAACATTA
50429 TTAATTTCCAT
66 TTAATTTCCAT
*
50440 ATAAATTAACAATCGATAAATTAATAACCTCTCTAAATTAATAATTTTTCATGGTCCCAACATTA
1 ATAAATTAACAATCGATAAATTAATAACCTCTCTAAATTAATAATTTTTCATAGTCCCAACATTA
50505 TTAATTT
66 TTAATTT
50512 ATAGAGGTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.39
Consensus pattern (76 bp):
ATAAATTAACAATCGATAAATTAATAACCTCTCTAAATTAATAATTTTTCATAGTCCCAACATTA
TTAATTTCCAT
Found at i:50845 original size:16 final size:14
Alignment explanation
Indices: 50817--50854 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
50807 CGTTTTCGTT
50817 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
50831 TTTTTGTTTCGTTTTG
1 TTTTTGTTT--TTTTG
50847 TTTTTGTT
1 TTTTTGTT
50855 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.82
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Found at i:52539 original size:63 final size:61
Alignment explanation
Indices: 52467--52874 Score: 391
Period size: 63 Copynumber: 6.6 Consensus size: 61
52457 TAAACTGTAT
* * * *
52467 ATAGCGGCGTTTAAATGTCGCTATATTTAAGGGTTTTAAAAAAAATAATACTTTAAATTATAC
1 ATAGGGGCGTTTAAACGCCGCTATATTTAAGGG-TTT-AAAAAAATAATACTTTAAATTATAG
* *
52530 ATAGGGGCGTTTAAACACCGTTATATTTAAGGGGTTTCAAAAAAAATAATACATTTAAATTATAG
1 ATAGGGGCGTTTAAACGCCGCTATATTTAA-GGGTTT--AAAAAAATAATAC-TTTAAATTATAG
* * *
52595 ATAGGGGCGATTAAATGCCGCTATATTTAAGGGGTT---AAAA-AA-ACTTTAAATTATAG
1 ATAGGGGCGTTTAAACGCCGCTATATTTAAGGGTTTAAAAAAATAATACTTTAAATTATAG
* * * *
52651 ATAGGGGCGTTTAAATGTCGCTATGTTTAAGGGGTTTAAAAAACATAATACTTTAAATTATAT
1 ATAGGGGCGTTTAAACGCCGCTATATTTAA-GGGTTTAAAAAA-ATAATACTTTAAATTATAG
* * * *
52714 ATAGGGACGTTTAAACGCCG-TTTTTTTAAAGGGGTTT-AAAAAATAATACATTTAAATTATGG
1 ATAGGGGCGTTTAAACGCCGCTATATTT-AA-GGGTTTAAAAAAATAATAC-TTTAAATTATAG
** * * * *
52776 ATAAAGGCGTTTAAACACCACTATATTTAAGAGGTTTAAAAAAATAATAAATTTTAATTATAG
1 ATAGGGGCGTTTAAACGCCGCTATATTTAAG-GGTTTAAAAAAATAAT-ACTTTAAATTATAG
* ** *
52839 GTAGGGGCGTTTAGGCGCCACTAT-TTTAAGGCGTTT
1 ATAGGGGCGTTTAAACGCCGCTATATTTAAGG-GTTT
52875 TCCTCAGTAG
Statistics
Matches: 289, Mismatches: 39, Indels: 35
0.80 0.11 0.10
Matches are distributed among these distances:
56 39 0.13
57 7 0.02
58 2 0.01
59 4 0.01
60 3 0.01
61 10 0.03
62 54 0.19
63 110 0.38
64 23 0.08
65 37 0.13
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (61 bp):
ATAGGGGCGTTTAAACGCCGCTATATTTAAGGGTTTAAAAAAATAATACTTTAAATTATAG
Found at i:52817 original size:125 final size:122
Alignment explanation
Indices: 52467--52869 Score: 422
Period size: 125 Copynumber: 3.3 Consensus size: 122
52457 TAAACTGTAT
* * * * *
52467 ATAGCGGCGTTTAAATGTCGCTATATTTAAGGGTTTTAAAAAAAATAATACTTTAAATTATACAT
1 ATAGGGGCGTTTAAACGCCGCTATATTTAAGGG-GTT--AAAAAATAATACTTTAAATTATAGAT
*
52532 AGGGGCGTTTAAACACCGTTATATTTAAGGGGTTTCAAAAAAAATAATACATTTAAATTATAG
63 AGGGGCGTTTAAACACCGCTATATTTAAGGGGTTT--AAAAAAATAATAC-TTTAAATTATAG
* *
52595 ATAGGGGCGATTAAATGCCGCTATATTTAAGGGGTT--AAAA-AA-ACTTTAAATTATAGATAGG
1 ATAGGGGCGTTTAAACGCCGCTATATTTAAGGGGTTAAAAAATAATACTTTAAATTATAGATAGG
*** * *
52656 GGCGTTTAAATGTCGCTATGTTTAAGGGGTTTAAAAAACATAATACTTTAAATTATAT
66 GGCGTTTAAACACCGCTATATTTAAGGGGTTTAAAAAA-ATAATACTTTAAATTATAG
* * * *
52714 ATAGGGACGTTTAAACGCCG-TTTTTTTAAAGGGGTTTAAAAAATAATACATTTAAATTATGGAT
1 ATAGGGGCGTTTAAACGCCGCTATATTT-AAGGGG-TTAAAAAATAATAC-TTTAAATTATAGAT
** * * * *
52778 AAAGGCGTTTAAACACCACTATATTTAAGAGGTTTAAAAAAATAATAAATTTTAATTATAG
63 AGGGGCGTTTAAACACCGCTATATTTAAGGGGTTTAAAAAAATAAT-ACTTTAAATTATAG
* ** *
52839 GTAGGGGCGTTTAGGCGCCACTAT-TTTAAGG
1 ATAGGGGCGTTTAAACGCCGCTATATTTAAGG
52870 CGTTTTCCTC
Statistics
Matches: 231, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
118 5 0.02
119 40 0.17
120 9 0.04
121 45 0.19
122 6 0.03
123 6 0.03
124 11 0.05
125 75 0.32
126 2 0.01
127 2 0.01
128 30 0.13
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (122 bp):
ATAGGGGCGTTTAAACGCCGCTATATTTAAGGGGTTAAAAAATAATACTTTAAATTATAGATAGG
GGCGTTTAAACACCGCTATATTTAAGGGGTTTAAAAAAATAATACTTTAAATTATAG
Found at i:52936 original size:32 final size:32
Alignment explanation
Indices: 52871--52950 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
52861 ATTTTAAGGC
*
52871 GTTTTCCTCAGTAGACGCCACTAAATAAGGGT
1 GTTTTCTTCAGTAGACGCCACTAAATAAGGGT
**
52903 GTTTTCTTCAGTAGACGCTGCTAAAT-AGTGGT
1 GTTTTCTTCAGTAGACGCCACTAAATAAG-GGT
*
52935 GTTTTCTTCGGTAGAC
1 GTTTTCTTCAGTAGAC
52951 ACCGGCAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 2 0.05
32 41 0.95
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (32 bp):
GTTTTCTTCAGTAGACGCCACTAAATAAGGGT
Found at i:58989 original size:51 final size:51
Alignment explanation
Indices: 58920--59030 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
58910 ATCATTTTGG
* ** *
58920 CAAAATGAAATTTAAAGATAGCGGCGTTTAT-GAAACAAAACGCCGCTATATA
1 CAAAATAAAATTCGAAGATAGAGGCGTTTATGGAAAC--AACGCCGCTATATA
*
58972 C-AAATAAAATTCGAAGATAGAGGCGTTTGTGGAAACAACGCCGCTATATA
1 CAAAATAAAATTCGAAGATAGAGGCGTTTATGGAAACAACGCCGCTATATA
59022 CAAAATAAA
1 CAAAATAAA
59031 TATTTTATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 15 0.29
51 31 0.60
52 6 0.12
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (51 bp):
CAAAATAAAATTCGAAGATAGAGGCGTTTATGGAAACAACGCCGCTATATA
Found at i:61519 original size:46 final size:46
Alignment explanation
Indices: 61460--61585 Score: 132
Period size: 46 Copynumber: 2.8 Consensus size: 46
61450 TGTATCCCTA
* * *
61460 AAAAAAATTCATAGGGAGCTTATCAAAATTTCATAGTCTGGGTCTC
1 AAAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTCTGGGTATC
* ** * *
61506 AAAAAATTTCATAGGAAGGTTA-CTGGAATTTCATAGTGTGGTTATC
1 AAAAAATTTCATAGGGAGGTTATC-AAAATTTCATAGTCTGGGTATC
* *
61552 --AAAATTTCATAGTGAGGTGATCAAAATTTCATAG
1 AAAAAATTTCATAGGGAGGTTATCAAAATTTCATAG
61586 GGAGGTTATC
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
44 27 0.42
45 2 0.03
46 36 0.55
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (46 bp):
AAAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTCTGGGTATC
Found at i:61557 original size:22 final size:22
Alignment explanation
Indices: 61462--61646 Score: 128
Period size: 22 Copynumber: 8.3 Consensus size: 22
61452 TATCCCTAAA
* * *
61462 AAAAATTCATAGGGAGCTTATC
1 AAAATTTCATAGTGAGGTTATC
** * *
61484 AAAATTTCATAGTCTGGGTCTC
1 AAAATTTCATAGTGAGGTTATC
61506 AAAAAATTTCATAG-GAAGGTTA-C
1 --AAAATTTCATAGTG-AGGTTATC
** *
61529 TGGAATTTCATAGTGTGGTTATC
1 -AAAATTTCATAGTGAGGTTATC
*
61552 AAAATTTCATAGTGAGGTGATC
1 AAAATTTCATAGTGAGGTTATC
*
61574 AAAATTTCATAGGGAGGTTATC
1 AAAATTTCATAGTGAGGTTATC
** * *
61596 GGAATTTCATAAG-GAGATTATA
1 AAAATTTCAT-AGTGAGGTTATC
61618 AAAATTTCAT-GATGTA-GTTATC
1 AAAATTTCATAG-TG-AGGTTATC
61640 AAAATTT
1 AAAATTT
61647 TATGGCATAA
Statistics
Matches: 125, Mismatches: 29, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
22 103 0.82
23 6 0.05
24 15 0.12
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAGTGAGGTTATC
Found at i:61580 original size:44 final size:43
Alignment explanation
Indices: 61462--61646 Score: 149
Period size: 44 Copynumber: 4.2 Consensus size: 43
61452 TATCCCTAAA
* * * * *
61462 AAAAATTCATAGGGAGCTTATCAAAATTTCATAGTCTGGGTCTC
1 AAAATTTCATA-GGAGGTTATCAAAATTTCATAGTGTGGTTATC
**
61506 AAAAAATTTCATAGGAAGGTTA-CTGGAATTTCATAGTGTGGTTATC
1 --AAAATTTCATAGG-AGGTTATC-AAAATTTCATAGTGTGGTTATC
* * *
61552 AAAATTTCATAGTGAGGTGATCAAAATTTCATAGGGAGGTTATC
1 AAAATTTCATAG-GAGGTTATCAAAATTTCATAGTGTGGTTATC
** * * *
61596 GGAATTTCATAAGGAGATTATAAAAATTTCAT-GATGTAGTTATC
1 AAAATTTCAT-AGGAGGTTATCAAAATTTCATAG-TGTGGTTATC
61640 AAAATTT
1 AAAATTT
61647 TATGGCATAA
Statistics
Matches: 111, Mismatches: 22, Indels: 14
0.76 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
44 71 0.64
45 7 0.06
46 32 0.29
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (43 bp):
AAAATTTCATAGGAGGTTATCAAAATTTCATAGTGTGGTTATC
Found at i:61864 original size:29 final size:31
Alignment explanation
Indices: 61832--61902 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 31
61822 CTGAGAGCTT
*
61832 AGGGGGCAAAACGTCCAAA-ATTA-AAGTTC
1 AGGGGGCAAAACGTCCAAACAGTACAAGTTC
* *
61861 AGGGGGCAAAATGTCCAAACCGTACAAGTTC
1 AGGGGGCAAAACGTCCAAACAGTACAAGTTC
61892 AGGGGGCAAAA
1 AGGGGGCAAAA
61903 AGGGTATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 18 0.49
30 2 0.05
31 17 0.46
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.14
Consensus pattern (31 bp):
AGGGGGCAAAACGTCCAAACAGTACAAGTTC
Found at i:62221 original size:44 final size:42
Alignment explanation
Indices: 62108--62231 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 42
62098 CTTTAGGATT
* * *
62108 TCAAAATTTCATTGTGTGGTTACCAAAATTTGATTGGTAGGTTA
1 TCAAAATTTCA-TGTGTGGTTATCAAAATTTCA-TAGTAGGTTA
* *
62152 TCAAAATTTGATG-GTAGAGTAATCAAAATTTCATAGTAAGGTTA
1 TCAAAATTTCATGTGT-G-GTTATCAAAATTTCATAGT-AGGTTA
*
62196 TTAAAATTTCATAGTGTGGTTATCAAAATTTCATAG
1 TCAAAATTTCAT-GTGTGGTTATCAAAATTTCATAG
62232 GGGATTATCA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
42 2 0.03
43 6 0.09
44 55 0.82
45 2 0.03
46 2 0.03
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (42 bp):
TCAAAATTTCATGTGTGGTTATCAAAATTTCATAGTAGGTTA
Found at i:62230 original size:22 final size:22
Alignment explanation
Indices: 62108--62231 Score: 119
Period size: 22 Copynumber: 5.6 Consensus size: 22
62098 CTTTAGGATT
*
62108 TCAAAATTTCATTGTGTGGTTA
1 TCAAAATTTCATAGTGTGGTTA
* * *
62130 CCAAAATTTGATTG-GTAGGTTA
1 TCAAAATTTCATAGTGT-GGTTA
* *
62152 TCAAAATTTGAT-G-GTAGAGTAA
1 TCAAAATTTCATAGTGT-G-GTTA
**
62174 TCAAAATTTCATAGTAAGGTTA
1 TCAAAATTTCATAGTGTGGTTA
*
62196 TTAAAATTTCATAGTGTGGTTA
1 TCAAAATTTCATAGTGTGGTTA
62218 TCAAAATTTCATAG
1 TCAAAATTTCATAG
62232 GGGATTATCA
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.08
22 77 0.90
23 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
TCAAAATTTCATAGTGTGGTTA
Found at i:62274 original size:22 final size:22
Alignment explanation
Indices: 62246--62297 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
62236 TTATCAATAC
*
62246 CAAAATTTAATACG-GAGGTTAT
1 CAAAATTTAACA-GTGAGGTTAT
*
62268 CAAAATTTCACAGTGAGGTTAT
1 CAAAATTTAACAGTGAGGTTAT
*
62290 CGAAATTT
1 CAAAATTT
62298 CGCATGGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (22 bp):
CAAAATTTAACAGTGAGGTTAT
Found at i:62309 original size:22 final size:21
Alignment explanation
Indices: 62260--62316 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
62250 ATTTAATACG
62260 GAGGTTATCAAAATTTCACAGT
1 GAGGTTATC-AAATTTCACAGT
*
62282 GAGGTTATCGAAATTTCGCA-T
1 GAGGTTATC-AAATTTCACAGT
*
62303 GGTGGTTATCAAAT
1 -GAGGTTATCAAAT
62317 ATTTGTTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (21 bp):
GAGGTTATCAAATTTCACAGT
Found at i:63620 original size:22 final size:22
Alignment explanation
Indices: 63579--63724 Score: 89
Period size: 22 Copynumber: 6.6 Consensus size: 22
63569 CGCAGGGTGG
* *
63579 TTATCAAAATTCCATTGGGAGA
1 TTATCAAAATTTCATAGGGAGA
*
63601 TTATCAAAATTTTATAGGGAGA
1 TTATCAAAATTTCATAGGGAGA
* * * *
63623 CTAACAAAATTTCAAAGGGAAGT
1 TTATCAAAATTTCATAGGG-AGA
*
63646 TTAACAAAATTTCATAGGTGA-A
1 TTATCAAAATTTCATAGG-GAGA
* * *** *
63668 TTCTCGAAA-TTCTATAGTTTGG
1 TTATCAAAATTTC-ATAGGGAGA
* * *
63690 TTATCAAAATTTTATAGTGAGG
1 TTATCAAAATTTCATAGGGAGA
*
63712 TTTTCAAAATTTC
1 TTATCAAAATTTC
63725 TTCCAAAAGA
Statistics
Matches: 94, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
21 3 0.03
22 69 0.73
23 21 0.22
24 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGA
Found at i:66798 original size:55 final size:55
Alignment explanation
Indices: 66714--66827 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
66704 CTCGTTATAA
* * *
66714 CTATCATAAACATGAATCCTCAGGATCATCATTTTTATTGGTTCCATAGTAACTC
1 CTATCATAAACATGAACCCTCAGGATCATCACTTTTACTGGTTCCATAGTAACTC
* *
66769 CTATCATAAACATGAACCCTTAGGTTCATCACTTTTACTGGTTCCATAGTAACTC
1 CTATCATAAACATGAACCCTCAGGATCATCACTTTTACTGGTTCCATAGTAACTC
66824 CTAT
1 CTAT
66828 GCACCCAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.36
Consensus pattern (55 bp):
CTATCATAAACATGAACCCTCAGGATCATCACTTTTACTGGTTCCATAGTAACTC
Found at i:73268 original size:130 final size:132
Alignment explanation
Indices: 73011--73268 Score: 385
Period size: 130 Copynumber: 2.0 Consensus size: 132
73001 GTCGTTACTG
*
73011 ACTCATTGAGTGTAACTGAACAAAATTCATAGCCTAAAAATTCGTCCTTGCTTCCTAACTACCGA
1 ACTCATTGACTGTAACTGAACAAAATTCATAGCCTAAAAATTCGTCCTTGCTTCCTAACTACCGA
* ** * * *
73076 ATTTAGTCTAACAAAGTAAAAGCTGTAACTTTAAACAGCATATCCTTTGCCTTGAGATAGAAGAA
66 ATTTAGTCTAACAAAGTAAAAGCTGTAACTTTAAACAGCACATCCTTCACATTAAGAAAGAAGAA
73141 TA
131 TA
* * * *
73143 ACTCATT-ACTGTAACTGAACGAAATTCATAGTCTAGAAATTCGT-CTTGCTTCCTACCTACCGA
1 ACTCATTGACTGTAACTGAACAAAATTCATAGCCTAAAAATTCGTCCTTGCTTCCTAACTACCGA
* *
73206 ATTTAGTCTAACAGAGTAAAAGCTGTAATTTTAAACAGCACATCCTTCACATTAAGAAAGAAG
66 ATTTAGTCTAACAAAGTAAAAGCTGTAACTTTAAACAGCACATCCTTCACATTAAGAAAGAAG
73269 TATGACCAAA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
130 73 0.65
131 33 0.29
132 7 0.06
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (132 bp):
ACTCATTGACTGTAACTGAACAAAATTCATAGCCTAAAAATTCGTCCTTGCTTCCTAACTACCGA
ATTTAGTCTAACAAAGTAAAAGCTGTAACTTTAAACAGCACATCCTTCACATTAAGAAAGAAGAA
TA
Found at i:77078 original size:14 final size:14
Alignment explanation
Indices: 77059--77092 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
77049 TTTTATAATT
77059 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
77073 ATTTTATTTTTACT
1 ATTTTATTTTTACC
77087 ATTTTA
1 ATTTTA
77093 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:77140 original size:15 final size:15
Alignment explanation
Indices: 77120--77150 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
77110 GATTAACCTG
77120 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
77135 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
77150 T
1 T
77151 AATGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:78005 original size:5 final size:5
Alignment explanation
Indices: 77995--78019 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
77985 GCTAGCTACC
77995 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
78020 TGCACCTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:82060 original size:2 final size:2
Alignment explanation
Indices: 82053--82087 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
82043 TCAAAAAGTA
82053 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
82088 TATTTTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83101 original size:45 final size:42
Alignment explanation
Indices: 83050--83145 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 42
83040 AACAACAATT
* * *
83050 AATATTAGATTTATTTTAATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGATTAATTTTAATGAATTACCCAGAGAT-GA--AGTAG
* *
83095 AATATTAGCTTAATTTTGATGAATTACCCAGAGATGAAGTAG
1 AATATTAGATTAATTTTAATGAATTACCCAGAGATGAAGTAG
83137 AAT-TTAGAT
1 AATATTAGAT
83146 AATGTACTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 5 0.11
42 8 0.18
44 2 0.04
45 30 0.67
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (42 bp):
AATATTAGATTAATTTTAATGAATTACCCAGAGATGAAGTAG
Found at i:83601 original size:23 final size:23
Alignment explanation
Indices: 83575--83621 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
83565 AATCCTATCC
*
83575 CCCTTAATTATCTAGAATTGTAA
1 CCCTTAATTATCTAGAACTGTAA
83598 CCCTTAATTATCTAGAACTGTAA
1 CCCTTAATTATCTAGAACTGTAA
83621 C
1 C
83622 ATCTCTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (23 bp):
CCCTTAATTATCTAGAACTGTAA
Found at i:86449 original size:12 final size:12
Alignment explanation
Indices: 86434--86487 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
86424 GGTGGTTTCC
86434 GTGGGGGCTATG
1 GTGGGGGCTATG
* *
86446 GTGGTGGCTCTG
1 GTGGGGGCTATG
*
86458 GCGGGGGCTATG
1 GTGGGGGCTATG
* *
86470 GTGGAGGCTTTG
1 GTGGGGGCTATG
86482 GTGGGG
1 GTGGGG
86488 ATTCTGGTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.06, C:0.11, G:0.57, T:0.26
Consensus pattern (12 bp):
GTGGGGGCTATG
Found at i:86463 original size:24 final size:24
Alignment explanation
Indices: 86436--86487 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
86426 TGGTTTCCGT
*
86436 GGGGGCTATGGTGGTGGCTCTGGC
1 GGGGGCTATGGTGGAGGCTCTGGC
* *
86460 GGGGGCTATGGTGGAGGCTTTGGT
1 GGGGGCTATGGTGGAGGCTCTGGC
86484 GGGG
1 GGGG
86488 ATTCTGGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.12, G:0.58, T:0.25
Consensus pattern (24 bp):
GGGGGCTATGGTGGAGGCTCTGGC
Found at i:92191 original size:24 final size:25
Alignment explanation
Indices: 92164--92225 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
92154 TGCTTTTTAG
* * *
92164 TTGATCT-GATTGGCTTCCAAGGAA
1 TTGATCTCAATTGGCTTCAAAAGAA
*
92188 TTGATCTCAATTGGTTTCAAAAGAA
1 TTGATCTCAATTGGCTTCAAAAGAA
92213 TTGATCTCAATTG
1 TTGATCTCAATTG
92226 TTCATTCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 7 0.21
25 26 0.79
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (25 bp):
TTGATCTCAATTGGCTTCAAAAGAA
Found at i:97620 original size:60 final size:60
Alignment explanation
Indices: 97522--97641 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
97512 TCACTCACTC
*
97522 GCATGCTTAATTTTGCACTTCATTTGTGTTAGGATCAAGCACCATAACGATGATAATCAT
1 GCATACTTAATTTTGCACTTCATTTGTGTTAGGATCAAGCACCATAACGATGATAATCAT
*
97582 GCATACTTAATTTTGCACTTCATTTGTGTTAGGATCAAGCACCATAACGATGATGATCAT
1 GCATACTTAATTTTGCACTTCATTTGTGTTAGGATCAAGCACCATAACGATGATAATCAT
97642 AATATATTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (60 bp):
GCATACTTAATTTTGCACTTCATTTGTGTTAGGATCAAGCACCATAACGATGATAATCAT
Found at i:98862 original size:14 final size:13
Alignment explanation
Indices: 98843--98881 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
98833 ACTCAACACT
98843 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
98857 AACTGACTCAACA
1 AACTGACTCAAAA
98870 AACTGACT-AAAA
1 AACTGACTCAAAA
98882 CCCGATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:98874 original size:13 final size:13
Alignment explanation
Indices: 98832--98877 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
98822 GCCAGACTCA
98832 GACTCAACACTAACT
1 GACTCAACA--AACT
*
98847 GACTCGAAAAAACT
1 GACTC-AACAAACT
98861 GACTCAACAAACT
1 GACTCAACAAACT
98874 GACT
1 GACT
98878 AAAACCCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:100152 original size:3 final size:3
Alignment explanation
Indices: 100144--100200 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
100134 GAAAAAGAAT
*
100144 ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
100192 ATA ATA ATA
1 ATA ATA ATA
100201 CCTCAATTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:104179 original size:43 final size:43
Alignment explanation
Indices: 104132--104221 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
104122 ATATTTAAAG
104132 GTTTATCAATTATTGGTTTTCCTTTTCCTTTTTTTAATTTGTA
1 GTTTATCAATTATTGGTTTTCCTTTTCCTTTTTTTAATTTGTA
104175 GTTTATCAATTATTGGTTTTCCTTTTCCTTTTTTTAATTTGTA
1 GTTTATCAATTATTGGTTTTCCTTTTCCTTTTTTTAATTTGTA
104218 -TTTA
1 GTTTA
104222 CTTTATGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 4 0.09
43 43 0.91
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (43 bp):
GTTTATCAATTATTGGTTTTCCTTTTCCTTTTTTTAATTTGTA
Found at i:109958 original size:7 final size:7
Alignment explanation
Indices: 109931--109961 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
109921 TATATATAAC
*
109931 TCTCCAC
1 TCTCCAG
109938 TCTCCAG
1 TCTCCAG
109945 TCTCCAG
1 TCTCCAG
109952 TCTCCAG
1 TCTCCAG
109959 TCT
1 TCT
109962 ATATATGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.45, G:0.10, T:0.32
Consensus pattern (7 bp):
TCTCCAG
Found at i:111435 original size:24 final size:24
Alignment explanation
Indices: 111408--111453 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
111398 AACAATTCGT
111408 GGATCTCTTTTAATAATTATAAAC
1 GGATCTCTTTTAATAATTATAAAC
111432 GGATCTCTTTTAATAATTATAA
1 GGATCTCTTTTAATAATTATAA
111454 CAAGCGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (24 bp):
GGATCTCTTTTAATAATTATAAAC
Found at i:112250 original size:219 final size:219
Alignment explanation
Indices: 111915--112311 Score: 758
Period size: 219 Copynumber: 1.8 Consensus size: 219
111905 AACATTTATT
111915 AAAACAAGACTCAAGGGCAAGAAATTGCTAGAAACTAACTTAGGGTCTTTTTAGTAATTTGGCAA
1 AAAACAAGACTCAAGGGCAAGAAATTGCTAGAAACTAACTTAGGGTCTTTTTAGTAATTTGGCAA
* * *
111980 GTGAGAAAAGACAGAAAAGGACAAAAAAAGTTAAAATGGAGCCTCCTCATCGATCCTCAAAAGGG
66 GTGAGAAAAGACAGAAAAAGACAAAAAAAATTAAAATGGAGCATCCTCATCGATCCTCAAAAGGG
*
112045 GCCTTTGGTAAATTCCCTGGGTCTTTCAAATACTATTTAGTATATATAAGAATTATTATAACATT
131 GCCTTTGGTAAATTCCCTGCGTCTTTCAAATACTATTTAGTATATATAAGAATTATTATAACATT
112110 TATGTGAAAGGAAAGGATAATTAC
196 TATGTGAAAGGAAAGGATAATTAC
112134 AAAACAAGACTCAAGGGCAAGAAATTGCTAGAAACTAACTTAGGGTCTTTTTAGTAATTTGGCAA
1 AAAACAAGACTCAAGGGCAAGAAATTGCTAGAAACTAACTTAGGGTCTTTTTAGTAATTTGGCAA
112199 GTGAGAAAAGACAGAAAAAGACAAAAAAAATTAAAATGGAGCATCCTCATCGATCCTCAAAAGGG
66 GTGAGAAAAGACAGAAAAAGACAAAAAAAATTAAAATGGAGCATCCTCATCGATCCTCAAAAGGG
112264 GCCTTTGGTAAATTCCCTGCGTCTTTCAAATACTATTTAGTATATATA
131 GCCTTTGGTAAATTCCCTGCGTCTTTCAAATACTATTTAGTATATATA
112312 TATATATATA
Statistics
Matches: 174, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
219 174 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (219 bp):
AAAACAAGACTCAAGGGCAAGAAATTGCTAGAAACTAACTTAGGGTCTTTTTAGTAATTTGGCAA
GTGAGAAAAGACAGAAAAAGACAAAAAAAATTAAAATGGAGCATCCTCATCGATCCTCAAAAGGG
GCCTTTGGTAAATTCCCTGCGTCTTTCAAATACTATTTAGTATATATAAGAATTATTATAACATT
TATGTGAAAGGAAAGGATAATTAC
Found at i:112311 original size:2 final size:2
Alignment explanation
Indices: 112304--112336 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
112294 TACTATTTAG
112304 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
112337 GTTCCCTCTT
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:113079 original size:59 final size:60
Alignment explanation
Indices: 112963--113098 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 60
112953 ATAAGAAAGT
* * * * *
112963 TTTGCTCAAATAGGACCTTAACGTATTCGGAAATACTCAAATAAGAGTTCATCTTTTTAA
1 TTTGGTCAAATAGGACCCTAACGTATACGAAAATACTCAAATAAGAGCTCATCTTTTTAA
* * * * *
113023 TTTGGTTAAATAGGGCCCTAACGTATAC-AAAATGCTCAAATAAGGGCTCATGTTTTTAA
1 TTTGGTCAAATAGGACCCTAACGTATACGAAAATACTCAAATAAGAGCTCATCTTTTTAA
113082 TTTGGTCAAATAGGACC
1 TTTGGTCAAATAGGACC
113099 ATAATATTTG
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 41 0.64
60 23 0.36
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTGGTCAAATAGGACCCTAACGTATACGAAAATACTCAAATAAGAGCTCATCTTTTTAA
Found at i:113113 original size:59 final size:60
Alignment explanation
Indices: 112963--113127 Score: 170
Period size: 59 Copynumber: 2.8 Consensus size: 60
112953 ATAAGAAAGT
* * * * ** * *
112963 TTTGCTCAAATAGGACCTTAACGTATTCGGAAATACTCAAATAAGAGTTCATCTTTTTAA
1 TTTGGTCAAATAGGACCATAACATATACAAAAATGCTCAAATAAGAGCTCATCTTTTTAA
* * * * * *
113023 TTTGGTTAAATAGGGCCCTAACGTATAC-AAAATGCTCAAATAAGGGCTCATGTTTTTAA
1 TTTGGTCAAATAGGACCATAACATATACAAAAATGCTCAAATAAGAGCTCATCTTTTTAA
* * *
113082 TTTGGTCAAATAGGACCATAATATTTGCAAAAATGCTCAAATAAGA
1 TTTGGTCAAATAGGACCATAACATATACAAAAATGCTCAAATAAGA
113128 TCCTGTTGTC
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 47 0.55
60 39 0.45
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (60 bp):
TTTGGTCAAATAGGACCATAACATATACAAAAATGCTCAAATAAGAGCTCATCTTTTTAA
Found at i:113213 original size:31 final size:32
Alignment explanation
Indices: 113173--113245 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
113163 GACATCGGGA
*
113173 CCCTATTTGAGCATTT-TCGCATACGTTAGGG
1 CCCTATTTGAGCATTTGTCACATACGTTAGGG
*
113204 CTCTATTTGAGCATTTGTCACATACGTTAGGG
1 CCCTATTTGAGCATTTGTCACATACGTTAGGG
113236 CCCTATTTGA
1 CCCTATTTGA
113246 CAAAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 15 0.39
32 23 0.61
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (32 bp):
CCCTATTTGAGCATTTGTCACATACGTTAGGG
Found at i:113294 original size:60 final size:60
Alignment explanation
Indices: 113207--113373 Score: 212
Period size: 60 Copynumber: 2.8 Consensus size: 60
113197 GTTAGGGCTC
* * *
113207 TATTTGAGCATTTGTCACATACGTTAGGGCCCTATTTGACAAAATTAAAAGTAT-GAGCCCT
1 TATTTGAGCATTT-TCACATACATTAGGGTCCTATTTGACAAAATTAAAAATATGGA-CCCT
* * *
113268 TATTTGAGGATTTTCACATACATTAGGGTCCTATTTGACTAAATTAAAAATATGGATCCT
1 TATTTGAGCATTTTCACATACATTAGGGTCCTATTTGACAAAATTAAAAATATGGACCCT
* * * *
113328 TATTTGAGCATTTCCAAATATATTAGGGTCCTATTTGA-ACAATTAA
1 TATTTGAGCATTTTCACATACATTAGGGTCCTATTTGACAAAATTAA
113374 CCAAAGTTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 6 0.06
60 73 0.78
61 14 0.15
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (60 bp):
TATTTGAGCATTTTCACATACATTAGGGTCCTATTTGACAAAATTAAAAATATGGACCCT
Found at i:121814 original size:2 final size:2
Alignment explanation
Indices: 121801--121830 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
121791 TAATTTTTGT
*
121801 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
121831 AAAGTACAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:124447 original size:176 final size:167
Alignment explanation
Indices: 124134--124473 Score: 441
Period size: 176 Copynumber: 2.0 Consensus size: 167
124124 ATAAAAGTAA
*
124134 GAATAATAGAAAACTTTATGTTTTCCGATTGTACCATTTTTTTCAAATACATTTCTAAATTAACA
1 GAATAATAGAAAACTTTATGTTTTCCGATTGCACCATTTTTTTCAAATACATTTCTAAATTAACA
* * * ** *
124199 ATATTAAAATTTATTGTTTAAAAATTAATTATAAAATTTCAATTTAGACTGAATTATAAGTTTGT
66 AAATTAAAATTTATTATTTAAAAATTAATTATAAAATTTAAATTTAGACCAAATTATAAGTTTAT
124264 AAAATTGATTTTCATTGATGAACATGCAAATTTCTAC
131 AAAATTGATTTTCATTGATGAACATGCAAATTTCTAC
* * *
124301 GAATAATGGGAAACTTTATGTTTTCCGATTGCACC-TTTTTTTCAAATATATTTCTAAATTGTCA
1 GAATAATAGAAAACTTTATGTTTTCCGATTGCACCATTTTTTTCAAATACATTTCTAAA-T-T-A
* *
124365 TTATTAAAATTTAGTATAATATTATTATTTAAAAATTAATTA-AAATTTTAAATTTAGACCAAAT
63 --A-CAAAA-TTA--A-AAT-TTATTATTTAAAAATTAATTATAAAATTTAAATTTAGACCAAAT
* *
124429 TATAAGTTTATCAAATTGATTTTCGTTGATGAACATGCAAATTTC
120 TATAAGTTTATAAAATTGATTTTCATTGATGAACATGCAAATTTC
124474 CTTTACTATT
Statistics
Matches: 148, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
166 22 0.15
167 33 0.22
168 1 0.01
169 1 0.01
171 1 0.01
172 3 0.02
173 3 0.02
175 1 0.01
176 63 0.43
177 20 0.14
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (167 bp):
GAATAATAGAAAACTTTATGTTTTCCGATTGCACCATTTTTTTCAAATACATTTCTAAATTAACA
AAATTAAAATTTATTATTTAAAAATTAATTATAAAATTTAAATTTAGACCAAATTATAAGTTTAT
AAAATTGATTTTCATTGATGAACATGCAAATTTCTAC
Found at i:124720 original size:22 final size:22
Alignment explanation
Indices: 124692--124889 Score: 166
Period size: 22 Copynumber: 8.9 Consensus size: 22
124682 TGTCTCTGTC
*
124692 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
124714 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
124737 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
124758 TGGTTACCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAGGA
** *
124780 AAGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
* * **
124802 AGGTTATCAAAATTCCATAATA
1 TGGTTATCAAAATTTCATAGGA
*
124824 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
124846 TCTGATTATTAAAATTTCTTAGGA
1 --TGGTTATCAAAATTTCATAGGA
* **
124870 AGGTTATTGAAATTTCATAG
1 TGGTTATCAAAATTTCATAG
124890 TACTATCAGA
Statistics
Matches: 138, Mismatches: 32, Indels: 12
0.76 0.18 0.07
Matches are distributed among these distances:
21 3 0.02
22 114 0.83
23 3 0.02
24 18 0.13
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:124798 original size:66 final size:66
Alignment explanation
Indices: 124692--124842 Score: 214
Period size: 66 Copynumber: 2.3 Consensus size: 66
124682 TGTCTCTGTC
* ** * * *
124692 TGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCATAG
1 TGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTCCATAA
*
124756 TG
65 TA
*
124758 TGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTCCATAAT
1 TGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTCCATAAT
124823 A
66 A
124824 TGGTTACCAAAATTTCATA
1 TGGTTACCAAAATTTCATA
124843 GGATCTGATT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
65 2 0.03
66 74 0.97
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (66 bp):
TGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTCCATAAT
A
Found at i:124951 original size:22 final size:22
Alignment explanation
Indices: 124926--125815 Score: 206
Period size: 22 Copynumber: 40.4 Consensus size: 22
124916 ATCAAAGAGA
* *
124926 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
124948 TTAT-AAGAATTTCATAGTGTA-G
1 TTATCAA-AATTTCATAGTG-AGG
*
124970 TTAACAAAATTTCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * * *
124992 TTA-CTGATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
125014 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
** * *
125036 TTATCAAAATTTTTTACTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
125058 TTATCAAAATTACATAAT-ATGA
1 TTATCAAAATTTCATAGTGA-GG
* * * *
125080 TTTTCAAAATTTAATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
125102 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
* ** *
125124 TTATCAGAATTTCATAAAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * **
125146 TTATCAAATTTTCAAAATGTGATC
1 TTATCAAAATTTC-ATA-GTGAGG
* *** * *
125170 ATAGT-GGTATTT-ATGGGGAGG
1 TTA-TCAAAATTTCATAGTGAGG
125191 TTATCAAAATTTCATAGT-ATGG
1 TTATCAAAATTTCATAGTGA-GG
*
125213 TTA-CCAAA--T--TAG-GAAGG
1 TTATCAAAATTTCATAGTG-AGG
* * * *
125230 CTATTAAACTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGAG-G
* * *
125252 TAATAAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
125272 ATATCAAAATTCCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
****
125294 TTATCAAAATTTCATAGTTTTTT
1 TTATCAAAATTTCATAG-TGAGG
* *
125317 TTTTGGCACAAATCAAAATTTCATA-AGAGGG
1 TTAT----C-AA----AATTTCATAGTGA-GG
*
125348 TTATCAAAATTTCATAGT-ATG
1 TTATCAAAATTTCATAGTGAGG
* *
125369 TAGATCAAAATTTCATAAG-GAGA
1 T-TATCAAAATTTCAT-AGTGAGG
* *
125392 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* ** * *
125414 TTATAAAAAAATCATGGGGAGG
1 TTATCAAAATTTCATAGTGAGG
125436 TTATC-AAATTT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
*
125452 TTATCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
125474 TTATCAAAATTTTATAGGGAGCT
1 TTATCAAAATTTCATAGTGAG-G
*
125497 TTATCAAAATTTTATAG-GCAGG
1 TTATCAAAATTTCATAGTG-AGG
*
125519 TTTATCAAAATTTCATAGCGAGG
1 -TTATCAAAATTTCATAGTGAGG
* * *
125542 TTATCACAATTTCATAGTGCGA
1 TTATCAAAATTTCATAGTGAGG
125564 TTA-CTAATAA-TTCATA-TGGAGG
1 TTATC-AA-AATTTCATAGT-GAGG
* * * **
125586 TTTTTAAATTTTCATA-ACATGG
1 TTATCAAAATTTCATAGTGA-GG
* *
125608 TTATCAATATATCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
125630 TTATCAATATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
125653 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * **
125675 TCT-TCAAAATTCCTTAGCAAGG
1 T-TATCAAAATTTCATAGTGAGG
* *
125697 TTAACAAAATTTCATAAG-AAGG
1 TTATCAAAATTTCAT-AGTGAGG
** ***
125719 TTAAAAAAAATTT-ATAAAAAGG
1 TT-ATCAAAATTTCATAGTGAGG
* * * *
125741 TTCTCGAAATTCCATAGT-ATCG
1 TTATCAAAATTTCATAGTGA-GG
**
125763 TTATTGAAATTTCATAG-GAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
125785 CTATCAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
*
125807 TCATCAAAA
1 TTATCAAAA
125816 ATAGTGTAAT
Statistics
Matches: 621, Mismatches: 168, Indels: 158
0.66 0.18 0.17
Matches are distributed among these distances:
16 6 0.01
17 13 0.02
18 4 0.01
19 4 0.01
20 13 0.02
21 45 0.07
22 416 0.67
23 93 0.15
24 8 0.01
25 1 0.00
26 2 0.00
27 2 0.00
28 2 0.00
31 3 0.00
32 9 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:125504 original size:23 final size:22
Alignment explanation
Indices: 125328--125815 Score: 221
Period size: 22 Copynumber: 22.3 Consensus size: 22
125318 TTTGGCACAA
*
125328 ATCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
125350 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
* *
125372 ATCAAAATTTCATAAGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
125394 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* ** *
125416 ATAAAAAAATCATGGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
125438 ATC-AAATTT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
125454 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
125476 ATCAAAATTTTATAGGGAGCTTT
1 ATCAAAATTTCATAGGGAG-GTT
* *
125499 ATCAAAATTTTATAGGCAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
125522 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
125544 ATCACAATTTCATAGTGCGATT
1 ATCAAAATTTCATAGGGAGGTT
*
125566 A-CTAATAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * **
125588 TTTAAATTTTCATA-ACATGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
125610 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
125632 ATCAATATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
*
125655 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* * **
125678 -TCAAAATTCCTTAGCAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
125699 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** ***
125721 AAAAAAAATTT-ATAAAAAGGTT
1 -ATCAAAATTTCATAGGGAGGTT
* * * * *
125743 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATAGGGA-GGTT
** * *
125765 ATTGAAATTTCATAGGAAGGCT
1 ATCAAAATTTCATAGGGAGGTT
* *
125787 ATCAAAATTTCATAAGGAGGTC
1 ATCAAAATTTCATAGGGAGGTT
125809 ATCAAAA
1 ATCAAAA
125816 ATAGTGTAAT
Statistics
Matches: 349, Mismatches: 94, Indels: 46
0.71 0.19 0.09
Matches are distributed among these distances:
16 6 0.02
17 7 0.02
19 2 0.01
21 18 0.05
22 241 0.69
23 75 0.21
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:129161 original size:21 final size:21
Alignment explanation
Indices: 129021--129188 Score: 85
Period size: 21 Copynumber: 7.8 Consensus size: 21
129011 TTATAGGGAG
* * *
129021 ATTAACAAAATCTCATAGGGA
1 ATTATCAAAATTTCATAGGTA
* *
129042 AGTTATCAAAA-ATCATATG-A
1 A-TTATCAAAATTTCATAGGTA
129062 AGGTTAT-AAAATTTCATAGG-A
1 A--TTATCAAAATTTCATAGGTA
* *
129083 AGGTTTATTAAAATTTCATAGTTA
1 A---TTATCAAAATTTCATAGGTA
* * *
129107 GGTTATC-AAAGTTCATATGGTG
1 -ATTATCAAAATTTCATA-GGTA
* *
129129 CTTATCACAATTTCATAGGTA
1 ATTATCAAAATTTCATAGGTA
*
129150 ATTATCAAAATTTCATAGCGTG
1 ATTATCAAAATTTCATAG-GTA
* *
129172 GTTACCAAAATTTCATA
1 ATTATCAAAATTTCATA
129189 AAAATATTCA
Statistics
Matches: 116, Mismatches: 21, Indels: 19
0.74 0.13 0.12
Matches are distributed among these distances:
20 6 0.05
21 53 0.46
22 44 0.38
23 12 0.10
24 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (21 bp):
ATTATCAAAATTTCATAGGTA
Found at i:129165 original size:43 final size:43
Alignment explanation
Indices: 129092--129188 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 43
129082 AAGGTTTATT
* * *
129092 AAAATTTCATAGTTAGGTTATCAAAGTTCATATG-GTGCTTATC
1 AAAATTTCATAGGTAGATTATCAAAGTTCATA-GCGTGCTTACC
* * *
129135 ACAATTTCATAGGTA-ATTATCAAAATTTCATAGCGTGGTTACC
1 AAAATTTCATAGGTAGATTATC-AAAGTTCATAGCGTGCTTACC
129178 AAAATTTCATA
1 AAAATTTCATA
129189 AAAATATTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
42 6 0.13
43 39 0.87
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (43 bp):
AAAATTTCATAGGTAGATTATCAAAGTTCATAGCGTGCTTACC
Found at i:129183 original size:22 final size:21
Alignment explanation
Indices: 129137--129188 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
129127 TGCTTATCAC
*
129137 AATTTCATAGGTAATTATCAA
1 AATTTCATAGGTAATTACCAA
**
129158 AATTTCATAGCGTGGTTACCAA
1 AATTTCATAG-GTAATTACCAA
129180 AATTTCATA
1 AATTTCATA
129189 AAAATATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (21 bp):
AATTTCATAGGTAATTACCAA
Found at i:129281 original size:16 final size:14
Alignment explanation
Indices: 129245--129290 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 14
129235 AGTTAAAACC
129245 AATATATATATATAT
1 AATATATATATA-AT
129260 ATATATATATATAAGT
1 A-ATATATATATAA-T
129276 GAATATATATATAAT
1 -AATATATATATAAT
129291 TTTAAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.11
16 24 0.86
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (14 bp):
AATATATATATAAT
Found at i:129288 original size:2 final size:2
Alignment explanation
Indices: 129246--129272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
129236 GTTAAAACCA
129246 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
129273 AGTGAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:129302 original size:22 final size:24
Alignment explanation
Indices: 129254--129302 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
129244 CAATATATAT
* *
129254 ATATATATATATATATATAAGTGA
1 ATATATATATATATATATAAATCA
*
129278 ATATATATATA-AT-TTTAAATCA
1 ATATATATATATATATATAAATCA
129300 ATA
1 ATA
129303 ATCAATAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 2 0.09
24 11 0.50
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
ATATATATATATATATATAAATCA
Found at i:132004 original size:21 final size:21
Alignment explanation
Indices: 131951--132005 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
131941 TATAGTATCA
* *
131951 AAAAATTATAGGGAGATTAAC
1 AAAAATCATAGGGAGATGAAC
* * *
131972 AAAATCTCATAGGGAGGTGATC
1 AAAA-ATCATAGGGAGATGAAC
131994 AAAAATCATAGG
1 AAAAATCATAGG
132006 AATTTTACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (21 bp):
AAAAATCATAGGGAGATGAAC
Found at i:132060 original size:65 final size:65
Alignment explanation
Indices: 131966--132156 Score: 165
Period size: 65 Copynumber: 2.9 Consensus size: 65
131956 TTATAGGGAG
* * *
131966 ATTAACAAAATCTCATAGGGAGGTGATCAAAA-ATCATAGGAATTTTA-CAAAATTTCATAGG-A
1 ATTATCAAAATTTCATAGGGAGGTGATCAAAATATCATAGGAAGTTTATCAAAATTTCATAGGTA
* ** * * * *
132028 AGGTTTATTAAAATTTCATAGTTAGGTTATCAAAATTTTATATGAAGTTTATCAAAATTTCATAG
1 A---TTATCAAAATTTCATAGGGAGGTGATCAAAATATCATAGGAAGTTTATCAAAATTTCATAG
132093 GTA
63 GTA
* * * * * * *
132096 ATTATCAAAATTTCATAGCGTGATTATCAAAATTTAATAGGGTAG-TTATCAAAATTTCATA
1 ATTATCAAAATTTCATAGGGAGGTGATCAAAATATCATA-GGAAGTTTATCAAAATTTCATA
132157 ATAATATTCA
Statistics
Matches: 104, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
62 1 0.01
65 73 0.70
66 14 0.13
67 14 0.13
68 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (65 bp):
ATTATCAAAATTTCATAGGGAGGTGATCAAAATATCATAGGAAGTTTATCAAAATTTCATAGGTA
Found at i:132062 original size:22 final size:22
Alignment explanation
Indices: 131971--132156 Score: 157
Period size: 22 Copynumber: 8.5 Consensus size: 22
131961 GGGAGATTAA
* * *
131971 CAAAATCTCATAGGGAGGTGAT
1 CAAAATTTCATAGGTAGGTTAT
* * **
131993 CAAAA-ATCATAGGAATTTTA-
1 CAAAATTTCATAGGTAGGTTAT
*
132013 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGTAGG-TTAT
* *
132036 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGTAGGTTAT
* * * *
132058 CAAAATTTTATATGAAGTTTAT
1 CAAAATTTCATAGGTAGGTTAT
*
132080 CAAAATTTCATAGGTA-ATTAT
1 CAAAATTTCATAGGTAGGTTAT
*
132101 CAAAATTTCATAGCGT-GATTAT
1 CAAAATTTCATAG-GTAGGTTAT
*
132123 CAAAATTTAATAGGGTA-GTTAT
1 CAAAATTTCATA-GGTAGGTTAT
132145 CAAAATTTCATA
1 CAAAATTTCATA
132157 ATAATATTCA
Statistics
Matches: 133, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.04
21 36 0.27
22 76 0.57
23 16 0.12
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGGTAGGTTAT
Found at i:135859 original size:21 final size:21
Alignment explanation
Indices: 135835--135877 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
135825 GTTTTGTGGC
135835 GGTATCTGGGTTATGGAGGTG
1 GGTATCTGGGTTATGGAGGTG
*
135856 GGTATCTGGGTTATGGTGGTG
1 GGTATCTGGGTTATGGAGGTG
135877 G
1 G
135878 TGTTCTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.12, C:0.05, G:0.49, T:0.35
Consensus pattern (21 bp):
GGTATCTGGGTTATGGAGGTG
Found at i:139717 original size:21 final size:21
Alignment explanation
Indices: 139691--139734 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
139681 TGTACCTGAA
139691 TTGCTAAATACCGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
**
139712 TTGCTACTTACCGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
139733 TT
1 TT
139735 TACACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.09, T:0.34
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCCCTT
Found at i:139849 original size:12 final size:12
Alignment explanation
Indices: 139834--139858 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
139824 CAATCTTGAA
139834 GAAAATCATGTC
1 GAAAATCATGTC
139846 GAAAATCATGTC
1 GAAAATCATGTC
139858 G
1 G
139859 GATTTTGTAG
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:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GAAAATCATGTC
Found at i:139980 original size:7 final size:7
Alignment explanation
Indices: 139970--140046 Score: 52
Period size: 7 Copynumber: 10.9 Consensus size: 7
139960 TTTTAATTAC
139970 TATTAAT
1 TATTAAT
139977 TATTTAAT
1 TA-TTAAT
139985 TATT-AT
1 TATTAAT
139991 TAATTTAAAT
1 T-A-TT-AAT
*
140001 TGTT-AT
1 TATTAAT
140007 TATTAAT
1 TATTAAT
140014 TA-TAAT
1 TATTAAT
*
140020 TAATAAT
1 TATTAAT
*
140027 TAATAAT
1 TATTAAT
*
140034 AATTAAT
1 TATTAAT
*
140041 AATTAA
1 TATTAA
140047 AAAAATATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
6 14 0.24
7 31 0.53
8 11 0.19
10 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (7 bp):
TATTAAT
Found at i:139984 original size:18 final size:18
Alignment explanation
Indices: 139961--139995 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
139951 TTTTTTATTT
139961 TTTAATTACTATTAATTA
1 TTTAATTACTATTAATTA
*
139979 TTTAATTATTATTAATT
1 TTTAATTACTATTAATT
139996 TAAATTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATTACTATTAATTA
Found at i:139991 original size:11 final size:10
Alignment explanation
Indices: 139962--140045 Score: 59
Period size: 10 Copynumber: 8.7 Consensus size: 10
139952 TTTTTATTTT
*
139962 TTAATTACTA
1 TTAATTATTA
139972 TTAATTA-T-
1 TTAATTATTA
139980 TTAATTATTA
1 TTAATTATTA
*
139990 TTAATT-TAAA
1 TTAATTAT-TA
*
140000 TT-GTTATTA
1 TTAATTATTA
*
140009 TTAATTATAA
1 TTAATTATTA
*
140019 TTAATAATTA
1 TTAATTATTA
* *
140029 ATAATAATTA
1 TTAATTATTA
*
140039 ATAATTA
1 TTAATTA
140046 AAAAAATATT
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
8 7 0.12
9 8 0.13
10 45 0.75
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (10 bp):
TTAATTATTA
Found at i:140006 original size:16 final size:15
Alignment explanation
Indices: 139978--140023 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
139968 ACTATTAATT
139978 ATTTAATTATTATTA
1 ATTTAATTATTATTA
*
139993 ATTTAAATTGTTATT-
1 ATTT-AATTATTATTA
*
140008 A-TTAATTATAATTA
1 ATTTAATTATTATTA
140022 AT
1 AT
140024 AATTAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 8 0.32
14 3 0.12
15 5 0.20
16 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTTAATTATTATTA
Found at i:140030 original size:17 final size:17
Alignment explanation
Indices: 140008--140046 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
139998 AATTGTTATT
*
140008 ATTAATTATAATTAATA
1 ATTAATAATAATTAATA
140025 ATTAATAATAATTAATA
1 ATTAATAATAATTAATA
140042 ATTAA
1 ATTAA
140047 AAAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAATAATAATTAATA
Found at i:140128 original size:21 final size:21
Alignment explanation
Indices: 140086--140130 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
140076 GCAAAATTGT
* ***
140086 CAAAAGGGGGGCGGTGTTTAG
1 CAAAAAGGGGGCGGTAAATAG
140107 CAAAAAGGGGGCGGTAAATAG
1 CAAAAAGGGGGCGGTAAATAG
140128 CAA
1 CAA
140131 CTCCCTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.40, T:0.13
Consensus pattern (21 bp):
CAAAAAGGGGGCGGTAAATAG
Found at i:141153 original size:2 final size:2
Alignment explanation
Indices: 141146--141181 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
141136 GAGAATGAAA
*
141146 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
141182 GGAGTAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:146869 original size:13 final size:13
Alignment explanation
Indices: 146851--146885 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
146841 GGTATCTATC
146851 GATATATCGAACG
1 GATATATCGAACG
146864 GATATATCG-ACG
1 GATATATCGAACG
146876 GATATATCGA
1 GATATATCGA
146886 GGTATCGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (13 bp):
GATATATCGAACG
Found at i:147888 original size:10 final size:10
Alignment explanation
Indices: 147873--147927 Score: 83
Period size: 10 Copynumber: 5.5 Consensus size: 10
147863 AATTTAATAT
*
147873 GATATTTACA
1 GATATTTACG
*
147883 GATATTTACA
1 GATATTTACG
*
147893 GATACTTACG
1 GATATTTACG
147903 GATATTTACG
1 GATATTTACG
147913 GATATTTACG
1 GATATTTACG
147923 GATAT
1 GATAT
147928 ATCGAGAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (10 bp):
GATATTTACG
Found at i:147967 original size:20 final size:20
Alignment explanation
Indices: 147926--147989 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
147916 ATTTACGGAT
*
147926 ATATCGAGAATATATCGA--G
1 ATATCGATAA-ATATCGACGG
147945 ATATCGATAAATATCGACGG
1 ATATCGATAAATATCGACGG
*
147965 ATACACGGAT--ATATCGACGG
1 ATA-TC-GATAAATATCGACGG
147985 ATATC
1 ATATC
147990 CGGTGACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.18
19 10 0.26
20 17 0.45
21 1 0.03
22 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (20 bp):
ATATCGATAAATATCGACGG
Found at i:154365 original size:32 final size:32
Alignment explanation
Indices: 154324--154384 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
154314 TATAAAACTT
*
154324 TTGAATCGACTATTATATCCTTATTTTTCTAA
1 TTGAATCGACCATTATATCCTTATTTTTCTAA
154356 TTGAATCGACCATTATATCCTTATTTTTC
1 TTGAATCGACCATTATATCCTTATTTTTC
154385 AAACATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (32 bp):
TTGAATCGACCATTATATCCTTATTTTTCTAA
Found at i:156834 original size:57 final size:58
Alignment explanation
Indices: 156739--156855 Score: 209
Period size: 57 Copynumber: 2.0 Consensus size: 58
156729 ATTTCATCCA
156739 CGTTTTTATAGTAATTCGACACTTGTTTTTCTCCGTTTTGCAAAACTGTGTCAGTACCC
1 CGTTTTTATAGTAATTCGA-ACTTGTTTTTCTCCGTTTTGCAAAACTGTGTCAGTACCC
*
156798 CGTTTTTATAGTGATTCG-ACTTGTTTTTCTCCGTTTTGCAAAACTGTGTCAGTACCC
1 CGTTTTTATAGTAATTCGAACTTGTTTTTCTCCGTTTTGCAAAACTGTGTCAGTACCC
156855 C
1 C
156856 ATCAGATCCC
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 40 0.70
59 17 0.30
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (58 bp):
CGTTTTTATAGTAATTCGAACTTGTTTTTCTCCGTTTTGCAAAACTGTGTCAGTACCC
Found at i:160678 original size:27 final size:27
Alignment explanation
Indices: 160640--160725 Score: 145
Period size: 27 Copynumber: 3.2 Consensus size: 27
160630 CTAACTACTA
160640 TGCTGGAACGCTTTCATTTCTTGTATC
1 TGCTGGAACGCTTTCATTTCTTGTATC
* *
160667 TGCTGGAACGCTTTCAGTTCTCGTATC
1 TGCTGGAACGCTTTCATTTCTTGTATC
*
160694 TGCTGGAACGATTTCATTTCTTGTATC
1 TGCTGGAACGCTTTCATTTCTTGTATC
160721 TGCTG
1 TGCTG
160726 TATCCTTTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (27 bp):
TGCTGGAACGCTTTCATTTCTTGTATC
Found at i:181724 original size:15 final size:15
Alignment explanation
Indices: 181708--181736 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
181698 CGGCTATGAT
181708 TTTC-CTTATATAAA
1 TTTCACTTATATAAA
181722 TTTCACTTATATAAA
1 TTTCACTTATATAAA
181737 CCTCCAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTCACTTATATAAA
Done.