Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002812.1 Hibiscus syriacus cultivar Beakdansim tig00005787_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: 199342
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3169 original size:21 final size:22
Alignment explanation
Indices: 3145--3192 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3135 ATTTCCTTGG
3145 CTAATTTCTCTC-TTGC-AACTC
1 CTAATTTCTCTCTTTGCAAAC-C
*
3166 CTAA-TTCTTTCTTTGCAAACC
1 CTAATTTCTCTCTTTGCAAACC
3187 CTAATT
1 CTAATT
3193 AACCTTCCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.23, C:0.29, G:0.04, T:0.44
Consensus pattern (22 bp):
CTAATTTCTCTCTTTGCAAACC
Found at i:6129 original size:30 final size:30
Alignment explanation
Indices: 6093--6159 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
6083 AGAATGCAGT
6093 TAAATTTTAGGAATTTATGTACTCTTTCTA
1 TAAATTTTAGGAATTTATGTACTCTTTCTA
6123 TAAATTTTAGGAATTTATGTACTCTTTCTA
1 TAAATTTTAGGAATTTATGTACTCTTTCTA
6153 TAAATTT
1 TAAATTT
6160 CATAGTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (30 bp):
TAAATTTTAGGAATTTATGTACTCTTTCTA
Found at i:12366 original size:27 final size:28
Alignment explanation
Indices: 12317--12371 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
12307 TTTTTAGCTT
12317 TTATTTTAAAAATTATTTAAAAACTTTA
1 TTATTTTAAAAATTATTTAAAAACTTTA
* *
12345 TTATTTTAAAAA-TATTTTAAAATTTTA
1 TTATTTTAAAAATTATTTAAAAACTTTA
12372 AAAATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTATTTTAAAAATTATTTAAAAACTTTA
Found at i:12687 original size:16 final size:16
Alignment explanation
Indices: 12668--12698 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12658 TTTTTCAAAG
12668 TTAAAAAATATTAAAT
1 TTAAAAAATATTAAAT
*
12684 TTAAAGAATATTAAA
1 TTAAAAAATATTAAA
12699 ATGTTTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TTAAAAAATATTAAAT
Found at i:17530 original size:95 final size:94
Alignment explanation
Indices: 17363--17542 Score: 272
Period size: 95 Copynumber: 1.9 Consensus size: 94
17353 GATTCAATCA
*
17363 GATACATGGTAAGGGTATCGATACCAAGCAACATCGAATCTAAAATCGATATCAATACCAGAAGG
1 GATACATGGTAAAGGTATCGATACCAAGCAACATCGAATCTAAAATCGATATCAATACCAGAAGG
17428 GGATATCGATACCATAGTATGGTAGTACC
66 GGATATCGATACCATAGTATGGTAGTACC
* * * * *
17457 GATACCATGGTAAATGTATCGATACCAGGCAACATCGAA-CTTAAAATCGATATCGATATCGGAA
1 GATA-CATGGTAAAGGTATCGATACCAAGCAACATCGAATC-TAAAATCGATATCAATACCAGAA
*
17521 GGGGGTATCGATACCATAGTAT
64 GGGGATATCGATACCATAGTAT
17543 ATAAGTATTG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
94 5 0.06
95 72 0.94
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (94 bp):
GATACATGGTAAAGGTATCGATACCAAGCAACATCGAATCTAAAATCGATATCAATACCAGAAGG
GGATATCGATACCATAGTATGGTAGTACC
Found at i:17989 original size:57 final size:57
Alignment explanation
Indices: 17895--18916 Score: 1499
Period size: 57 Copynumber: 17.8 Consensus size: 57
17885 ATTACCAAAT
* * *
17895 GGCACTTCGTGTACAAAAATGTTAAGAAATTCATACTAAGTATATGAATTTCCATATTG
1 GGCACTTCGTGTGC-AAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
17954 GGCACTTCGTGTGCAAAAGTTAATAAATTCATACTAAGTGTATGAATTTCTGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
18011 GGCACTTCATGTGCAAAAATGTTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGC-AAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
18070 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAACTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
** *
18127 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTAAAAATTTCCGTATTA
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
18184 GGCAATTCGTGTACAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * *
18241 GACACTTCGTGTGTAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCGGTATTA
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * **
18298 GACAATTCGTGTGCAAAAGTTAAGAATTTCATACTAAGTGTATGAATTTCTGTATCC
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
18355 GGAACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
18412 GGCACTTCGTGTACAAAAGTTAAGAAATTCATACAAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * *
18469 GGCACTTCGTCTGTAAAAGTTAAGAGATTCATACAAAGT-TATGAATTTCCTTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
18525 GGCAC-TCGTGTGCAAAAGTTAAGATATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * *
18581 GACACTTCTTGTGCAAAAATGTTTAGAAATTCATATTAAGTGTATGAATTTCTGTATTG
1 GGCACTTCGTGTGC-AAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* **
18640 GGCACTTCGTGTGCAAAAGTTGAGAAATTCATACTAAGTGTATGAATTTCAATATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
18697 GGCACTTCGAGTGTAAAAGTTAAAAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
18754 GACACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTTTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* **
18811 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTTTGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * *
18868 GGTACTTTGTGTGCAAATTGTTAAGAGATTCATACTAAGTGTATGAATT
1 GGCACTTCGTGTGCAAA-AGTTAAGAAATTCATACTAAGTGTATGAATT
18917 ATCAGATGAG
Statistics
Matches: 870, Mismatches: 86, Indels: 15
0.90 0.09 0.02
Matches are distributed among these distances:
55 29 0.03
56 41 0.05
57 643 0.74
58 48 0.06
59 109 0.13
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (57 bp):
GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
Found at i:23026 original size:73 final size:74
Alignment explanation
Indices: 22888--23030 Score: 200
Period size: 73 Copynumber: 1.9 Consensus size: 74
22878 GAAAATTTCA
* **
22888 TTCATGATTCTTTAGTTGCTTTAAAGCATAAACCAAAACTTTTCCTCTTGTACGAACACGTATCC
1 TTCATGATTC-TTAGTTGCTTTAAAGCATAAACCAAAACTTTTCCTCTTGTACAAACACACATCC
22953 CAAACAAAAT
65 CAAACAAAAT
* * *
22963 TTCATGATTC-TAGTTGTTTTAATA-CATAAACCAAAACTTTTCCTCTTGTATAAATACACATCC
1 TTCATGATTCTTAGTTGCTTTAA-AGCATAAACCAAAACTTTTCCTCTTGTACAAACACACATCC
23026 CAAAC
65 CAAAC
23031 CATTTTAAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
73 50 0.82
74 1 0.02
75 10 0.16
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (74 bp):
TTCATGATTCTTAGTTGCTTTAAAGCATAAACCAAAACTTTTCCTCTTGTACAAACACACATCCC
AAACAAAAT
Found at i:26946 original size:21 final size:21
Alignment explanation
Indices: 26922--26989 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
26912 GTTAAACATA
26922 TTGAAAGAAAAATAAAGTAAC
1 TTGAAAGAAAAATAAAGTAAC
** * * * *
26943 TTGAAACCATACT-TAG-AATT
1 TTGAAAGAAAAATAAAGTAA-C
26963 TTGAAAGAAAAATAAAGTAAC
1 TTGAAAGAAAAATAAAGTAAC
26984 TTGAAA
1 TTGAAA
26990 AATAAAAAGA
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
19 2 0.06
20 11 0.34
21 17 0.53
22 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.25
Consensus pattern (21 bp):
TTGAAAGAAAAATAAAGTAAC
Found at i:27270 original size:23 final size:23
Alignment explanation
Indices: 27244--27288 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
27234 CTACTTCGAT
27244 CTTCAAGAAGTTGTTGACTGGGC
1 CTTCAAGAAGTTGTTGACTGGGC
* *
27267 CTTCTAGAAGTTGTTGATTGGG
1 CTTCAAGAAGTTGTTGACTGGG
27289 TACCATGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.36
Consensus pattern (23 bp):
CTTCAAGAAGTTGTTGACTGGGC
Found at i:28673 original size:16 final size:15
Alignment explanation
Indices: 28648--28677 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28638 TTCAAAGTTA
28648 TAAAAATATTAAATT
1 TAAAAATATTAAATT
28663 TAAAGAATATTAAAT
1 TAAA-AATATTAAAT
28678 GTTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TAAAAATATTAAATT
Found at i:31547 original size:19 final size:19
Alignment explanation
Indices: 31523--31568 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
31513 AAAGGCCAAT
* *
31523 GGAGCATACGAGAAGGTGA
1 GGAGCAGACGAGAACGTGA
*
31542 GGAGCAGATGAGAACGTGA
1 GGAGCAGACGAGAACGTGA
31561 GGAGCAGA
1 GGAGCAGA
31569 TTTATCTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.43, T:0.09
Consensus pattern (19 bp):
GGAGCAGACGAGAACGTGA
Found at i:31569 original size:19 final size:19
Alignment explanation
Indices: 31532--31569 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31522 TGGAGCATAC
*
31532 GAGAAGGTGAGGAGCAGAT
1 GAGAACGTGAGGAGCAGAT
31551 GAGAACGTGAGGAGCAGAT
1 GAGAACGTGAGGAGCAGAT
31570 TTATCTCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.45, T:0.11
Consensus pattern (19 bp):
GAGAACGTGAGGAGCAGAT
Found at i:39608 original size:15 final size:15
Alignment explanation
Indices: 39573--39609 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
39563 AGAGGAAGAA
39573 GTTGATTCTGAATAT
1 GTTGATTCTGAATAT
**
39588 ACTGATTCTGAATAT
1 GTTGATTCTGAATAT
39603 GTTGATT
1 GTTGATT
39610 GTCTGAATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (15 bp):
GTTGATTCTGAATAT
Found at i:45394 original size:36 final size:36
Alignment explanation
Indices: 45326--45394 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
45316 ACTTTTAAAT
* *
45326 AAAGTAAATAAAAACTTTAAAAAGTAAAAAAGTGAG
1 AAAGGAAATAAAAACTTTAAAAAATAAAAAAGTGAG
*
45362 AAAGGAAA-AAAAACTTTAAAAAAATAACAAAGT
1 AAAGGAAATAAAAACTTT-AAAAAATAAAAAAGT
45395 AATTCGAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 9 0.31
36 20 0.69
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.17
Consensus pattern (36 bp):
AAAGGAAATAAAAACTTTAAAAAATAAAAAAGTGAG
Found at i:49342 original size:22 final size:21
Alignment explanation
Indices: 49315--49367 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
49305 ATATTTCTAG
49315 AAACTATATAAAGTGTTTTAAA
1 AAACTATATAAAGTGTTTT-AA
* *
49337 AAACTATAGT-ATGTGTTTTCA
1 AAACTATA-TAAAGTGTTTTAA
49358 AAACTATATA
1 AAACTATATA
49368 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 9 0.33
22 16 0.59
23 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (21 bp):
AAACTATATAAAGTGTTTTAA
Found at i:62602 original size:13 final size:13
Alignment explanation
Indices: 62584--62609 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62574 TACATACGCG
62584 CATATGAAGACTA
1 CATATGAAGACTA
62597 CATATGAAGACTA
1 CATATGAAGACTA
62610 TTCAACTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
CATATGAAGACTA
Found at i:65943 original size:27 final size:27
Alignment explanation
Indices: 65886--65942 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
65876 GAAAGGACTG
* ** *
65886 AAATACCCTTAAATCGTAAAATGACCA
1 AAATACCCCTAAAGAGTAAAATAACCA
65913 AAATACCCCTAAAGAGTAAAATAATCCA
1 AAATACCCCTAAAGAGTAAAATAA-CCA
65941 AA
1 AA
65943 TTATCTCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (27 bp):
AAATACCCCTAAAGAGTAAAATAACCA
Found at i:83930 original size:23 final size:23
Alignment explanation
Indices: 83903--83948 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
83893 CTCCACGCCA
* *
83903 CTGCTGATTGGATCTTCTAGAAG
1 CTGCTGAATGGACCTTCTAGAAG
*
83926 CTGCTGAATGGGCCTTCTAGAAG
1 CTGCTGAATGGACCTTCTAGAAG
83949 TTGTTGACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (23 bp):
CTGCTGAATGGACCTTCTAGAAG
Found at i:84040 original size:23 final size:23
Alignment explanation
Indices: 83972--84040 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
83962 GTCATGTCAC
* *
83972 CTACCATGTCATCACTACATCAA
1 CTACCATGTCATCACCACATCAG
* * **
83995 CTGCCATGTCATAACCATGTCAG
1 CTACCATGTCATCACCACATCAG
84018 CTACCATGTCATCACCACATCAG
1 CTACCATGTCATCACCACATCAG
84041 ACGTTGACTA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.35, G:0.10, T:0.25
Consensus pattern (23 bp):
CTACCATGTCATCACCACATCAG
Found at i:85248 original size:10 final size:10
Alignment explanation
Indices: 85233--85264 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
85223 AAAAATTTAC
85233 TATTTTAAAA
1 TATTTTAAAA
85243 TATTTT-AAA
1 TATTTTAAAA
85252 -ATTTTAAAA
1 TATTTTAAAA
85261 TATT
1 TATT
85265 AAATTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.25
9 6 0.30
10 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:86993 original size:95 final size:95
Alignment explanation
Indices: 86825--87049 Score: 333
Period size: 95 Copynumber: 2.4 Consensus size: 95
86815 TACCAAGGAG
* ** *
86825 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTCACATCGAATCTAAAATGGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAACATCGAATCAAAAATGGGTATCGAT
** *
86890 ACTGGAAGGGGGTATTGGTACCATAATATA
66 ACCCGAAGGGGGTATCGGTACCATAATATA
* * * *
86920 GTAGTATCAATACCATTGTAAGGGTATCGATACTAGGAAACATCGAATCAAAAATTGGTATTGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAACATCGAATCAAAAATGGGTATCGAT
*
86985 ACCCGAAGGGGGTATCGGTACCATAGTATA
66 ACCCGAAGGGGGTATCGGTACCATAATATA
*
87015 GTAGTATCGATACCATGGTAGGGGTATCGATACTA
1 GTAGTATCGATACCATGGTAAGGGTATCGATACTA
87050 TAGAGCTAGA
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 115 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAACATCGAATCAAAAATGGGTATCGAT
ACCCGAAGGGGGTATCGGTACCATAATATA
Found at i:87459 original size:55 final size:55
Alignment explanation
Indices: 87380--87541 Score: 200
Period size: 55 Copynumber: 2.9 Consensus size: 55
87370 ATGGCACTAG
* **
87380 GTGTGCAAAAATTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGAACTTT
1 GTGTGCAAAAA--TAAGAAATTCATACTAAGTGTATGAATTTCAGTATGGGAACCAT
*
87437 GTGTGCAAAAATAAGAAATTCATACTAAGTGTATGAATTTCAGTATGGGCACCAT
1 GTGTGCAAAAATAAGAAATTCATACTAAGTGTATGAATTTCAGTATGGGAACCAT
* ** * * * *
87492 GGGTG-TGAACTGAGAAATTCATACTAAGTGTATTAATTTCCGTATGGGAA
1 GTGTGCAAAAATAAGAAATTCATACTAAGTGTATGAATTTCAGTATGGGAA
87542 ATATATGTGA
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 38 0.41
55 44 0.47
57 11 0.12
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (55 bp):
GTGTGCAAAAATAAGAAATTCATACTAAGTGTATGAATTTCAGTATGGGAACCAT
Found at i:88160 original size:68 final size:68
Alignment explanation
Indices: 87751--88142 Score: 622
Period size: 68 Copynumber: 5.8 Consensus size: 68
87741 AAAAGATTAT
* * * *
87751 AGGCCTAACTGTGCTAATGACATAAAAGTGTCATTTATGCCAGTTATATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
87816 TTG
66 TTG
*
87819 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGTCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
87884 TTG
66 TTG
* *
87887 AGGCCTAACTGTGCAAATAACAGAAAGGTGTCATTTATGCCAGTTAGATAAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
87952 TTG
66 TTG
* *
87955 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGGCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
88020 TTG
66 TTG
* * * * *
88023 AGGCCTAACTGTGCAAATGAAAGAAATGTTTCATTTATGCAAGTTAGATGAAAGGGTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
88088 TTG
66 TTG
* * * *
88091 AGGCCTAATTGTGGAATTGGCAGAAAGGTGTCATTTATGCCAGTTAGATGAA
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
88143 CGATTAAATA
Statistics
Matches: 298, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 298 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:88231 original size:81 final size:81
Alignment explanation
Indices: 88092--88488 Score: 521
Period size: 81 Copynumber: 4.9 Consensus size: 81
88082 GTGCCTTTGA
* * * * *
88092 GGCCTAATTGTGGAATTGGCAGAAAGGTGTCATTTATGCCAGTTAGATGAACGATTAAATACAGT
1 GGCCTAACTGTGCAATTGGAAGAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAATACAGT
*
88157 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAATAAT
* * * *
88173 GGCCTAACTATGTAATTGGAAGAAATGTGTCATTTATGCCAGTTAAATGAACGGTTAAATACCGT
1 GGCCTAACTGTGCAATTGGAAGAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAATACAGT
88238 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * *
88254 AGCCTAACTGTGCAATTGGCAGAAATGTGTCATTTATGCCAGTTTGATGAACGGTTAAATACAGT
1 GGCCTAACTGTGCAATTGGAAGAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAATACAGT
88319 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * **
88335 GGCCTAACTGTGTAATT-GATAGAAAGGTCTCATTTATTCCAGTTAGATGAACGGTTAAATATTG
1 GGCCTAACTGTGCAATTGGA-AGAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAATACAG
88399 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
* * * * * *
88416 GGCCTAAATGTGCAATT-GACAGAAATGTGTCAATTATG-TAGTTATATGAACGGTTAAACACTG
1 GGCCTAACTGTGCAATTGGA-AGAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAATACAG
*
88479 TTGATTAAAA
65 TTGAGTAAAA
88489 TATTGAAGCT
Statistics
Matches: 278, Mismatches: 37, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
80 31 0.11
81 247 0.89
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (81 bp):
GGCCTAACTGTGCAATTGGAAGAAATGTGTCATTTATGCCAGTTAGATGAACGGTTAAATACAGT
TGAGTAAAAGAATAAT
Found at i:94147 original size:24 final size:25
Alignment explanation
Indices: 94114--94165 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
94104 ATCAGCAAAG
*
94114 AAATTGAAGCACTC-AAAAGAAGAA
1 AAATTCAAGCACTCAAAAAGAAGAA
94138 AAATTCAAGCACTCAAAAAGAAGAA
1 AAATTCAAGCACTCAAAAAGAAGAA
94163 AAA
1 AAA
94166 AGAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.12
Consensus pattern (25 bp):
AAATTCAAGCACTCAAAAAGAAGAA
Found at i:99694 original size:75 final size:75
Alignment explanation
Indices: 99550--99695 Score: 247
Period size: 75 Copynumber: 1.9 Consensus size: 75
99540 AAAATATTTC
* *
99550 TTTCATGATTCTCTAGTTGCTTTAAAGCATAAACCATAACTTTTCCTCTTGTAAGAACACACATT
1 TTTCATGATTCTCTAGTTGCTTTAAAGCATAAACCAAAACTTTTCCTCTTGTAAGAACACACATC
99615 TCAAACGAAA
66 TCAAACGAAA
* **
99625 TTTCATGATTCTCTAGTTGCTTTAAAGCATAAACCAAAACTTTTCCTCTTGTACGAACAGGCATC
1 TTTCATGATTCTCTAGTTGCTTTAAAGCATAAACCAAAACTTTTCCTCTTGTAAGAACACACATC
99690 TCAAAC
66 TCAAAC
99696 CATTATGAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (75 bp):
TTTCATGATTCTCTAGTTGCTTTAAAGCATAAACCAAAACTTTTCCTCTTGTAAGAACACACATC
TCAAACGAAA
Found at i:103265 original size:20 final size:20
Alignment explanation
Indices: 103206--103258 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
103196 AACCGCCGCT
103206 AAGTGTGTTCACATTAAGTC
1 AAGTGTGTTCACATTAAGTC
103226 AAGTGTGTTCACATTAAGTC
1 AAGTGTGTTCACATTAAGTC
103246 AAGTGTGTTCACA
1 AAGTGTGTTCACA
103259 GGAAGTCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (20 bp):
AAGTGTGTTCACATTAAGTC
Found at i:111147 original size:18 final size:19
Alignment explanation
Indices: 111125--111167 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
111115 TGGTAAAAAA
111125 AATTAAAATAA-TAAAAGC
1 AATTAAAATAAGTAAAAGC
*
111143 GATT-AAATAAGTAAAAGC
1 AATTAAAATAAGTAAAAGC
111161 AATTAAA
1 AATTAAA
111168 GTAAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.63, C:0.05, G:0.09, T:0.23
Consensus pattern (19 bp):
AATTAAAATAAGTAAAAGC
Found at i:125216 original size:3 final size:3
Alignment explanation
Indices: 125208--125292 Score: 125
Period size: 3 Copynumber: 27.7 Consensus size: 3
125198 TTATTTATTA
*
125208 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* *
125255 AAT AAT TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
125293 ATTTAAATGA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
3 68 0.92
4 6 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:125553 original size:76 final size:76
Alignment explanation
Indices: 125419--126366 Score: 1711
Period size: 76 Copynumber: 12.5 Consensus size: 76
125409 GATGGAAATG
*
125419 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
125484 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
125495 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
125560 CCCGAATGCTT
66 CCCGAAGGCTT
125571 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
125636 CCCGAAGGCTT
66 CCCGAAGGCTT
125647 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
125712 CCCGAAGGCTT
66 CCCGAAGGCTT
125723 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
125788 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
125799 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCTG-AGGTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGC
*
125863 TCCCGAATGCTT
65 TCCCGAAGGCTT
125875 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
125940 CCCGAAGGCTTT
66 CCCGAAGGC-TT
*
125952 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
126016 CCCGAAGGCTT
66 CCCGAAGGCTT
*
126027 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
126092 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
126103 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
126168 CCCGAAGGCTT
66 CCCGAAGGCTT
126179 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
126244 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
126255 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
126320 CCCGAAGGTTTT
66 CCCGAAGG-CTT
126332 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
126367 TGGGAAATAG
Statistics
Matches: 843, Mismatches: 24, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
75 60 0.07
76 688 0.82
77 95 0.11
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:129815 original size:116 final size:114
Alignment explanation
Indices: 129588--129807 Score: 325
Period size: 116 Copynumber: 1.9 Consensus size: 114
129578 GATCATGCAG
* **
129588 TTCATCTTTCAATTCCAATGATAGGTTCTGGGGTTCCTACCAAATTAGATCAGATAACTCAAAGA
1 TTCATCTTTCAATTCCAATGATAGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
129653 ACACTTCCAGAAGATGCTATTGGGTCTCCTTGTTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCAAA
* * *
129702 TTCATCTTTCAGA-TCCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATTAGATAACTCAA
1 TTCATCTTTCA-ATTCCAATGATAGG--TTCTGGGGTTCATACCAAACCAGATCAGATAACTCAA
*
129766 AGAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTAC
63 AGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTAC
129808 TTTGAGCACA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
114 22 0.23
115 1 0.01
116 71 0.76
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAATTCCAATGATAGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCAAA
Found at i:132128 original size:15 final size:15
Alignment explanation
Indices: 132099--132139 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
132089 CTTGATTCAA
*
132099 TTTTCCTTC-TTTTT
1 TTTTCTTTCTTTTTT
132113 TTTTCTTTCTTTTTT
1 TTTTCTTTCTTTTTT
132128 TTTTCTTTCTTT
1 TTTTCTTTCTTT
132140 GCTGGATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTCTTTTTT
Found at i:136789 original size:20 final size:21
Alignment explanation
Indices: 136742--136790 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
136732 AAAAAATAAT
*
136742 AAAA-AATAAAAAATTGAAAG
1 AAAAGAATTAAAAATTGAAAG
*
136762 AAAAGAATTAAAAATT-AAAT
1 AAAAGAATTAAAAATTGAAAG
*
136782 AAATGAATT
1 AAAAGAATT
136791 TTTAATTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (21 bp):
AAAAGAATTAAAAATTGAAAG
Found at i:139063 original size:3 final size:3
Alignment explanation
Indices: 139055--139172 Score: 168
Period size: 3 Copynumber: 39.7 Consensus size: 3
139045 TTATTTATTA
*
139055 AAT AAT AAT AAT -AT ATAT AAT ATT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
139099 AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
139147 AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
139173 ATTTAAATGA
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
2 4 0.04
3 95 0.93
4 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:140314 original size:75 final size:75
Alignment explanation
Indices: 140191--140372 Score: 193
Period size: 75 Copynumber: 2.4 Consensus size: 75
140181 TATAAATAAA
* * * *
140191 GTCAAATATCAAGACTCAAACCAAAATATTAAGTTTAGAACAATAAAATCCATAAGCAAATCACA
1 GTCAAATATCAAGACTCAAACCAAAATATTAACTCTAAAACAATAAAATCCATAAGCAAACCACA
140256 ATATTAAAAT
66 ATATTAAAAT
* * * * * * ** *
140266 GTCAAATATCAATATTCAAACTACAATATTAACTCTAAAATAATAAAATCTATAATTAAACCATA
1 GTCAAATATCAAGACTCAAACCAAAATATTAACTCTAAAACAATAAAATCCATAAGCAAACCACA
*
140331 ATATTAAAGT
66 ATATTAAAAT
* * * * *
140341 GTCAAATCTTAATACTGAAACCATAATATTAA
1 GTCAAATATCAAGACTCAAACCAAAATATTAA
140373 GTTTAGAAAA
Statistics
Matches: 87, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
75 87 1.00
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (75 bp):
GTCAAATATCAAGACTCAAACCAAAATATTAACTCTAAAACAATAAAATCCATAAGCAAACCACA
ATATTAAAAT
Found at i:166709 original size:20 final size:22
Alignment explanation
Indices: 166670--166710 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
166660 TCACCATTTA
166670 TCTTCTTCTTCATCTCCTTGTTT
1 TCTTCTTCTTCA-CTCCTTGTTT
166693 TCTTCTTCTTC-CT-CTTGT
1 TCTTCTTCTTCACTCCTTGT
166711 GAGTGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
23 11 0.61
ACGTcount: A:0.02, C:0.32, G:0.05, T:0.61
Consensus pattern (22 bp):
TCTTCTTCTTCACTCCTTGTTT
Found at i:170823 original size:45 final size:45
Alignment explanation
Indices: 170772--171093 Score: 348
Period size: 45 Copynumber: 7.1 Consensus size: 45
170762 AAATGAATGA
* ** *
170772 ATAAATGAAATGCATAATGAG-ACATTATCATAATGAAAGGATGAC
1 ATAAATGAAATGCATAATG-GTGCATTATCAGCATGAAAGGATGCC
* * * * *
170817 ATAAATGAAATGTATAATGATGGATTATCGGCATAAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCAGCATGAAAGGATGCC
170862 ATAAATGAAATGCATAATGGTGCATTAT-AGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCA-GCATGAAAGGATGCC
170907 ATAAATGAAATGCATAATGGTGCATTAT-AGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCA-GCATGAAAGGATGCC
* ** * *
170952 ATAAATAAAATAAATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCAGCATGAAAGGATGCC
* * * *
170997 ATAAATGAAATGTATAACGGTGCATTAAT-GGCATGGAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATT-ATCAGCATGAAAGGATGCC
* ** * *
171042 GTAAATGAAAATGCATAACAGTGCATTAT-AGGCATGAAATGATGCT
1 ATAAATG-AAATGCATAATGGTGCATTATCA-GCATGAAAGGATGCC
171088 ATAAAT
1 ATAAAT
171094 AAAAATAAAG
Statistics
Matches: 240, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
45 204 0.85
46 36 0.15
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.25
Consensus pattern (45 bp):
ATAAATGAAATGCATAATGGTGCATTATCAGCATGAAAGGATGCC
Found at i:170979 original size:135 final size:135
Alignment explanation
Indices: 170772--171102 Score: 425
Period size: 135 Copynumber: 2.4 Consensus size: 135
170762 AAATGAATGA
* ** * * ** *
170772 ATAAATGAAATGCATAATGAG-ACATTATCA-TAATGAAAGGATGACATAAATGAAATGTATAAT
1 ATAAATGAAATGCATAATG-GTGCATTAT-AGGCATGAAAGGATGCCATAAATAAAATAAATAAC
* *
170835 GATGGATTATCGGCATAAAAGGATGCCATAAATGAAATGCATAATGGTGCATT-ATAGGCATGAA
64 GATGCATTATCGGCATAAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAT-GGCATGAA
170899 AGGATGCC
128 AGGATGCC
*
170907 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCCATAAATAAAATAAATAACGG
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCCATAAATAAAATAAATAACGA
* * *
170972 TGCATTATCGGCATGAAAGGATGCCATAAATGAAATGTATAACGGTGCATTAATGGCATGGAAGG
66 TGCATTATCGGCATAAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAATGGCATGAAAGG
171037 ATGCC
131 ATGCC
* ** * *
171042 GTAAATGAAAATGCATAACAGTGCATTATAGGCATGAAATGATGCTATAAATAAAAATAAA
1 ATAAATG-AAATGCATAATGGTGCATTATAGGCATGAAAGGATGCCATAAAT-AAAATAAA
171103 GAATAATGGG
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
134 2 0.01
135 120 0.70
136 42 0.24
137 8 0.05
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.24
Consensus pattern (135 bp):
ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCCATAAATAAAATAAATAACGA
TGCATTATCGGCATAAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAATGGCATGAAAGG
ATGCC
Found at i:175529 original size:22 final size:21
Alignment explanation
Indices: 175479--175529 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
175469 CTTCAAGTGG
*
175479 TAAGGCTATAATTTATGGCCA
1 TAAGACTATAATTTATGGCCA
* *
175500 TAAAACTATAATTTATGTGGCA
1 TAAGACTATAATTTATG-GCCA
175522 TAAGACTA
1 TAAGACTA
175530 GCCTTTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (21 bp):
TAAGACTATAATTTATGGCCA
Found at i:188953 original size:25 final size:27
Alignment explanation
Indices: 188915--188974 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
188905 CCCTATGGGG
*
188915 AAAATAACCAAAATGCC-CTTAAGTGT
1 AAAATAACCAAAATGCCTCTGAAGTGT
*
188941 AAAATGACC-AAATGCCTCTGAAGTGT
1 AAAATAACCAAAATGCCTCTGAAGTGT
188967 -AAATAACC
1 AAAATAACC
188975 TAAAGTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (27 bp):
AAAATAACCAAAATGCCTCTGAAGTGT
Found at i:191543 original size:40 final size:39
Alignment explanation
Indices: 191343--191529 Score: 230
Period size: 39 Copynumber: 4.8 Consensus size: 39
191333 GAAAAATAAA
* * * *
191343 AAATTCAACAATTTATTTCCTTTTACAAAACATAAATAT
1 AAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGAT
* * * *
191382 AAATTCAACGATTTATTTTCTTTTACAAAATAAAAAGAT
1 AAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGAT
* * * *
191421 AAATCTAACGATTTATTTTCTTTTATAAAACAGAATGAT
1 AAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGAT
* *
191460 AAATCCAACGATTTATTTCCGTTTACAAAACAGAAAAAT
1 AAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGAT
*
191499 AAATCCAAATGATTTATTTCCTTTTACAAAA
1 AAATCC-AACGATTTATTTCCTTTTACAAAA
191530 TGAGGAAATA
Statistics
Matches: 128, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 106 0.83
40 22 0.17
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (39 bp):
AAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGAT
Found at i:191549 original size:28 final size:28
Alignment explanation
Indices: 191517--191572 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
191507 ATGATTTATT
** *
191517 TCCTTTTACAAAATGAGGAAATAAATCA
1 TCCTTTTACAAAACAAGAAAATAAATCA
*
191545 TCCTTTTACAGAACAAGAAAATAAATCA
1 TCCTTTTACAAAACAAGAAAATAAATCA
191573 AATGATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (28 bp):
TCCTTTTACAAAACAAGAAAATAAATCA
Found at i:191661 original size:39 final size:38
Alignment explanation
Indices: 191596--191760 Score: 174
Period size: 39 Copynumber: 4.3 Consensus size: 38
191586 TTTTATTTTC
*
191596 TTTCTTTTACAAAATAGGAAACTAAATCCAAAGATTTA
1 TTTCTTTTACAAAATAGGAAAATAAATCCAAAGATTTA
*
191634 TTTCCTTTTTACAATATA-GAAAATAAATCCAACA-ATTTA
1 TTT-C-TTTTACAAAATAGGAAAATAAATCCAA-AGATTTA
** * * * *
191673 TTTCTTTTACAAACCAGTAAACTAAAT-TATATGATTTA
1 TTTCTTTTACAAAATAGGAAAATAAATCCA-AAGATTTA
* *
191711 TTTACTTTTTCAAAATAGGAAAATAAATCCAACGATTTA
1 TTT-CTTTTACAAAATAGGAAAATAAATCCAAAGATTTA
191750 TTTCTTTTACA
1 TTTCTTTTACA
191761 TATAATAATC
Statistics
Matches: 102, Mismatches: 17, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
37 10 0.10
38 28 0.27
39 51 0.50
40 13 0.13
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (38 bp):
TTTCTTTTACAAAATAGGAAAATAAATCCAAAGATTTA
Found at i:191695 original size:77 final size:77
Alignment explanation
Indices: 191596--191760 Score: 226
Period size: 77 Copynumber: 2.1 Consensus size: 77
191586 TTTTATTTTC
* * *
191596 TTTCTTTTACAAAATAGGAAACTAAATCCA-AAGATTTATTTCCTTTTTACAATATA-GAAAATA
1 TTTCTTTTACAAAACAGGAAACTAAAT-CATAAGATTTATTTACTTTTT-CAAAATAGGAAAATA
191659 AATCCAACAATTTA
64 AATCCAACAATTTA
* * * *
191673 TTTCTTTTACAAACCAGTAAACTAAATTATATGATTTATTTACTTTTTCAAAATAGGAAAATAAA
1 TTTCTTTTACAAAACAGGAAACTAAATCATAAGATTTATTTACTTTTTCAAAATAGGAAAATAAA
*
191738 TCCAACGATTTA
66 TCCAACAATTTA
191750 TTTCTTTTACA
1 TTTCTTTTACA
191761 TATAATAATC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
76 7 0.09
77 71 0.91
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (77 bp):
TTTCTTTTACAAAACAGGAAACTAAATCATAAGATTTATTTACTTTTTCAAAATAGGAAAATAAA
TCCAACAATTTA
Found at i:191984 original size:40 final size:41
Alignment explanation
Indices: 191881--192031 Score: 180
Period size: 44 Copynumber: 3.6 Consensus size: 41
191871 GACTCTCAGG
191881 AAAATAAATTCAACAATTTATTTCCTTTTACATAATAGGAAAATA
1 AAAATAAATTCAACAATTTATTTCCTTTTAC--AATA-GAAAA-A
*
191926 AAAAT-TATTCAACAATTTATTTCCTTTTACAA-AGAAAAA
1 AAAATAAATTCAACAATTTATTTCCTTTTACAATAGAAAAA
* * * *
191965 AAAATAAATCCAACGATTTATTTCCTTTTAAAAATAGATATAAG
1 AAAATAAATTCAACAATTTATTTCCTTTT-ACAATAGA-A-AAA
192009 AAAATAAATTCAACAATTTATTT
1 AAAATAAATTCAACAATTTATTT
192032 TTTATTTAGG
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
39 6 0.06
40 25 0.27
41 4 0.04
42 5 0.05
43 1 0.01
44 47 0.51
45 5 0.05
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (41 bp):
AAAATAAATTCAACAATTTATTTCCTTTTACAATAGAAAAA
Found at i:192103 original size:58 final size:59
Alignment explanation
Indices: 192048--192171 Score: 171
Period size: 57 Copynumber: 2.1 Consensus size: 59
192038 TAGGATTCCC
* * *
192048 AAAAAAATTAAATTTAACAATTTATT-TCATTTAACAAAATAGAA-CATTTAAGATTCT
1 AAAAAAAATAAATTTAACAATGTATTAACATTTAACAAAATAGAATCATTTAAGATTCT
* * * *
192105 TAAGAAAATAAATTTAACAATGTATTAACTTTTTACAAAATAGAATCATTTAAGATTCT
1 AAAAAAAATAAATTTAACAATGTATTAACATTTAACAAAATAGAATCATTTAAGATTCT
192164 AAAAAAAA
1 AAAAAAAA
192172 ATATGAACAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 22 0.39
58 15 0.27
59 19 0.34
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (59 bp):
AAAAAAAATAAATTTAACAATGTATTAACATTTAACAAAATAGAATCATTTAAGATTCT
Found at i:192300 original size:58 final size:58
Alignment explanation
Indices: 192238--192381 Score: 168
Period size: 57 Copynumber: 2.5 Consensus size: 58
192228 TAATTTGTAG
192238 AATTTATTTTTCTTACAAAGTTA-AAGTCATTCAAGATT-TCCAAAGAAATAAATTCAAA
1 AATTTATTTTTCTTACAAAGTTAGAA-TCATTCAAGATTCT-CAAAGAAATAAATTCAAA
* * * * * * *
192296 AATTTATTTAT-TTACCAAGTTAGAATCATTTAATATTCTGAAGGAAATAAATTCAAC
1 AATTTATTTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAAAGAAATAAATTCAAA
* *
192353 AATCTATTTTCCTTACAAAGTTAGAATCA
1 AATTTATTTTTCTTACAAAGTTAGAATCA
192382 ACGCAAGATT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
57 43 0.60
58 29 0.40
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (58 bp):
AATTTATTTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAAAGAAATAAATTCAAA
Found at i:192706 original size:14 final size:15
Alignment explanation
Indices: 192687--192719 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
192677 GTTATATGGT
192687 AATAATACCAT-AAC
1 AATAATACCATGAAC
*
192701 AATAATATCATGAAC
1 AATAATACCATGAAC
192716 AATA
1 AATA
192720 TAATGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATACCATGAAC
Done.