Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007698.1 Hibiscus syriacus cultivar Beakdansim tig00109908_pilon, 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: 347831
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 1 of 2
Found at i:1441 original size:21 final size:21
Alignment explanation
Indices: 1372--1441 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1362 CATGTGAATC
*
1372 GGACTCTTGAATGGTGGGA-G
1 GGACTCTTGAACGGTGGGAGG
* * ** *
1392 GGACCTCTTCAACGATGACAGT
1 GGA-CTCTTGAACGGTGGGAGG
*
1414 GGCCTCTTGAACGGTGGGAGG
1 GGACTCTTGAACGGTGGGAGG
1435 GGACTCT
1 GGACTCT
1442 CGAGGAATGA
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 3 0.09
21 30 0.86
22 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
GGACTCTTGAACGGTGGGAGG
Found at i:1460 original size:42 final size:41
Alignment explanation
Indices: 1375--1497 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1365 GTGAATCGGA
* * * *
1375 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
*
1417 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1459 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGATAGG
1498 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:3522 original size:20 final size:18
Alignment explanation
Indices: 3490--3649 Score: 93
Period size: 20 Copynumber: 8.8 Consensus size: 18
3480 TCTTTTGGTT
3490 GAAATGAAATCGCAACGA
1 GAAATGAAATCGCAACGA
*
3508 GATAATGAGAATCGCAACGCG
1 GA-AATGA-AATCGCAACG-A
*
3529 GAAATGACTATCGCAACGA
1 GAAATGA-AATCGCAACGA
*
3548 G--A-G-AATCGCAACGC
1 GAAATGAAATCGCAACGA
* * *
3562 GAAATGACTATCGCGACCA
1 GAAATGA-AATCGCAACGA
* *
3581 G--A--CAATCGCAACGC
1 GAAATGAAATCGCAACGA
*
3595 GAAATGAAAATCGCAACCGC
1 GAAATG-AAATCGCAA-CGA
*
3615 GAAATGAAAATCGCAACGC
1 GAAATG-AAATCGCAACGA
3634 GAAATGAAAATCGCAA
1 GAAATG-AAATCGCAA
3650 TGCGATTTTG
Statistics
Matches: 112, Mismatches: 16, Indels: 27
0.72 0.10 0.17
Matches are distributed among these distances:
14 18 0.16
16 3 0.03
17 3 0.03
18 2 0.02
19 41 0.37
20 43 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGA
Found at i:3571 original size:33 final size:33
Alignment explanation
Indices: 3514--3612 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
3504 ACGAGATAAT
*
3514 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
3548 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
3581 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
3613 GCGAAATGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:3606 original size:19 final size:19
Alignment explanation
Indices: 3490--3654 Score: 136
Period size: 19 Copynumber: 9.1 Consensus size: 19
3480 TCTTTTGGTT
*
3490 GAAATG-AAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3508 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3528 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
3546 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
3562 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
3580 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3595 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
3615 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3634 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3653 GA
1 GA
3655 TTTTGGTTTC
Statistics
Matches: 120, Mismatches: 13, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 6 0.05
19 46 0.38
20 41 0.34
21 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3672 original size:19 final size:19
Alignment explanation
Indices: 3650--3697 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3640 AAAATCGCAA
*
3650 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
3669 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
3689 TGCGATTTT
1 TGCGATTTT
3698 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:4258 original size:20 final size:21
Alignment explanation
Indices: 4209--4261 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
4199 GCGCTATGTA
4209 AATCG-CGTTGCGAAAGCCAG
1 AATCGTCGTTGCGAAAGCCAG
*
4229 AATCGT-GTTGCGAAAGTCAG
1 AATCGTCGTTGCGAAAGCCAG
*
4249 TATC-TCGTTGCGA
1 AATCGTCGTTGCGA
4262 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (21 bp):
AATCGTCGTTGCGAAAGCCAG
Found at i:4435 original size:21 final size:21
Alignment explanation
Indices: 4374--4427 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
4364 ACTGTATACC
4374 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
4395 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
4416 ATCGCAACGCGA
1 ATCGCAACGCGA
4428 AATGCAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAACT
Found at i:8028 original size:20 final size:20
Alignment explanation
Indices: 8005--8055 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
7995 CACAGAATGT
*
8005 AAGATTATCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
8025 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
8045 AAGATTACCAG
1 AAGATTACCAG
8056 AGAATAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:12156 original size:21 final size:21
Alignment explanation
Indices: 12126--12173 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
12116 TAATTTTCAA
*
12126 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
12147 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
12168 ACATTG
1 ACATTG
12174 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:16803 original size:21 final size:21
Alignment explanation
Indices: 16773--16821 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
16763 TAATTTTCAA
*
16773 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
16794 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
16815 ACATTGT
1 ACATTGT
16822 AATATTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:19595 original size:30 final size:30
Alignment explanation
Indices: 19551--19609 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
19541 GGTGAAGAAT
*
19551 CTAAAGACGCCATGTACTCTGGCCGTCTTA
1 CTAAAAACGCCATGTACTCTGGCCGTCTTA
* *
19581 CTAAAAACGTCATGTGCTCTGGCCGTCTT
1 CTAAAAACGCCATGTACTCTGGCCGTCTT
19610 CCGGAGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (30 bp):
CTAAAAACGCCATGTACTCTGGCCGTCTTA
Found at i:21764 original size:316 final size:316
Alignment explanation
Indices: 21190--21823 Score: 1058
Period size: 316 Copynumber: 2.0 Consensus size: 316
21180 GCAAAGGTTT
*
21190 CGAGACAAAACACTCAAATTCGATGTAACACTCAAACTCAACAAAAAATAATTCTTCACTTCAAC
1 CGAGACAAAACACTCAAATTCGATGTAACACTCAAACTCAACAAAAAACAATTCTTCACTTCAAC
* * * *
21255 GAACAAGTTTTCCACCTCTTCCACAACACCCCTCAAAGGGTTAATCTTCAGTAATGGACATCGAC
66 GAACAAGTTCTCCACCTCTTCCACAACACCCCTCAAAGGGGTAATCTTCAGTAATGGACACCAAC
21320 CGAATCCAAGCTTTTTCTAGGCTTAGATTTAGTCTTCACATCGACATGGTTATCATAAGTGTCAA
131 CGAATCCAAGCTTTTTCTAGGCTTAGATTTAGTCTTCACATCGACATGGTTATCATAAGTGTCAA
* * *
21385 CTTTGCTTACAAATGTTTCACCACGAGCAATATCATGCATATCACAATCTCGATCATCAATGATA
196 CTTTGCTCACAAATGTTTAACCAAGAGCAATATCATGCA-ATCACAATCTCGATCATCAATGATA
* * *
21450 GTTATATCTTCAAATTCATTATGTTCATGAAATTGAACTCTTTTCTGCTTCATATAA
260 ATTATATCTTCAAATTCATTATGTTCACGAAATTGAACTCTTTTCTGCTTCACATAA
*
21507 CGAGACAAAACACTCAAATTCGATGTGACACTCAAACTCAAC-AAAAACAATTCTTCACTTCAAC
1 CGAGACAAAACACTCAAATTCGATGTAACACTCAAACTCAACAAAAAACAATTCTTCACTTCAAC
*
21571 GAACAAGTTCTCTACCTCTTCCACAACACCCCTCAAAGGGGTAATCTTCAGTAATGGACACCAAC
66 GAACAAGTTCTCCACCTCTTCCACAACACCCCTCAAAGGGGTAATCTTCAGTAATGGACACCAAC
* *
21636 CGAATCCAAGCTTTTTCTAGGGTTGGATTTAGTCTTCACATCGACATGGTTATCATAAGTGTCAA
131 CGAATCCAAGCTTTTTCTAGGCTTAGATTTAGTCTTCACATCGACATGGTTATCATAAGTGTCAA
*
21701 CTTTGCTCACAAATGTTTAACCAAGAGCAATATCACGTGC-ATCGCAATC-CTGATCATCAATGA
196 CTTTGCTCACAAATGTTTAACCAAGAGCAATATCA--TGCAATCACAATCTC-GATCATCAATGA
*
21764 TAATTATATCTTCAAATTCATTATGTTCACGAAATTGAACTCTTTTCTTCTTCACATAA
258 TAATTATATCTTCAAATTCATTATGTTCACGAAATTGAACTCTTTTCTGCTTCACATAA
21823 C
1 C
21824 TATTCTGCCC
Statistics
Matches: 297, Mismatches: 17, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
315 1 0.00
316 252 0.85
317 41 0.14
318 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (316 bp):
CGAGACAAAACACTCAAATTCGATGTAACACTCAAACTCAACAAAAAACAATTCTTCACTTCAAC
GAACAAGTTCTCCACCTCTTCCACAACACCCCTCAAAGGGGTAATCTTCAGTAATGGACACCAAC
CGAATCCAAGCTTTTTCTAGGCTTAGATTTAGTCTTCACATCGACATGGTTATCATAAGTGTCAA
CTTTGCTCACAAATGTTTAACCAAGAGCAATATCATGCAATCACAATCTCGATCATCAATGATAA
TTATATCTTCAAATTCATTATGTTCACGAAATTGAACTCTTTTCTGCTTCACATAA
Found at i:34342 original size:18 final size:18
Alignment explanation
Indices: 34319--34359 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
34309 AGGCATTTGA
* *
34319 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
34337 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
34355 TCCTC
1 TCCTC
34360 ATGTTGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:43342 original size:45 final size:44
Alignment explanation
Indices: 43221--43390 Score: 232
Period size: 44 Copynumber: 3.8 Consensus size: 44
43211 ATTCAATATT
* *
43221 TTACCATTATTTAACCATAATCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATT-TTT--CCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
43268 TTACCATTTATCCATAAGCTCGTAAGCTTATCTTACCATTATAC
1 TTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
43312 TTACCATTTGTTCCATAAGTTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTT-TTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* *
43357 TTGCCATTATTCCATAAGCTCGTAAGCTTATTTT
1 TTACCATTTTTCCATAAGCTCGTAAGCTTATTTT
43391 TCAGTTTATC
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
44 62 0.56
45 38 0.35
46 2 0.02
47 8 0.07
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (44 bp):
TTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:59453 original size:12 final size:13
Alignment explanation
Indices: 59430--59454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59420 ATTTTAATCG
59430 AAAATACAAAAAA
1 AAAATACAAAAAA
59443 AAAATACAAAAA
1 AAAATACAAAAA
59455 CTTAAAACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATACAAAAAA
Found at i:76138 original size:29 final size:29
Alignment explanation
Indices: 76093--76150 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
76083 GTGTTTGTCG
76093 TAGGTCACCATGCCTTCC-GGACGACCTAC
1 TAGGTCACCATGCCTTCCTGG-CGACCTAC
* *
76122 TAGGTCGCCATGTCTTCCTGGCGACCTAC
1 TAGGTCACCATGCCTTCCTGGCGACCTAC
76151 GAGAGATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.17, C:0.36, G:0.22, T:0.24
Consensus pattern (29 bp):
TAGGTCACCATGCCTTCCTGGCGACCTAC
Found at i:76325 original size:29 final size:29
Alignment explanation
Indices: 76293--76349 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
76283 GAGCAAGGGT
* *
76293 AGGTCGTCCGGAGAGCATGGCGATCTATA
1 AGGTCGCCCGGAGAGCATGGCGACCTATA
*
76322 AGGTCGCCCGGAGGGCATGGCGACCTAT
1 AGGTCGCCCGGAGAGCATGGCGACCTAT
76350 GTGTTGGGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.37, T:0.18
Consensus pattern (29 bp):
AGGTCGCCCGGAGAGCATGGCGACCTATA
Found at i:77389 original size:29 final size:30
Alignment explanation
Indices: 77326--77391 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
77316 GGACTAGCAA
*
77326 TGAACCGACTGAAAATCGGTAAAATCGGGG
1 TGAACCGACTGAAAACCGGTAAAATCGGGG
* **
77356 TGAACCGGCTGAAAACCGGT-AAATCGGTT
1 TGAACCGACTGAAAACCGGTAAAATCGGGG
77385 TGAACCG
1 TGAACCG
77392 TCGGTACACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (30 bp):
TGAACCGACTGAAAACCGGTAAAATCGGGG
Found at i:80685 original size:21 final size:22
Alignment explanation
Indices: 80661--80701 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
80651 CCAAAACAGG
*
80661 GAGTATCGATA-TTCCTTTAAT
1 GAGTATCGATACTACCTTTAAT
*
80682 GAGTATTGATACTACCTTTA
1 GAGTATCGATACTACCTTTA
80702 TAATATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (22 bp):
GAGTATCGATACTACCTTTAAT
Found at i:82243 original size:21 final size:20
Alignment explanation
Indices: 82219--82267 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
82209 CTCGAAATCA
*
82219 TTTTTCAAAATTTAATTTTG
1 TTTTTCAAAATCTAATTTTG
82239 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
82259 -CTTTCAAAA
1 TTTTTCAAAA
82268 GAAATCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:83834 original size:79 final size:79
Alignment explanation
Indices: 83670--83827 Score: 284
Period size: 78 Copynumber: 2.0 Consensus size: 79
83660 TTTCTAACAA
*
83670 ATTCACTAATTTGTTCTTTCTTTTTTCTAGGCTCAATAGTAACCTTTACAAAACCCTTAGTTTTT
1 ATTCACTAATTTGTTCTTTCATTTTTCTAGGCTCAATAGTAACCTTTACAAAACCCTTAGTTTTT
83735 TTAATGACTAAACT
66 TTAATGACTAAACT
83749 ATTCACTAATTTGTTCTTT-ATTTTTCTAGGCTCAATAGTAACCTTTACAAAACCCTTAG-TTTT
1 ATTCACTAATTTGTTCTTTCATTTTTCTAGGCTCAATAGTAACCTTTACAAAACCCTTAGTTTTT
*
83812 TTAATGAGTAAACT
66 TTAATGACTAAACT
83826 AT
1 AT
83828 AATCACTCCC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
77 19 0.25
78 39 0.51
79 19 0.25
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (79 bp):
ATTCACTAATTTGTTCTTTCATTTTTCTAGGCTCAATAGTAACCTTTACAAAACCCTTAGTTTTT
TTAATGACTAAACT
Found at i:85066 original size:19 final size:19
Alignment explanation
Indices: 85042--85103 Score: 124
Period size: 19 Copynumber: 3.3 Consensus size: 19
85032 ATTTATAAAT
85042 AAAACTTTACAATTATAAG
1 AAAACTTTACAATTATAAG
85061 AAAACTTTACAATTATAAG
1 AAAACTTTACAATTATAAG
85080 AAAACTTTACAATTATAAG
1 AAAACTTTACAATTATAAG
85099 AAAAC
1 AAAAC
85104 ATTCTAAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAACTTTACAATTATAAG
Found at i:88169 original size:76 final size:77
Alignment explanation
Indices: 88042--88185 Score: 209
Period size: 76 Copynumber: 1.9 Consensus size: 77
88032 TATGAAGTAT
* * * *
88042 GTGGTTATAATGTAGGTTTGTTGTTGGAATGTGAAATTGATTCCATTCTTTTTC-ATTATCTATG
1 GTGGTTACAATGTAGGTTTGTTGTTGGAATGTGAAATTAATTCCATCCTTTTCCTATTATCTATG
88106 TATATTTCATAA
66 TATATTTCATAA
* * * *
88118 GTGGTTACGATGTAGGTTTGTTGTTGTAATGTGAAATTAATTTCATCCTTTTCCTTTTATCTATG
1 GTGGTTACAATGTAGGTTTGTTGTTGGAATGTGAAATTAATTCCATCCTTTTCCTATTATCTATG
88183 TAT
66 TAT
88186 GGGTTATGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
76 47 0.80
77 12 0.20
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.49
Consensus pattern (77 bp):
GTGGTTACAATGTAGGTTTGTTGTTGGAATGTGAAATTAATTCCATCCTTTTCCTATTATCTATG
TATATTTCATAA
Found at i:91949 original size:12 final size:12
Alignment explanation
Indices: 91932--91956 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
91922 ATCCATGTTC
91932 CTTGTATGTTGT
1 CTTGTATGTTGT
91944 CTTGTATGTTGT
1 CTTGTATGTTGT
91956 C
1 C
91957 ATCGCGGTGA
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:0.08, C:0.12, G:0.24, T:0.56
Consensus pattern (12 bp):
CTTGTATGTTGT
Found at i:92860 original size:20 final size:19
Alignment explanation
Indices: 92827--92865 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
92817 AAACCATATA
92827 AAATAATATAATATTCTCAT
1 AAATAATATAATATT-TCAT
* *
92847 AAATAATTTTATATTTCAT
1 AAATAATATAATATTTCAT
92866 GAACCAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATAATATAATATTTCAT
Found at i:93338 original size:60 final size:62
Alignment explanation
Indices: 93274--93546 Score: 271
Period size: 60 Copynumber: 4.5 Consensus size: 62
93264 AAACTAGTTT
93274 TCAAATTCGCAAAGCGAATATGT-AAA-TCGCAACACATAAGTCAAATTCGCAACACAAAAG
1 TCAAATTCGCAAAGCGAATATGTCAAATTCGCAACACATAAGTCAAATTCGCAACACAAAAG
* ** * **
93334 TCAAATTCGCAACGCG-ATA-GTCAAATTCGCAATGCGAT-AGTCAAATTCACAACACTGAAG
1 TCAAATTCGCAAAGCGAATATGTCAAATTCGCAACAC-ATAAGTCAAATTCGCAACACAAAAG
* * * * *
93394 TCAAATTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAAGTCAAGTTCGCAACACAGAAG
1 TCAAATTCGCAAAGCGAATATGTCAAATTCGCAACACATAAGTCAAATTCGCAACACAAAAG
* * * * * * *
93454 TCAAATTCACAACA-C-AAAATTTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAG
1 TCAAATTCGCAA-AGCGAATATGTCAAATTCGCAACACATAAGTCAAATTCGCAACACAAAAG
* *
93515 TCAAATTTGCAATGCGAA-A-GTCAAATTCGCAA
1 TCAAATTCGCAAAGCGAATATGTCAAATTCGCAA
93547 AGCGCGTTTA
Statistics
Matches: 174, Mismatches: 28, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
58 2 0.01
59 11 0.06
60 110 0.63
61 47 0.27
62 4 0.02
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (62 bp):
TCAAATTCGCAAAGCGAATATGTCAAATTCGCAACACATAAGTCAAATTCGCAACACAAAAG
Found at i:93480 original size:21 final size:20
Alignment explanation
Indices: 93300--93546 Score: 219
Period size: 20 Copynumber: 12.3 Consensus size: 20
93290 AATATGTAAA
*
93300 TCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
93320 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
93340 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
** * *
93360 TCGCAATGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* **
93380 TCACAACACTGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* **
93400 TCGCAACGCGAATCTGT-AAA-
1 TCGCAACAC-AA-AAGTCAAAT
* *
93420 TCGCAACACAGAAGTCAAGT
1 TCGCAACACAAAAGTCAAAT
*
93440 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
93460 TCACAACACAAAATTTCAAAT
1 TCGCAACACAAAA-GTCAAAT
93481 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
93501 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* ** *
93521 TTGCAATGCGAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
93541 TCGCAA
1 TCGCAA
93547 AGCGCGTTTA
Statistics
Matches: 187, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
18 2 0.01
19 3 0.02
20 159 0.85
21 21 0.11
22 2 0.01
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:97244 original size:24 final size:24
Alignment explanation
Indices: 97217--97270 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
97207 ATGAAACATC
*
97217 ATCAAAATCCGATTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
97241 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
97265 ATCAAA
1 ATCAAA
97271 CTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:97284 original size:24 final size:24
Alignment explanation
Indices: 97217--97284 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
97207 ATGAAACATC
* * *
97217 ATCAAAATCCGATTATTGACCAAG
1 ATCAAACTCCGAATACTGACCAAG
* ** *
97241 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAACTCCGAATACTGACCAAG
*
97265 ATCAAACTTCGAATACTGAC
1 ATCAAACTCCGAATACTGAC
97285 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAACTCCGAATACTGACCAAG
Found at i:98045 original size:14 final size:15
Alignment explanation
Indices: 98009--98046 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
97999 GAAATCATTG
98009 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
98024 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
98039 AAAAATTA
1 AAAAATTA
98047 AAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:98671 original size:15 final size:15
Alignment explanation
Indices: 98651--98693 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
98641 TTTCGAAAAA
98651 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
98666 TGAATTATTGGAATT
1 TGAATTACTGGAATT
98681 TGAATTACTGGAA
1 TGAATTACTGGAA
98694 CTGAAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:99034 original size:34 final size:34
Alignment explanation
Indices: 98968--99034 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
98958 TAATTTATTT
* *
98968 AATATTAATGTTTTTTTATAATTTTATTAATAAA
1 AATAATAATGTTTTTTTATAATTTTATAAATAAA
99002 AATAATAAT-TTTTTTTAT-ATTTTAGTGAAATAA
1 AATAATAATGTTTTTTTATAATTTTA-T-AAATAA
99035 TATATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.21
33 10 0.34
34 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (34 bp):
AATAATAATGTTTTTTTATAATTTTATAAATAAA
Found at i:99173 original size:19 final size:19
Alignment explanation
Indices: 99145--99194 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
99135 TTTAAATATA
99145 TAAATAATATTATTCATTAT
1 TAAAT-ATATTATTCATTAT
* **
99165 TAAATATATAATTTTTTAT
1 TAAATATATTATTCATTAT
99184 T--ATATATTATT
1 TAAATATATTATT
99195 TAAATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.35
19 12 0.46
20 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TAAATATATTATTCATTAT
Found at i:99240 original size:58 final size:58
Alignment explanation
Indices: 99128--99250 Score: 132
Period size: 58 Copynumber: 2.1 Consensus size: 58
99118 TCTTTACTAA
*
99128 AATATTATTTAAATATATAAATAATATTATTCATTATTAAATATATAATTTTTTAT-T
1 AATATTATTTAAATATAAAAATAATATTATTCATTATTAAATATATAATTTTTTATAT
*
99185 ATATATTATTTAAATA-AAAATATAATA-TA-T-A-TATTATAATATAATTGATTATTTTATAT
1 A-ATATTATTTAAATATAAAA-ATAATATTATTCATTATTA-AATAT-A-TAATT-TTTTATAT
99244 AATATTA
1 AATATTA
99251 AAAATATTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
54 5 0.09
55 6 0.11
56 2 0.04
57 10 0.18
58 32 0.56
59 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (58 bp):
AATATTATTTAAATATAAAAATAATATTATTCATTATTAAATATATAATTTTTTATAT
Found at i:99533 original size:42 final size:42
Alignment explanation
Indices: 99475--99591 Score: 189
Period size: 42 Copynumber: 2.8 Consensus size: 42
99465 ATGAATTACA
*
99475 TTCCGGAAAACCAATTACATGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
* *
99517 TTCCGGAAAACGAATTACGTGAAATAAACACGGGAAAACATT
1 TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
* *
99559 TTCCGAAAAACTAATTACGTGAAACAAACACGG
1 TTCCGGAAAACCAATTACGTGAAACAAACACGG
99592 AAATTCGGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
Found at i:118091 original size:3 final size:3
Alignment explanation
Indices: 118083--118110 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
118073 ATGTTCTGTT
118083 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
118111 ACGCATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:119810 original size:19 final size:19
Alignment explanation
Indices: 119718--119806 Score: 67
Period size: 18 Copynumber: 4.8 Consensus size: 19
119708 TTATTTTAAT
119718 AATTATAATAATATTATTA
1 AATTATAATAATATTATTA
* * *
119737 AATTATATTAAAATGATT-
1 AATTATAATAATATTATTA
** * * * *
119755 TTTTATTATTATTTTAAT-
1 AATTATAATAATATTATTA
119773 AATTATAATAATATTATTA
1 AATTATAATAATATTATTA
*
119792 AATTATTATAA-ATTA
1 AATTATAATAATATTA
119807 ATTATTTTCA
Statistics
Matches: 50, Mismatches: 19, Indels: 3
0.69 0.26 0.04
Matches are distributed among these distances:
18 25 0.50
19 25 0.50
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
AATTATAATAATATTATTA
Found at i:121815 original size:19 final size:19
Alignment explanation
Indices: 121791--121829 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
121781 TCGAATGCAT
121791 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
121810 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
121829 T
1 T
121830 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:121846 original size:65 final size:63
Alignment explanation
Indices: 121727--121936 Score: 219
Period size: 65 Copynumber: 3.3 Consensus size: 63
121717 TTATTCAAAG
* *
121727 TCATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGC
1 TCATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGC
121789 ATT
61 ATT
*
121792 CCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATT
1 TCATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATT
* * *** * **
121857 TGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATT
1 TCATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATT
*
121921 TCATGCATCGATGCAC
1 TCATGCACCGATGCAC
121937 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 7 0.06
64 53 0.42
65 64 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (63 bp):
TCATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATT
Found at i:121952 original size:64 final size:64
Alignment explanation
Indices: 121727--121957 Score: 227
Period size: 64 Copynumber: 3.6 Consensus size: 64
121717 TTATTCAAAG
* * * *
121727 TCATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGC
1 TCATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGC
121789 ATT
62 ATT
* * * *
121792 CCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATT
1 TCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATT
* ** **
121857 TGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATT
1 TCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATT
*** *
121921 TCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 TCATGCATCGATGCACACTCCATGCATCGATGCATCA
121958 AGTGTTCCAA
Statistics
Matches: 139, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
63 6 0.04
64 69 0.50
65 64 0.46
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
TCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATT
Found at i:123530 original size:16 final size:16
Alignment explanation
Indices: 123511--123544 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
123501 CAATATACGA
123511 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
123527 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
123543 AT
1 AT
123545 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:123621 original size:16 final size:18
Alignment explanation
Indices: 123589--123622 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
123579 TATTAATGTA
123589 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
123607 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
123623 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:124759 original size:35 final size:35
Alignment explanation
Indices: 124709--124784 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
124699 AATCTGACAT
* *
124709 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
124744 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
124779 AATTGA
1 AATTGA
124785 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:142777 original size:43 final size:43
Alignment explanation
Indices: 142725--142808 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
142715 GGGTTTAGAT
*
142725 CCAGGCGTTTACGAATAAAGTAAATTGGGTTGAAAGGGTCGAC
1 CCAGGCGTTTACGAATAAAGTAAATTGGGTTGAAAAGGTCGAC
142768 CCAGGCGTTTACGAATAAAGTAAATTGGGTTGAAAAGGTCG
1 CCAGGCGTTTACGAATAAAGTAAATTGGGTTGAAAAGGTCG
142809 CCCTTGCCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (43 bp):
CCAGGCGTTTACGAATAAAGTAAATTGGGTTGAAAAGGTCGAC
Found at i:155876 original size:2 final size:2
Alignment explanation
Indices: 155869--155947 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
155859 TTTCACAATA
*
155869 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155911 AT AT AT AT AT 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 AT AT AT AT AT A
155948 AGATTGCGAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:164751 original size:17 final size:19
Alignment explanation
Indices: 164718--164758 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
164708 ATGTTATTTT
*
164718 AATAAAATTTCATTAAAA-
1 AATAAAACTTCATTAAAAC
164736 AATAAAACTT-ATTAAAAC
1 AATAAAACTTCATTAAAAC
164754 AATAA
1 AATAA
164759 TTTTATATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAAAACTTCATTAAAAC
Found at i:166448 original size:6 final size:6
Alignment explanation
Indices: 166437--166469 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
166427 TTATCTACCC
166437 TTTAAT TTTAAT TTTAAT TTTAATT TTTAAT TT
1 TTTAAT TTTAAT TTTAAT TTTAA-T TTTAAT TT
166470 ATTTATCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:171260 original size:49 final size:49
Alignment explanation
Indices: 171180--171274 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
171170 GACACTTGTG
** *
171180 GAGGGGTTGCTTGGGATACCCCGGACACCATGGAGGTCCACCCCTGGAT
1 GAGGGGTTGCCCGAGATACCCCGGACACCATGGAGGTCCACCCCTGGAT
* *
171229 GAGGGGTTGCCCGAGATACCCCAGG-CTCCATGGAGGTCCGCCCCTG
1 GAGGGGTTGCCCGAGATACCCC-GGACACCATGGAGGTCCACCCCTG
171275 TCCGTCACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 38 0.95
50 2 0.05
ACGTcount: A:0.17, C:0.32, G:0.35, T:0.17
Consensus pattern (49 bp):
GAGGGGTTGCCCGAGATACCCCGGACACCATGGAGGTCCACCCCTGGAT
Found at i:176070 original size:45 final size:45
Alignment explanation
Indices: 176006--176093 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
175996 GATCCATCTT
*
176006 AATTTTGGAATAGATTGGATTTTTTTAAATAAATAAATAAATTTG
1 AATTTTGGAAAAGATTGGATTTTTTTAAATAAATAAATAAATTTG
176051 AATTTTGGAAAAGATTGGATTTTTTTAAATAAATAAATAAATT
1 AATTTTGGAAAAGATTGGATTTTTTTAAATAAATAAATAAATT
176094 GGAGTCGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.43
Consensus pattern (45 bp):
AATTTTGGAAAAGATTGGATTTTTTTAAATAAATAAATAAATTTG
Found at i:179992 original size:128 final size:128
Alignment explanation
Indices: 179762--180088 Score: 582
Period size: 128 Copynumber: 2.6 Consensus size: 128
179752 AGTAACATAC
179762 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* *
179827 ACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGGGCG
66 ACACTATTCATATCAGTACCTATTATTTCTCAAGGGACTTGAAGGCGCGTTCCCGGGGGAGCG
* * *
179890 CCTTCCATTATTTTGTTAGAGAATATGTTATCATTTCCCTATTATGTCACTCATGTCCCTCGGAG
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
*
179955 ACACTATTCATATCAGTACCTATTATTTCTCAAGGGACTTGAATGCGCGTTCCCGGGGGAGCG
66 ACACTATTCATATCAGTACCTATTATTTCTCAAGGGACTTGAAGGCGCGTTCCCGGGGGAGCG
* *
180018 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTGTTATGTCACTCATGTCCCTTGGGG
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
180083 ACACTA
66 ACACTA
180089 GATGGATTGT
Statistics
Matches: 188, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 188 1.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (128 bp):
CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
ACACTATTCATATCAGTACCTATTATTTCTCAAGGGACTTGAAGGCGCGTTCCCGGGGGAGCG
Found at i:180523 original size:34 final size:34
Alignment explanation
Indices: 180484--180584 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 34
180474 TAAGTTGAAA
* *
180484 TTTAATGTTACATTTCGAATACTATAATTTATAT
1 TTTAATGTTAAATTTCGAATAATATAATTTATAT
*
180518 TTTAATTTTAAATTTCGAAT-A-AT-A-TTAT-T
1 TTTAATGTTAAATTTCGAATAATATAATTTATAT
* * *
180547 TTT-ATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATGTTAAATTTCGAATAATATAATTTATAT
180580 TTTAA
1 TTTAA
180585 AAACATTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
28 15 0.27
29 5 0.09
30 6 0.11
31 2 0.04
32 5 0.09
33 4 0.07
34 19 0.34
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATAATATAATTTATAT
Found at i:180547 original size:28 final size:27
Alignment explanation
Indices: 180515--180585 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 27
180505 CTATAATTTA
180515 TATTTTAATTTTAAATTTCGAATAATAT
1 TATTTT-ATTTTAAATTTCGAATAATAT
*
180543 TATTTTTATTTTAAATTTTGAATAATAT
1 TA-TTTTATTTTAAATTTCGAATAATAT
*
180571 AATTTGTATTTTAAA
1 TATTT-TATTTTAAA
180586 AACATTTATC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 3 0.08
28 32 0.82
29 4 0.10
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (27 bp):
TATTTTATTTTAAATTTCGAATAATAT
Found at i:181134 original size:21 final size:21
Alignment explanation
Indices: 181104--181260 Score: 196
Period size: 21 Copynumber: 7.5 Consensus size: 21
181094 TATGGTATAA
181104 AACCCTGCGGGCTA-GACATGT
1 AACCCTGCGGGCTAGGA-ATGT
181125 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
181146 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
* *
181167 AA-CCTGGCAGGCTAGGAATAT
1 AACCCT-GCGGGCTAGGAATGT
* *
181188 AACCCTGTGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
181209 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
181230 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
181251 AACCCTGCGG
1 AACCCTGCGG
181261 AGATGACATA
Statistics
Matches: 118, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
20 9 0.08
21 98 0.83
22 11 0.09
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:181167 original size:42 final size:42
Alignment explanation
Indices: 181104--181254 Score: 250
Period size: 42 Copynumber: 3.6 Consensus size: 42
181094 TATGGTATAA
*
181104 AACCCTGCGGGCT-AGACATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGA-ATGTAACCTGGCGGGCTAGGAATGT
* *
181146 AACCCTGCGGGCTCGGAATGTAACCTGGCAGGCTAGGAATAT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
*
181188 AACCCTGTGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
181230 AACCCTGCGGGCTCGGAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
181255 CTGCGGAGAT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
42 99 0.98
43 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.32, T:0.19
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:183088 original size:34 final size:31
Alignment explanation
Indices: 183045--183133 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
183035 TTAATAATTC
183045 TAAAAAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
183079 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
183110 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
183134 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.34
33 2 0.04
34 23 0.49
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:183110 original size:31 final size:33
Alignment explanation
Indices: 183045--183124 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 33
183035 TTAATAATTC
*
183045 TAAAAAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
183079 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
183110 TATAAAATATAATAA
1 TA-AAAAAATAATAA
183125 CTATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.24
33 2 0.05
34 23 0.56
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:183919 original size:2 final size:2
Alignment explanation
Indices: 183879--183905 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
183869 ACACACACGC
183879 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
183906 AACTAATAAT
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:188286 original size:2 final size:2
Alignment explanation
Indices: 188279--188306 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
188269 GTTAGAAATA
188279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
188307 GTTTAAGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194007 original size:2 final size:2
Alignment explanation
Indices: 194000--194032 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
193990 ATCAAAATCA
194000 AT AT AT 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 AT AT AT A
194033 CACACCTGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:199236 original size:16 final size:16
Alignment explanation
Indices: 199215--199250 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
199205 ACCTGAAGTA
*
199215 AGTACTAAATATCAAT
1 AGTACTAAATATCAAC
199231 AGTACTAAATATCAAC
1 AGTACTAAATATCAAC
199247 AGTA
1 AGTA
199251 GTTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (16 bp):
AGTACTAAATATCAAC
Found at i:202216 original size:18 final size:18
Alignment explanation
Indices: 202183--202217 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
202173 ATCCCTGTTC
*
202183 TCTTCCTTCTCTTCTTCT
1 TCTTCCTTCTCATCTTCT
*
202201 TCTTCCTTTTCATCTTC
1 TCTTCCTTCTCATCTTC
202218 CTCCATAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTCCTTCTCATCTTCT
Found at i:215114 original size:11 final size:11
Alignment explanation
Indices: 215098--215131 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
215088 TGATCGTTTA
215098 ATTTTAAAATG
1 ATTTTAAAATG
* *
215109 ATTTTAGAATA
1 ATTTTAAAATG
215120 ATTTTAAAATG
1 ATTTTAAAATG
215131 A
1 A
215132 ATTAATTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (11 bp):
ATTTTAAAATG
Found at i:217069 original size:23 final size:23
Alignment explanation
Indices: 217015--217069 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
217005 TTTGTGTTCA
*
217015 ATTCGTTTAGCACTCACGAACAT
1 ATTCGTTTAACACTCACGAACAT
** *
217038 ATTTTTTTAACATTCAC-AGACAT
1 ATTCGTTTAACACTCACGA-ACAT
217061 ATTCGTTTA
1 ATTCGTTTA
217070 GTGACCACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTCGTTTAACACTCACGAACAT
Found at i:222238 original size:20 final size:20
Alignment explanation
Indices: 222213--222260 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
222203 AGAACTGGTA
* *
222213 TGAGTCAACTCGGACCGAAC-
1 TGAGTCAACCCGAACCG-ACT
222233 TGAGTCAACCCGAACCGACT
1 TGAGTCAACCCGAACCGACT
222253 TGAGTCAA
1 TGAGTCAA
222261 TATGAACCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (20 bp):
TGAGTCAACCCGAACCGACT
Found at i:222455 original size:13 final size:14
Alignment explanation
Indices: 222439--222473 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
222429 TAATTTAAAT
*
222439 ATTTATTTAAGTG-
1 ATTTAATTAAGTGC
222452 ATTTAATTAAGTGC
1 ATTTAATTAAGTGC
222466 ATTTAATT
1 ATTTAATT
222474 TGAGGGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (14 bp):
ATTTAATTAAGTGC
Found at i:223099 original size:36 final size:36
Alignment explanation
Indices: 223048--223117 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
223038 AAGTCTCTAC
**
223048 AGGTTCAACTTCGATCAAACTGGTAATTCCTTATAT
1 AGGTTCAACACCGATCAAACTGGTAATTCCTTATAT
*
223084 AGGTTCAACACCGATCAAGCTGGTAATTCCTTAT
1 AGGTTCAACACCGATCAAACTGGTAATTCCTTAT
223118 GGATCTAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (36 bp):
AGGTTCAACACCGATCAAACTGGTAATTCCTTATAT
Found at i:231726 original size:28 final size:28
Alignment explanation
Indices: 231693--231748 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
231683 CCTTTCCATG
231693 ATGAACATGCCTTTGAAACCATTTCATC
1 ATGAACATGCCTTTGAAACCATTTCATC
231721 ATGAACATGCCTTTGAAACCATTTCATC
1 ATGAACATGCCTTTGAAACCATTTCATC
231749 CCATGATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (28 bp):
ATGAACATGCCTTTGAAACCATTTCATC
Found at i:234206 original size:41 final size:41
Alignment explanation
Indices: 234161--234401 Score: 227
Period size: 41 Copynumber: 5.9 Consensus size: 41
234151 CATTTTTTCA
* * *
234161 ACAAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTCTAG
1 ACAAACGCCGCAACAGACTAGTACTTTAGTGGCGTTTTTAT
* * **
234202 ACAAACGCCGCAACAGAGTAGTACTTTAGAGGTATTTTTAT
1 ACAAACGCCGCAACAGACTAGTACTTTAGTGGCGTTTTTAT
* * * *
234243 ACAAACGCCGCTATAGACTTGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCAACAGACTAGTACTTTAGTGGCGTTTTTAT
* * * *
234284 ATAAGCACC-CTATACA-A-TTGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGC-A-ACAGACTAGTACTTTAGTGGCGTTTTTAT
* * * * *
234324 ACAAACACCGCTATACACTTGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCAACAGACTAGTACTTTAGTGGCGTTTTTAT
* * * *
234365 ACAAACGCTGCTATACACTAGTACTTTAGTGGCGTTT
1 ACAAACGCCGCAACAGACTAGTACTTTAGTGGCGTTT
234402 GTATTTATAA
Statistics
Matches: 171, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 31 0.18
41 136 0.80
42 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (41 bp):
ACAAACGCCGCAACAGACTAGTACTTTAGTGGCGTTTTTAT
Found at i:234335 original size:81 final size:82
Alignment explanation
Indices: 234220--234401 Score: 249
Period size: 81 Copynumber: 2.2 Consensus size: 82
234210 CGCAACAGAG
* ** * *
234220 TAGTACTTTAGAGGTATTTTTATACAAACGCCGCTATAGACTTGTACTTTAGTGGCATTTTTATA
1 TAGTACTTTAGTGGCGTTTTTATACAAACACCGCTATACACTTGTACTTTAGTGGCATTTTTATA
* *
234285 TAAGCAC-CCTATACAA
66 CAAACACTCCTATACAA
* *
234301 TTGTACTTTAGTGGCGTTTTTATACAAACACCGCTATACACTTGTACTTTAGTGGCGTTTTTATA
1 TAGTACTTTAGTGGCGTTTTTATACAAACACCGCTATACACTTGTACTTTAGTGGCATTTTTATA
* * *
234366 CAAACGCTGCTATACAC
66 CAAACACTCCTATACAA
234383 TAGTACTTTAGTGGCGTTT
1 TAGTACTTTAGTGGCGTTT
234402 GTATTTATAA
Statistics
Matches: 87, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 62 0.71
82 25 0.29
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (82 bp):
TAGTACTTTAGTGGCGTTTTTATACAAACACCGCTATACACTTGTACTTTAGTGGCATTTTTATA
CAAACACTCCTATACAA
Found at i:234758 original size:41 final size:40
Alignment explanation
Indices: 234693--235111 Score: 255
Period size: 41 Copynumber: 10.2 Consensus size: 40
234683 ATAACATTAA
* *
234693 TGGCGTTTTTCAATAAACGCCGCTAAAACTCATACTTTAG
1 TGGCGTTTTTAAACAAACGCCGCTAAAACTCATACTTTAG
** * *
234733 TGGCGTTTATTCGACAAACGTCGCTAAAGA-TAAGTACTTTAG
1 TGGCGTTT-TTAAACAAACGCCGCTAAA-ACTCA-TACTTTAG
** *
234775 TGGCGTTTTTAAACAAACGCCG-TAATAGGGT-ATA-TATATTG
1 TGGCGTTTTTAAACAAACGCCGCTAA-A-ACTCATACT-T-TAG
* * *
234816 TGGCGTTTTTAGATAAACGCCGTTAAAAC-CTAGTACTTTAG
1 TGGCGTTTTTAAACAAACGCCGCTAAAACTC-A-TACTTTAG
* * * *
234857 AGGCGTTTTATGCAA-AAATGCCGCTAAAACTCGTACTTTAG
1 TGGCGTTTT-T-AAACAAACGCCGCTAAAACTCATACTTTAG
* * ** *
234898 TGGCGTTTGTAAACAAACGCCGCCATAGAA-TTGTTCTTTAG
1 TGGCGTTTTTAAACAAACGCCG-C-TAAAACTCATACTTTAG
** * *
234939 TGGCGTTTTTAAACAAACGCCG-TAATAGGGTACATA-TATCG
1 TGGCGTTTTTAAACAAACGCCGCTAA-A-ACT-CATACTTTAG
* * *
234980 TTGCGTTTTTAAATAAACGCCGCTAAAACCTAATACTTTAG
1 TGGCGTTTTTAAACAAACGCCGCTAAAA-CTCATACTTTAG
*
235021 TGGCGTTTTATTCAA-AAACGCCGCTAAATACTCATACTTTAG
1 TGGCG-TTT-TTAAACAAACGCCGCTAAA-ACTCATACTTTAG
* * * * ** *
235063 TGACGATTTTAGACAAACGTCGCTAAAACCTTGTACTTTAT
1 TGGCGTTTTTAAACAAACGCCGCTAAAA-CTCATACTTTAG
235104 TGGCGTTT
1 TGGCGTTT
235112 AACCATTAAC
Statistics
Matches: 294, Mismatches: 55, Indels: 59
0.72 0.13 0.14
Matches are distributed among these distances:
38 2 0.01
39 4 0.01
40 29 0.10
41 174 0.59
42 77 0.26
43 8 0.03
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (40 bp):
TGGCGTTTTTAAACAAACGCCGCTAAAACTCATACTTTAG
Found at i:234843 original size:123 final size:123
Alignment explanation
Indices: 234693--234919 Score: 302
Period size: 123 Copynumber: 1.8 Consensus size: 123
234683 ATAACATTAA
* * * *
234693 TGGCGTTTTTCAATAAACGCCGCTAAAA-CTCA-TACTTTAGTGGCG-TTTATTCGACAAACGTC
1 TGGCGTTTTTCAATAAACGCCGCTAAAACCT-AGTACTTTAGAGGCGTTTTATGC-AAAAACGCC
*
234755 GCTAAAGA-TAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGTAATAGGGTATATATATTG
64 GCTAAA-ACT-AGTACTTTAGTGGCGTTTGTAAACAAACGCCGTAATAGGGTATATATATTG
* *
234816 TGGCGTTTTT-AGATAAACGCCGTTAAAACCTAGTACTTTAGAGGCGTTTTATGCAAAAATGCCG
1 TGGCGTTTTTCA-ATAAACGCCGCTAAAACCTAGTACTTTAGAGGCGTTTTATGCAAAAACGCCG
*
234880 CTAAAACTCGTACTTTAGTGGCGTTTGTAAACAAACGCCG
65 CTAAAACTAGTACTTTAGTGGCGTTTGTAAACAAACGCCG
234920 CCATAGAATT
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
122 1 0.01
123 57 0.63
124 27 0.30
125 6 0.07
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (123 bp):
TGGCGTTTTTCAATAAACGCCGCTAAAACCTAGTACTTTAGAGGCGTTTTATGCAAAAACGCCGC
TAAAACTAGTACTTTAGTGGCGTTTGTAAACAAACGCCGTAATAGGGTATATATATTG
Found at i:234946 original size:164 final size:162
Alignment explanation
Indices: 234694--235081 Score: 528
Period size: 164 Copynumber: 2.4 Consensus size: 162
234684 TAACATTAAT
* * *
234694 GGCGTTTT-TCAATAAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGTCGCT
1 GGCGTTTTATCAA-AAACGCCGCTAAAACTCATACTTTAGTGGCG-TT-TTAGACAAACGCCGCC
* *
234758 AAAGATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGTAATAGGGTATATATATTGTGGCGTT
63 AAAGATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGTAATAGGGTACATATATCGTGGCGTT
* * *
234823 TTTAGATAAACGCCGTTAAAACCTAGTACTTTAGA
128 TTTAAATAAACGCCGCTAAAACCTAATACTTTAGA
* * *
234858 GGCGTTTTATGCAAAAATGCCGCTAAAACTCGTACTTTAGTGGCGTTTGTAAACAAACGCCGCCA
1 GGCGTTTTAT-CAAAAACGCCGCTAAAACTCATACTTTAGTGGCGTTT-TAGACAAACGCCGCCA
* * * *
234923 TAGA-ATTGTTCTTTAGTGGCGTTTTTAAACAAACGCCGTAATAGGGTACATATATCGTTGCGTT
64 AAGATA-AGTACTTTAGTGGCGTTTTTAAACAAACGCCGTAATAGGGTACATATATCGTGGCGTT
*
234987 TTTAAATAAACGCCGCTAAAACCTAATACTTTAGT
128 TTTAAATAAACGCCGCTAAAACCTAATACTTTAGA
*
235022 GGCGTTTTATTCAAAAACGCCGCTAAATACTCATACTTTAGTGACGATTTTAGACAAACG
1 GGCGTTTTA-TCAAAAACGCCGCTAAA-ACTCATACTTTAGTGGCG-TTTTAGACAAACG
235082 TCGCTAAAAC
Statistics
Matches: 197, Mismatches: 20, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
163 2 0.01
164 133 0.68
165 56 0.28
166 6 0.03
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (162 bp):
GGCGTTTTATCAAAAACGCCGCTAAAACTCATACTTTAGTGGCGTTTTAGACAAACGCCGCCAAA
GATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGTAATAGGGTACATATATCGTGGCGTTTTT
AAATAAACGCCGCTAAAACCTAATACTTTAGA
Found at i:234957 original size:123 final size:123
Alignment explanation
Indices: 234693--234961 Score: 289
Period size: 123 Copynumber: 2.2 Consensus size: 123
234683 ATAACATTAA
* * * * * *
234693 TGGCGTTTTTCAATAAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGTCGCT
1 TGGCGTTTTTAAATAAACGCCGTTAAAACTCATACTTTAGAGGCGTTTATGCGAAAAACGCCGCT
* * **
234758 AAAGATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGTAATAGGGTATATATATTG
66 AAAGATAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAATATATATATTG
* *
234816 TGGCGTTTTTAGATAAACGCCGTTAAAAC-CTAGTACTTTAGAGGCGTTTTATGC-AAAAATGCC
1 TGGCGTTTTTAAATAAACGCCGTTAAAACTC-A-TACTTTAGAGGCG-TTTATGCGAAAAACGCC
* * * *
234879 GCTAAA-ACT-CGTACTTTAGTGGCGTTTGTAAACAAACGCCGCCATAGAAT-TGT-TCTTTAG
63 GCTAAAGA-TAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAATATATAT-ATT-G
*
234939 TGGCGTTTTTAAACAAACGCCGT
1 TGGCGTTTTTAAATAAACGCCGT
234962 AATAGGGTAC
Statistics
Matches: 122, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
121 1 0.01
122 5 0.04
123 85 0.70
124 25 0.20
125 6 0.05
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (123 bp):
TGGCGTTTTTAAATAAACGCCGTTAAAACTCATACTTTAGAGGCGTTTATGCGAAAAACGCCGCT
AAAGATAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCAATAGAATATATATATTG
Found at i:241141 original size:20 final size:20
Alignment explanation
Indices: 241097--241158 Score: 106
Period size: 20 Copynumber: 3.0 Consensus size: 20
241087 TGATTTATTA
*
241097 TTATGGATTTCAAGTTTTTTG
1 TTATGGATTTCAAG-TTTGTG
241118 TTATGGATTTCAAGTTTGTG
1 TTATGGATTTCAAGTTTGTG
241138 TTATGGATTTCAAGTTTGTG
1 TTATGGATTTCAAGTTTGTG
241158 T
1 T
241159 CTTAATTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.19, C:0.05, G:0.23, T:0.53
Consensus pattern (20 bp):
TTATGGATTTCAAGTTTGTG
Found at i:241407 original size:43 final size:43
Alignment explanation
Indices: 241291--241660 Score: 531
Period size: 43 Copynumber: 8.8 Consensus size: 43
241281 GTTTGTATAG
* *
241291 AAAAAC-CCGCTATAAATCTCAACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
*
241333 -AAAACGCCGCTATAGATCT-GACCTTTTGCGGCATTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* * *
241374 AAAAATGCCGCTATAAATCTCGACCTTTAGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* *
241417 AAAAACG-CGTTATAGATCTCGACATTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
241459 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* * *
241502 AAAAACGCTGCTATAAATCTTGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
*
241545 -AAAACGCCGCTATAGATCTCGACCTTTTACGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* * *
241587 AAAAATGCCGCTATAGATCTCGACCTTTTACAGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* *
241630 AAAAATGCCGCTAT--ATCTTGACC-TTTGCGGC
1 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGC
241661 ATTTTTGTTC
Statistics
Matches: 297, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
40 6 0.02
41 33 0.11
42 105 0.35
43 153 0.52
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (43 bp):
AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
Found at i:241517 original size:128 final size:128
Alignment explanation
Indices: 241273--241660 Score: 563
Period size: 128 Copynumber: 3.1 Consensus size: 128
241263 TGAAAGGTAA
* ** * * *
241273 TTAGCGACGTTTGTATAGAAAAACCCGCTATAAATCTCAACCTTTTGCGGCGTTTGTTCC-AAAA
1 TTAGCGGCGTTTGT-TCCAAAAACGCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAA
* *
241337 CGCCGCTATAGATCT-GACCTTTTGCGGCATTTGTTCCAAAAATGCCGCTATAAATCTCGACCT
65 CGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAAATCTTGACCT
* *
241400 TTAGCGGCGTTTGTTCCAAAAACGCGTTATAGATCTCGACATTTTGCGGCGTTTGTTCCAAAAAC
1 TTAGCGGCGTTTGTTCCAAAAACGCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAAC
* *
241465 GCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCTGCTATAAATCTTGACCT
66 GCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAAATCTTGACCT
* *
241528 TTTGCGGCGTTTGTTCC-AAAACGCCGCTATAGATCTCGACCTTTTACGGCGTTTGTTCCAAAAA
1 TTAGCGGCGTTTGTTCCAAAAACG-CGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAA
* * *
241592 TGCCGCTATAGATCTCGACCTTTTACAGCGTTTGTTCCAAAAATGCCGCTAT--ATCTTGACCT
65 CGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAAATCTTGACCT
241654 TT-GCGGC
1 TTAGCGGC
241661 ATTTTTGTTC
Statistics
Matches: 237, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
125 5 0.02
126 50 0.21
127 38 0.16
128 144 0.61
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (128 bp):
TTAGCGGCGTTTGTTCCAAAAACGCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAAC
GCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAAATCTTGACCT
Found at i:241670 original size:85 final size:85
Alignment explanation
Indices: 241291--241660 Score: 520
Period size: 85 Copynumber: 4.4 Consensus size: 85
241281 GTTTGTATAG
*
241291 AAAAAC-CCGCTATAAATCTCAACCTTTTGCGGCGTTTGTTCC-AAAACGCCGCTATAGATCT-G
1 AAAAACGCCGCTAT-AATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
*
241353 ACCTTTTGCGGCATTTGTTCC
65 ACCTTTTGCGGCGTTTGTTCC
* * *
241374 AAAAATGCCGCTATAAATCTCGACCTTTAGCGGCGTTTGTTCCAAAAACG-CGTTATAGATCTCG
1 AAAAACGCCGCTAT-AATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
*
241438 ACATTTTGCGGCGTTTGTTCC
65 ACCTTTTGCGGCGTTTGTTCC
* * *
241459 AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCTGCTATAAATCTTG
1 AAAAACGCCGCTATA-ATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
241524 ACCTTTTGCGGCGTTTGTTCC
65 ACCTTTTGCGGCGTTTGTTCC
* *
241545 -AAAACGCCGCTATAGATCTCGACCTTTTACGGCGTTTGTTCCAAAAATGCCGCTATAGATCTCG
1 AAAAACGCCGCTATA-ATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
* *
241609 ACCTTTTACAGCGTTTGTTCC
65 ACCTTTTGCGGCGTTTGTTCC
* *
241630 AAAAATGCCGCTAT-ATCTTGACC-TTTGCGGC
1 AAAAACGCCGCTATAATCTCGACCTTTTGCGGC
241661 ATTTTTGTTC
Statistics
Matches: 258, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
83 12 0.05
84 54 0.21
85 150 0.58
86 42 0.16
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (85 bp):
AAAAACGCCGCTATAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGA
CCTTTTGCGGCGTTTGTTCC
Found at i:244524 original size:18 final size:20
Alignment explanation
Indices: 244473--244525 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
244463 AGTTTGTTTG
*
244473 GAATTTTATCATTTTTAAAT
1 GAATTTCATCATTTTTAAAT
244493 GAATTTCATCATTTTT-AAT
1 GAATTTCATCATTTTTAAAT
244512 GAATTTC-TCATTTT
1 GAATTTCATCATTTT
244526 AGCTTAGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 7 0.22
19 10 0.31
20 15 0.47
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (20 bp):
GAATTTCATCATTTTTAAAT
Found at i:245082 original size:43 final size:42
Alignment explanation
Indices: 245021--245293 Score: 269
Period size: 43 Copynumber: 6.5 Consensus size: 42
245011 GTTTCGATTA
* *
245021 GCGGCATTTGTTCTAAAAACGCCGTTATAGAATTGACCTTTT
1 GCGGCGTTTGTTCTAAAAACGCCGCTATAGAATTGACCTTTT
*
245063 GCGGCGTTTTGTT-TAAAAAATGCCGCTATAGAATTGACCTTTT
1 GCGGCG-TTTGTTCT-AAAAACGCCGCTATAGAATTGACCTTTT
* * *
245106 GTGGCGTTTGTTCAAAAAACG-CGCTATAG-ATCTGACATTTT
1 GCGGCGTTTGTTCTAAAAACGCCGCTATAGAAT-TGACCTTTT
* *
245147 GCGGCGTTTGTTCTGAAAACGCCTCTATAG-ATTCGGACCTTTT
1 GCGGCGTTTGTTCTAAAAACGCCGCTATAGAATT--GACCTTTT
* * *
245190 GCGGCGTTTGTATCT-AAAATGCC-ATATAGAA-CGACCTTTT
1 GCGGCGTTTGT-TCTAAAAACGCCGCTATAGAATTGACCTTTT
* * *
245230 GTGGCGTTTTTGTTCTAAAAACG-CGCTATA-TATCTGACATTTT
1 GCGGCG--TTTGTTCTAAAAACGCCGCTATAGAAT-TGACCTTTT
245273 GCGGCG-TTGTTCTAAAAACGC
1 GCGGCGTTTGTTCTAAAAACGC
245294 TTCTTGCGGC
Statistics
Matches: 193, Mismatches: 22, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
40 29 0.15
41 40 0.21
42 46 0.24
43 75 0.39
44 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (42 bp):
GCGGCGTTTGTTCTAAAAACGCCGCTATAGAATTGACCTTTT
Found at i:245186 original size:84 final size:84
Alignment explanation
Indices: 245021--245293 Score: 278
Period size: 84 Copynumber: 3.3 Consensus size: 84
245011 GTTTCGATTA
* * *
245021 GCGGCATTTGTTCTAAAAACGCCGTTATAGAAT-TGACCTTTTGCGGCGTTTTGTT-TAAAAAAT
1 GCGGCGTTTGTTCTAAAAACG-CGCTATAG-ATCTGACCTTTTGCGGCGTTTTGTTCT-AAAAAC
245084 GCCGCTATAGAATT-GACCTTTT
63 GCCGCTATAG-ATTCGACCTTTT
* * * *
245106 GTGGCGTTTGTTCAAAAAACGCGCTATAGATCTGACATTTTGCGGCG-TTTGTTCTGAAAACGCC
1 GCGGCGTTTGTTCTAAAAACGCGCTATAGATCTGACCTTTTGCGGCGTTTTGTTCTAAAAACGCC
*
245170 TCTATAGATTCGGACCTTTT
66 GCTATAGATTC-GACCTTTT
* * *
245190 GCGGCGTTTGTATCT-AAAATGC-CATATAGAAC-GACCTTTTGTGGCGTTTTTGTTCTAAAAAC
1 GCGGCGTTTGT-TCTAAAAACGCGC-TATAGATCTGACCTTTTGCGGCG-TTTTGTTCTAAAAAC
* *
245252 G-CGCTATATA-TCTGACATTTT
63 GCCGCTATAGATTC-GACCTTTT
245273 GCGGCG-TTGTTCTAAAAACGC
1 GCGGCGTTTGTTCTAAAAACGC
245294 TTCTTGCGGC
Statistics
Matches: 159, Mismatches: 20, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
81 3 0.02
82 13 0.08
83 49 0.31
84 60 0.38
85 34 0.21
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (84 bp):
GCGGCGTTTGTTCTAAAAACGCGCTATAGATCTGACCTTTTGCGGCGTTTTGTTCTAAAAACGCC
GCTATAGATTCGACCTTTT
Found at i:245250 original size:126 final size:126
Alignment explanation
Indices: 245021--245293 Score: 378
Period size: 126 Copynumber: 2.2 Consensus size: 126
245011 GTTTCGATTA
* *
245021 GCGGCATTTGTTCTAAAAACGCCGTTATAGAATTGACCTTTTGCGGCGTTTTGTTTAAAAAATGC
1 GCGGCGTTTGTTCTAAAAACGCCGTTATAGAATTGACCTTTTGCGGCGTTTTGTATAAAAAATGC
* *
245086 CGCTATAGAATTGACCTTTTGTGGCGTTTGTTCAAAAAACGCGCTATAGATCTGACATTTT
66 CGATATAGAATCGACCTTTTGTGGCGTTTGTTCAAAAAACGCGCTATAGATCTGACATTTT
* **
245147 GCGGCGTTTGTTCTGAAAACGCC-TCTATAG-ATTCGGACCTTTTGCGGCG-TTTGTATCTAAAA
1 GCGGCGTTTGTTCTAAAAACGCCGT-TATAGAATT--GACCTTTTGCGGCGTTTTGTATAAAAAA
* *
245209 TGCC-ATATAGAA-CGACCTTTTGTGGCGTTTTTGTTCTAAAAACGCGCTATATATCTGACATTT
63 TGCCGATATAGAATCGACCTTTTGTGGCG--TTTGTTCAAAAAACGCGCTATAGATCTGACATTT
245272 T
126 T
245273 GCGGCG-TTGTTCTAAAAACGC
1 GCGGCGTTTGTTCTAAAAACGC
245294 TTCTTGCGGC
Statistics
Matches: 132, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
124 14 0.11
125 25 0.19
126 79 0.60
127 14 0.11
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (126 bp):
GCGGCGTTTGTTCTAAAAACGCCGTTATAGAATTGACCTTTTGCGGCGTTTTGTATAAAAAATGC
CGATATAGAATCGACCTTTTGTGGCGTTTGTTCAAAAAACGCGCTATAGATCTGACATTTT
Found at i:247347 original size:18 final size:19
Alignment explanation
Indices: 247318--247353 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
247308 ACACACACAT
247318 TATATGCATATAAAATTAC
1 TATATGCATATAAAATTAC
*
247337 TATAT-CATATAGAATTA
1 TATATGCATATAAAATTA
247354 TGGGGATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (19 bp):
TATATGCATATAAAATTAC
Found at i:248919 original size:20 final size:20
Alignment explanation
Indices: 248894--248943 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
248884 ATGGTTTTAT
248894 GTCTTCAAAGGTCTGCAGAC
1 GTCTTCAAAGGTCTGCAGAC
248914 GTCTTCAAAGGTCTGCAGAC
1 GTCTTCAAAGGTCTGCAGAC
248934 GTCTTCAAAG
1 GTCTTCAAAG
248944 AACATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (20 bp):
GTCTTCAAAGGTCTGCAGAC
Found at i:248993 original size:22 final size:22
Alignment explanation
Indices: 248965--249218 Score: 154
Period size: 22 Copynumber: 11.5 Consensus size: 22
248955 TATTTAAATC
248965 TATTTTAAAATATAGATTGATT
1 TATTTTAAAATATAGATTGATT
*
248987 TATTTTAAAATGA-A-A---AAT
1 TATTTTAAAAT-ATAGATTGATT
249005 TATTTTAAAATATAGATTGATT
1 TATTTTAAAATATAGATTGATT
**
249027 TATTTTAAAATAT-GA---AAA
1 TATTTTAAAATATAGATTGATT
* *
249045 AAATTTAAAATATAGATTGATT
1 TATTTTAAAATATAGATTGATT
*
249067 TATTTTAAAATATAAAAAAAATATGGATT
1 TATTTTAAAATAT-----AGAT-T-GATT
* * *** *
249096 GATTTATTTTAAAATATAAAAAAAAT
1 TATTT----TAAAATATAGATTGATT
*
249122 TATTTTAAAATATAGATT-AAT
1 TATTTTAAAATATAGATTGATT
249143 TATTTTAAAAATATTA-ATTGATT
1 TATTTT-AAAATA-TAGATTGATT
249166 TATTTTAAAATATAGATTGATT
1 TATTTTAAAATATAGATTGATT
* *
249188 TATTTTAAAATTTGGATTGATT
1 TATTTTAAAATATAGATTGATT
*
249210 T-TTTAAAAA
1 TATTTTAAAA
249219 ATTTATTATT
Statistics
Matches: 183, Mismatches: 24, Indels: 51
0.71 0.09 0.20
Matches are distributed among these distances:
17 1 0.01
18 26 0.14
19 3 0.02
21 21 0.11
22 92 0.50
23 11 0.06
26 6 0.03
27 3 0.02
28 4 0.02
29 8 0.04
33 8 0.04
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
TATTTTAAAATATAGATTGATT
Found at i:249011 original size:40 final size:40
Alignment explanation
Indices: 248960--249197 Score: 237
Period size: 40 Copynumber: 5.9 Consensus size: 40
248950 AAAATTATTT
248960 AAATCTATTTTAAAATATAGATTGATTTATTTT-AAAATGAA
1 AAAT-TATTTTAAAATATAGATTGATTTATTTTAAAAAT-AA
249001 AAATTATTTTAAAATATAGATTGATTTATTTTAAAATATGAA
1 AAATTATTTTAAAATATAGATTGATTTATTTTAAAA-AT-AA
* *
249043 AAA--AATTTAAAATATAGATTGATTTATTTT-AAAATAT
1 AAATTATTTTAAAATATAGATTGATTTATTTTAAAAATAA
*
249080 AAA--A----AAAATATGGATTGATTTATTTTAAAATATAAAAA
1 AAATTATTTTAAAATATAGATTGATTTATTTTAAAA-AT---AA
*
249118 AAATTATTTTAAAATATAGATT-AATTATTTTAAAAATATTA
1 AAATTATTTTAAAATATAGATTGATTTATTTTAAAAATA--A
*
249159 ATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAA
1 A---AATTATTTTAAAATATAGATTGATTTATTTTAAAA
249198 TTTGGATTGA
Statistics
Matches: 170, Mismatches: 8, Indels: 34
0.80 0.04 0.16
Matches are distributed among these distances:
33 21 0.12
34 3 0.02
35 2 0.01
37 5 0.03
38 6 0.04
39 4 0.02
40 55 0.32
41 9 0.05
42 10 0.06
43 12 0.07
44 31 0.18
45 12 0.07
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.44
Consensus pattern (40 bp):
AAATTATTTTAAAATATAGATTGATTTATTTTAAAAATAA
Found at i:249027 original size:18 final size:18
Alignment explanation
Indices: 248966--249027 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
248956 ATTTAAATCT
248966 ATTTTAAAATATAGATTG
1 ATTTTAAAATATAGATTG
* *
248984 ATTTATTTTAAAATGAAAAATT-
1 ----ATTTTAAAAT-ATAGATTG
249006 ATTTTAAAATATAGATTG
1 ATTTTAAAATATAGATTG
249024 ATTT
1 ATTT
249028 ATTTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 5 0.15
18 14 0.41
22 10 0.29
23 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
ATTTTAAAATATAGATTG
Found at i:249109 original size:33 final size:33
Alignment explanation
Indices: 249011--249121 Score: 150
Period size: 33 Copynumber: 3.2 Consensus size: 33
249001 AAATTATTTT
249011 AAAATATAGATTGATTTATTTTAAAATATGAAAAAAA
1 AAAATATAGATTGATTTATTTTAAAATAT----AAAA
249048 TTTAAAATATAGATTGATTTATTTTAAAATATAAAA
1 ---AAAATATAGATTGATTTATTTTAAAATATAAAA
*
249084 AAAATATGGATTGATTTATTTTAAAATATAAAA
1 AAAATATAGATTGATTTATTTTAAAATATAAAA
249117 AAAAT
1 AAAAT
249122 TATTTTAAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
33 37 0.53
36 4 0.06
40 29 0.41
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (33 bp):
AAAATATAGATTGATTTATTTTAAAATATAAAA
Found at i:249219 original size:66 final size:67
Alignment explanation
Indices: 249082--249220 Score: 174
Period size: 66 Copynumber: 2.1 Consensus size: 67
249072 TAAAATATAA
*
249082 AAAAAATATGGATTGATTTATTTTAAAATATAAAAAAAATTATTTTAAAATATAGATTAATTATT
1 AAAAAATATGAATTGATTTATTTTAAAATATAAAAAAAATTATTTTAAAATATAGATTAATTATT
249147 TT
66 TT
* * *** * * * *
249149 -AAAAATATTAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATTTGGATTGATT-TT
1 AAAAAATATGAATTGATTTATTTTAAAATATAAAAAAAATTATTTTAAAATATAGATTAATTATT
249212 TT
66 TT
249214 AAAAAAT
1 AAAAAAT
249221 TTATTATTGT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 4 0.07
66 57 0.93
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (67 bp):
AAAAAATATGAATTGATTTATTTTAAAATATAAAAAAAATTATTTTAAAATATAGATTAATTATT
TT
Found at i:249451 original size:23 final size:23
Alignment explanation
Indices: 249421--249471 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
249411 TCTTCTGCTA
249421 CAGATGCTTGCAGATATGATCCG
1 CAGATGCTTGCAGATATGATCCG
*
249444 CAGATGCTTGCAGATATGATCCT
1 CAGATGCTTGCAGATATGATCCG
249467 CAGAT
1 CAGAT
249472 TACAGACCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (23 bp):
CAGATGCTTGCAGATATGATCCG
Found at i:254563 original size:76 final size:76
Alignment explanation
Indices: 254437--254587 Score: 302
Period size: 76 Copynumber: 2.0 Consensus size: 76
254427 TATCGTCGGG
254437 AAAAACTTAAATTCACCGCCGATCGTTGTTCCGTTTACGACACCTCCTGCACCATCGTGTTCCTT
1 AAAAACTTAAATTCACCGCCGATCGTTGTTCCGTTTACGACACCTCCTGCACCATCGTGTTCCTT
254502 GTGTCGTTGCA
66 GTGTCGTTGCA
254513 AAAAACTTAAATTCACCGCCGATCGTTGTTCCGTTTACGACACCTCCTGCACCATCGTGTTCCTT
1 AAAAACTTAAATTCACCGCCGATCGTTGTTCCGTTTACGACACCTCCTGCACCATCGTGTTCCTT
254578 GTGTCGTTGC
66 GTGTCGTTGC
254588 GAGTCCGCCG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (76 bp):
AAAAACTTAAATTCACCGCCGATCGTTGTTCCGTTTACGACACCTCCTGCACCATCGTGTTCCTT
GTGTCGTTGCA
Found at i:254858 original size:9 final size:10
Alignment explanation
Indices: 254825--254890 Score: 75
Period size: 10 Copynumber: 6.8 Consensus size: 10
254815 GCTGCTAGAA
254825 AACCGGTTTG
1 AACCGGTTTG
*
254835 -ACCAGTTTTG
1 AACC-GGTTTG
254845 AACCGGTTTG
1 AACCGGTTTG
*
254855 -ACCGGTCTG
1 AACCGGTTTG
254864 AACC-GTTTG
1 AACCGGTTTG
*
254873 AACCGGTCTG
1 AACCGGTTTG
254883 AACCGGTT
1 AACCGGTT
254891 GACCCGACCC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
9 19 0.41
10 24 0.52
11 3 0.07
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:254867 original size:19 final size:19
Alignment explanation
Indices: 254825--254894 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
254815 GCTGCTAGAA
* *
254825 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
254845 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
254864 AACC-GTTTGAACCGGTCTG
1 AACCGGTTTG-ACCGGTCTG
254883 AACCGG-TTGACC
1 AACCGGTTTGACC
254895 CGACCCGACT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.17
19 24 0.52
20 14 0.30
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:254910 original size:17 final size:17
Alignment explanation
Indices: 254888--254945 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
254878 GTCTGAACCG
254888 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
254905 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
254922 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
254939 GTTGACC
1 GTTGACC
254946 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:256781 original size:15 final size:15
Alignment explanation
Indices: 256761--256842 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
256751 TTCTAGAAAA
256761 TGAATTACTGGAATT
1 TGAATTACTGGAATT
256776 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
256791 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
256806 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
256821 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
256835 TGAATTAC
1 TGAATTAC
256843 ATTTATGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:256795 original size:30 final size:30
Alignment explanation
Indices: 256761--256842 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
256751 TTCTAGAAAA
**
256761 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
256791 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
256821 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
256843 ATTTATGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:256807 original size:45 final size:44
Alignment explanation
Indices: 256756--256842 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
256746 TGGTTTTCTA
**
256756 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
256801 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
256843 ATTTATGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:256854 original size:20 final size:20
Alignment explanation
Indices: 256828--256894 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
256818 ATTTGAATTC
256828 TGGAAAATGAATTACATTTA
1 TGGAAAATGAATTACATTTA
* *
256848 TGTAAAATGAATTACATTTC
1 TGGAAAATGAATTACATTTA
*
256868 TGGAAAATGAATTACATTTC
1 TGGAAAATGAATTACATTTA
256888 TGGAAAA
1 TGGAAAA
256895 CATCTGGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.34
Consensus pattern (20 bp):
TGGAAAATGAATTACATTTA
Found at i:257109 original size:23 final size:27
Alignment explanation
Indices: 257054--257115 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
257044 TTTACTAAAA
257054 TATTATTGAAATATATAAATAATATAT
1 TATTATTGAAATATATAAATAATATAT
* *
257081 TCATTATT-AAATATATAAAAAATTTAT
1 T-ATTATTGAAATATATAAATAATATAT
257108 TATATATT
1 TAT-TATT
257116 ATTAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
27 23 0.74
28 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TATTATTGAAATATATAAATAATATAT
Found at i:257153 original size:29 final size:28
Alignment explanation
Indices: 257105--257220 Score: 93
Period size: 29 Copynumber: 4.2 Consensus size: 28
257095 ATAAAAAATT
*
257105 TATTATATATTATTAAAATAAAAATATAA
1 TATT-TATATTATTATAATAAAAATATAA
*
257134 TATCTTATATTATTATAAT-ATAATGAT--
1 TAT-TTATATTATTATAATAAAAAT-ATAA
*
257161 TATTTATA-TA--ATATTAAAAATATAA
1 TATTTATATTATTATAATAAAAATATAA
*
257186 TA-TTATATTATTATTATTAATAAATATAAA
1 TATTTATATTATTA-TAATAA-AAATAT-AA
257216 TATTT
1 TATTT
257221 TAATAATTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
23 6 0.08
24 9 0.13
25 6 0.08
26 5 0.07
27 4 0.06
28 10 0.14
29 24 0.34
30 5 0.07
31 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTATATTATTATAATAAAAATATAA
Found at i:257176 original size:14 final size:14
Alignment explanation
Indices: 257140--257196 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
257130 ATAATATCTT
257140 ATATTATTATAATATA
1 ATATTATT-T-ATATA
257156 ATGATTATTTATATA
1 AT-ATTATTTATATA
***
257171 ATATTAAAAATATA
1 ATATTATTTATATA
257185 ATATTATATTAT
1 ATATTAT-TTAT
257197 TATTATTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
14 15 0.45
15 9 0.27
16 3 0.09
17 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
ATATTATTTATATA
Found at i:257452 original size:42 final size:42
Alignment explanation
Indices: 257405--257524 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
257395 ATGAATTACA
* *
257405 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
257447 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
257489 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAA
257525 TTCGGAAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
Found at i:258016 original size:25 final size:25
Alignment explanation
Indices: 257982--258032 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
257972 TTATTATTAG
257982 TCAATGAGATTTAGGGGTTGTTTGA
1 TCAATGAGATTTAGGGGTTGTTTGA
258007 TCAATGAGATTTAGGGGTTGTTTGA
1 TCAATGAGATTTAGGGGTTGTTTGA
258032 T
1 T
258033 TAAATCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.41
Consensus pattern (25 bp):
TCAATGAGATTTAGGGGTTGTTTGA
Found at i:258075 original size:17 final size:17
Alignment explanation
Indices: 258053--258088 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
258043 TGATTTAGCG
*
258053 TTGAATGATTCAATGGC
1 TTGAATGATTCAAAGGC
258070 TTGAATGATTCAAAGGC
1 TTGAATGATTCAAAGGC
258087 TT
1 TT
258089 TGTATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (17 bp):
TTGAATGATTCAAAGGC
Found at i:260497 original size:30 final size:30
Alignment explanation
Indices: 260456--260524 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
260446 AACCTATCTA
*
260456 TCCACAAGAGTAGAAGATGAAAATGATAAG
1 TCCAGAAGAGTAGAAGATGAAAATGATAAG
260486 TCCAGAAGAGTAGAAGATGAAAATGATAAG
1 TCCAGAAGAGTAGAAGATGAAAATGATAAG
260516 TCCAGAAGA
1 TCCAGAAGA
260525 CAAGATTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.25, T:0.16
Consensus pattern (30 bp):
TCCAGAAGAGTAGAAGATGAAAATGATAAG
Found at i:261702 original size:21 final size:21
Alignment explanation
Indices: 261678--261727 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
261668 ATTTTTTTTC
*
261678 TCATGGTTGAATTTGACATCG
1 TCATGATTGAATTTGACATCG
* *
261699 TCATAATTGGATTTGACATCG
1 TCATGATTGAATTTGACATCG
*
261720 CCATGATT
1 TCATGATT
261728 AATCAAGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (21 bp):
TCATGATTGAATTTGACATCG
Found at i:268578 original size:20 final size:22
Alignment explanation
Indices: 268545--268588 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
268535 CACTCGCTGC
268545 ATCCATCCACCCAT-TA-ATAT
1 ATCCATCCACCCATATATATAT
* *
268565 ATCCATCTATCCATATATATAT
1 ATCCATCCACCCATATATATAT
268587 AT
1 AT
268589 ATATTATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (22 bp):
ATCCATCCACCCATATATATAT
Found at i:269172 original size:17 final size:17
Alignment explanation
Indices: 269123--269172 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
269113 TTGTTCATGT
269123 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
269140 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
269154 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
269171 TT
1 TT
269173 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:274200 original size:6 final size:6
Alignment explanation
Indices: 274189--274235 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
274179 ACTCGCGCAC
274189 GCACAA GCACAA GCACAA GCACAA GCACAA GCACAA GCACAA GCACA
1 GCACAA GCACAA GCACAA GCACAA GCACAA GCACAA GCACAA GCACA
274236 CACACTACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.49, C:0.34, G:0.17, T:0.00
Consensus pattern (6 bp):
GCACAA
Found at i:276589 original size:18 final size:18
Alignment explanation
Indices: 276563--276597 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
276553 TCGAAAGGAC
*
276563 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
276581 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
276598 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:281808 original size:18 final size:18
Alignment explanation
Indices: 281782--281816 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
281772 TCGAAAGGAC
*
281782 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
281800 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
281817 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:285468 original size:9 final size:9
Alignment explanation
Indices: 285454--285483 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
285444 GCAGTTGTAA
285454 TTTTAAATT
1 TTTTAAATT
*
285463 TTTTAAAAT
1 TTTTAAATT
285472 TTTTAAATT
1 TTTTAAATT
285481 TTT
1 TTT
285484 CATACAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTAAATT
Found at i:287603 original size:42 final size:44
Alignment explanation
Indices: 287533--287632 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 44
287523 TTTTTTGAAT
* * *
287533 AAACGCCACAAAAAGTTATGATATATAGCGGCGTGTCTAGA-AA
1 AAACGCCGCAAAAGGTCATGATATATAGCGGCGTGTCTAGATAA
* * * * *
287576 AAACGCCGCAAAAGGTCA-GATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATGATATATAGCGGCGTGTCTAGATAA
287619 AAACGCCGCAAAAG
1 AAACGCCGCAAAAG
287633 AGAAGACATA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 18 0.38
43 30 0.62
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (44 bp):
AAACGCCGCAAAAGGTCATGATATATAGCGGCGTGTCTAGATAA
Found at i:287623 original size:43 final size:43
Alignment explanation
Indices: 287576--287756 Score: 208
Period size: 43 Copynumber: 4.2 Consensus size: 43
287566 TGTCTAGAAA
* *
287576 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACAC
* *
287619 AAACGCCGCAAAAGAG-AAGACATATA-CTGGCGTTTTTGGACAC
1 AAACGCCGCAAAAG-GTCAGACCTATAGC-GGCGTTTTTGGACAC
** *
287662 AAACGCCGCAAAAGGTCAGACCTATAATGGCGTTTTTGAACAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACAC
** *
287705 AAACGCCGCAAAAATTCA-AGCCTATAGCGGCGTTTATT-GATAC
1 AAACGCCGCAAAAGGTCAGA-CCTATAGCGGCGTTT-TTGGACAC
287748 AAACGCCGC
1 AAACGCCGC
287757 TAATTACCTT
Statistics
Matches: 118, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
42 3 0.03
43 112 0.95
44 3 0.03
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACAC
Found at i:292144 original size:125 final size:125
Alignment explanation
Indices: 291991--292371 Score: 459
Period size: 125 Copynumber: 3.0 Consensus size: 125
291981 ACACTTAAAA
* *
291991 TTTGTAAACACAAACGCCACTATAGTACAAATGTATAGCGGCGCTTGAATAAAAACGCCACTAAA
1 TTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCCACTAAA
* *
292056 GTACGACTCTTTAGCGGCATTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCG
66 GTACGACTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCG
* *
292116 TTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTAAA
1 TTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCCACTAAA
* * *
292181 GTACG-CGCCTTTAGTGGCGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGGCG
66 GTACGAC-TCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCG
* * * ** * *
292241 TTTGTATA-A-AAACGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAA-ACACAAACGCCACT
1 TTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTG-AATA-A-AAACGCCACT
* * * * * * *
292303 ATAGTAC-A-TGTGTATAACGACGTTTGTATAAAAATGCCACTAAAGTACAATTCTATAGCGGCG
63 AAAGTACGACTCT-T-TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCG
292366 TTTGTA
1 TTTGTA
292372 TAAAAATGCC
Statistics
Matches: 221, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
123 31 0.14
124 6 0.03
125 184 0.83
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (125 bp):
TTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCCACTAAA
GTACGACTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCG
Found at i:292280 original size:166 final size:166
Alignment explanation
Indices: 292006--292411 Score: 605
Period size: 166 Copynumber: 2.4 Consensus size: 166
291996 AAACACAAAC
* *** * * * *
292006 GCCACTATAGTACAAATGTATAGCGGCGCTTGAATAAAAACGCCACTAAAGTACGACTCTTTAGC
1 GCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGC
* *
292071 GGCATTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCAC
66 GGCGTTTGTATAAAAACGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCAC
*
292136 TATAGTACAAGTGTATAACGGCGTTTGAATAAAAAT
131 TATAGTACAAGTGTATAACGACGTTTGAATAAAAAT
** * * *
292172 GCCACTAAAGTACGCGCCTTTAGTGGCGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTAGC
1 GCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGC
*
292237 GGCGTTTGTATAAAAACGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCAC
66 GGCGTTTGTATAAAAACGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCAC
* *
292302 TATAGTACATGTGTATAACGACGTTTGTATAAAAAT
131 TATAGTACAAGTGTATAACGACGTTTGAATAAAAAT
** * *
292338 GCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTTGC
1 GCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGC
292403 GGCGTTTGT
66 GGCGTTTGT
292412 TGAAAAAATG
Statistics
Matches: 212, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
166 212 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (166 bp):
GCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGC
GGCGTTTGTATAAAAACGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCAC
TATAGTACAAGTGTATAACGACGTTTGAATAAAAAT
Found at i:292372 original size:125 final size:124
Alignment explanation
Indices: 292026--292411 Score: 420
Period size: 125 Copynumber: 3.1 Consensus size: 124
292016 TACAAATGTA
* * * * * *
292026 TAGCGGCGCTTG-AATAAAAACGCCACTAAAGTACGAC-TCTTTAGCGGCATTTGTATAAAAATG
1 TAGCGGCGTTTGTAATAAAAACGCCACTAAAGTAC-ACGCCTATAACGACGTTTGTATAAAAATG
* * * * * * *
292089 CCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTA
65 CCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A-AAACGCCACTAAATTACGAGTCTT
* * * * ** *
292151 TAACGGCGTTTG-AATAAAAATGCCACTAAAGTACGCGCCTTTAGTGGCGTTTGTATAAAAATGC
1 TAGCGGCGTTTGTAATAAAAACGCCACTAAAGTACACGCCTATAACGACGTTTGTATAAAAATGC
* *
292215 CACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTATGAGTCTT
66 CACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTACGAGTCTT
* * **
292274 TAGCGGCGTTTGTAA-ACACAAACGCCACTATAGTACATGTGTATAACGACGTTTGTATAAAAAT
1 TAGCGGCGTTTGTAATA-A-AAACGCCACTAAAGTACACGCCTATAACGACGTTTGTATAAAAAT
* * * *
292338 GCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTT
64 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTACGAGTCTT
*
292399 TTGCGGCGTTTGT
1 TAGCGGCGTTTGT
292412 TGAAAAAATG
Statistics
Matches: 223, Mismatches: 34, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
123 30 0.13
124 5 0.02
125 188 0.84
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (124 bp):
TAGCGGCGTTTGTAATAAAAACGCCACTAAAGTACACGCCTATAACGACGTTTGTATAAAAATGC
CACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTACGAGTCTT
Found at i:292418 original size:41 final size:41
Alignment explanation
Indices: 292026--292425 Score: 426
Period size: 41 Copynumber: 9.6 Consensus size: 41
292016 TACAAATGTA
* * * *
292026 TAGCGGCGCTTGAATAAAAACGCCACTAAAGTACGACTCTT
1 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTT
* *
292067 TAGCGGCATTTGTATAAAAATGCCACTAAATTACGAGTCTT
1 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTT
* * * * * *
292108 TAGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTA
1 TAGCGGCGTTTGTATA-A-AAATGCCACTAAAGTACGAGTCTT
* * * *
292151 TAACGGCGTTTGAATAAAAATGCCACTAAAGTACGCGCCTT
1 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTT
* *
292192 TAGTGGCGTTTGTATAAAAATGCCACTAAAGTATGAGTCTT
1 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTT
* * *
292233 TAGCGGCGTTTGTATAAAAACGCCACTAAATTATGAGTCTT
1 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTT
* * * * *
292274 TAGCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTA
1 TAGCGGCGTTTGTATA-A-AAATGCCACTAAAGTACGA-GTCTT
* * * * *
292317 TAACGACGTTTGTATAAAAATGCCACTAAAGTACAATTCTA
1 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTT
*
292358 TAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTT
1 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTT
*
292399 TTGCGGCGTTTGT-TGAAAAAATGCCAC
1 TAGCGGCGTTTGTAT--AAAAATGCCAC
292426 AATAGATGAA
Statistics
Matches: 298, Mismatches: 53, Indels: 15
0.81 0.14 0.04
Matches are distributed among these distances:
40 1 0.00
41 219 0.73
42 17 0.06
43 61 0.20
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTT
Found at i:294760 original size:50 final size:50
Alignment explanation
Indices: 294666--294761 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
294656 CTATTTTTTG
* *
294666 GTACTGCACTTTTTATCGTTGTTGGCAGCTAATCACCTTCTGTCACATTA
1 GTACTGCACTTTTTATCGTTGTTGACAGCTAATCACCCTCTGTCACATTA
* * *
294716 GTACTGTACTTTTTATCGTTGTTGATAGTTAATCACCACT-TGTCAC
1 GTACTGCACTTTTTATCGTTGTTGACAGCTAATCACC-CTCTGTCAC
294762 CGGTTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 39 0.98
51 1 0.03
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.42
Consensus pattern (50 bp):
GTACTGCACTTTTTATCGTTGTTGACAGCTAATCACCCTCTGTCACATTA
Found at i:302379 original size:20 final size:20
Alignment explanation
Indices: 302364--302402 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
302354 AATAATTCTT
*
302364 ATGATCTTGGTCTAATTTTG
1 ATGATCTTGATCTAATTTTG
302384 ATGATCTTGATCTAATTTT
1 ATGATCTTGATCTAATTTT
302403 TTAGTGGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (20 bp):
ATGATCTTGATCTAATTTTG
Done.