Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011617.1 Kokia drynarioides strain JFW-HI SEQ_126607, 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: 128244
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:558 original size:15 final size:15
Alignment explanation
Indices: 532--605 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
522 GGGCACTTTA
*
532 TAATTGGACCATTTG
1 TAATTGGGCCATTTG
*
547 TATTTGGGCCATTTG
1 TAATTGGGCCATTTG
*
562 TAACTGGGCCATTTG
1 TAATTGGGCCATTTG
* * *
577 TATTTGGGTCATCTG
1 TAATTGGGCCATTTG
*
592 TAACTGGGCCATTT
1 TAATTGGGCCATTT
606 ATTTTGGATT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (15 bp):
TAATTGGGCCATTTG
Found at i:576 original size:30 final size:30
Alignment explanation
Indices: 540--605 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
530 TATAATTGGA
*
540 CCATTTGTATTTGGGCCATTTGTAACTGGG
1 CCATTTGTATTTGGGCCATCTGTAACTGGG
*
570 CCATTTGTATTTGGGTCATCTGTAACTGGG
1 CCATTTGTATTTGGGCCATCTGTAACTGGG
600 CCATTT
1 CCATTT
606 ATTTTGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41
Consensus pattern (30 bp):
CCATTTGTATTTGGGCCATCTGTAACTGGG
Found at i:698 original size:17 final size:17
Alignment explanation
Indices: 638--700 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
628 CGGACTTTTC
* *
638 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
*
655 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
672 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
689 TAAACTTAAATT
1 TAAATTTAAATT
701 CAATTTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1612 original size:9 final size:10
Alignment explanation
Indices: 1598--1639 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1588 ATTAAAACCC
1598 AAGAAA-AAA
1 AAGAAAGAAA
1607 AAGAAAGAAA
1 AAGAAAGAAA
1617 AA-AAAGAGAA
1 AAGAAAGA-AA
*
1627 AAGAAGGAAA
1 AAGAAAGAAA
1637 AAG
1 AAG
1640 TTAAGATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 11 0.38
10 14 0.48
11 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:1614 original size:13 final size:13
Alignment explanation
Indices: 1598--1623 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1588 ATTAAAACCC
1598 AAGAAAAAAAAGA
1 AAGAAAAAAAAGA
1611 AAGAAAAAAAAGA
1 AAGAAAAAAAAGA
1624 GAAAAGAAGG
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAGA
Found at i:2497 original size:18 final size:18
Alignment explanation
Indices: 2442--2500 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
2432 AATAATAAAT
2442 AAAAAAAGAAGAGAAAAAG
1 AAAAAAAGAAG-GAAAAAG
2461 AAAAAATAGAA-GAAAAAG
1 AAAAAA-AGAAGGAAAAAG
* *
2479 AAAAAAACAAGGAAGAAG
1 AAAAAAAGAAGGAAAAAG
2497 AAAA
1 AAAA
2501 TGAGAGGTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
17 3 0.08
18 23 0.64
19 6 0.17
20 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAGGAAAAAG
Found at i:2874 original size:114 final size:114
Alignment explanation
Indices: 2735--2942 Score: 308
Period size: 114 Copynumber: 1.8 Consensus size: 114
2725 ACTGTTTTGT
** * *
2735 CCCACTTCTTTGTACCTCACTAGGAAAATGGGAGTTGAAGTCTCACTCCACTCCACTGTATCCTC
1 CCCACTTCTCCGTACCTCACCAGGAAAATGGGAGTTGAAGTCTCACTCCACACCACTGTATCCTC
*
2800 AGGGACGTTGAGCTTGACTTCATTGTTTTGATTCAAGATATTGTATTGA
66 AGGGACGTTGAGCTCGACTTCATTGTTTTGATTCAAGATATTGTATTGA
* * * *
2849 CCCACTTCTCCGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACACCATTGTATCCTT
1 CCCACTTCTCCGTACCTCACCAGGAAAATGGGAGTTGAAGTCTCACTCCACACCACTGTATCCTC
* * *
2914 AGGGATGTTGAGCTCGGCTTCGTTGTTTT
66 AGGGACGTTGAGCTCGACTTCATTGTTTT
2943 AATCTGCTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
114 82 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (114 bp):
CCCACTTCTCCGTACCTCACCAGGAAAATGGGAGTTGAAGTCTCACTCCACACCACTGTATCCTC
AGGGACGTTGAGCTCGACTTCATTGTTTTGATTCAAGATATTGTATTGA
Found at i:3192 original size:49 final size:49
Alignment explanation
Indices: 3139--3454 Score: 241
Period size: 49 Copynumber: 6.4 Consensus size: 49
3129 TGCTTCTCCT
* **
3139 CATCTTCAGGGTATAAGATTCGCCATTGCGGCTTCAATATTTCCCTTCA
1 CATCTTCAGGGTATAAGATTCACCATTGCGGCTTCAACCTTTCCCTTCA
* * * * * *
3188 CATC-TCTAAGGTATAAGGTTCACCGTTGCAGCTTAAACCTTTCCC-TCTG
1 CATCTTC-AGGGTATAAGATTCACCATTGCGGCTTCAACCTTTCCCTTC-A
* * * * *
3237 CATC-TCTAGGGTATAAGATTCGCTATTGTGGCTTCAATCTTTCCGTTCA
1 CATCTTC-AGGGTATAAGATTCACCATTGCGGCTTCAACCTTTCCCTTCA
* * * * *
3286 TATCTTTAGGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCA
1 CATCTTCAGGGTATAAGATTCACCATTGCGGCTTCAACCTTTCCCTTCA
* * * ** *
3335 CAT-GTCTAGGGTATAAGGA-GCACCGTTATGACTTCAACCTTTCCC-TCTA
1 CATCTTC-AGGGTATAA-GATTCACCATTGCGGCTTCAACCTTTCCCTTC-A
* * * *
3384 CATCTTTAGGGTATAAGATTCACCATTGCGGCTTTAATCTTTCCTTTCA
1 CATCTTCAGGGTATAAGATTCACCATTGCGGCTTCAACCTTTCCCTTCA
* *
3433 CATCGTT-AGAGTATAGGATTCA
1 CATC-TTCAGGGTATAAGATTCA
3455 ATATTTCCTT
Statistics
Matches: 205, Mismatches: 51, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
48 8 0.04
49 188 0.92
50 9 0.04
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (49 bp):
CATCTTCAGGGTATAAGATTCACCATTGCGGCTTCAACCTTTCCCTTCA
Found at i:3308 original size:98 final size:98
Alignment explanation
Indices: 3146--3351 Score: 304
Period size: 98 Copynumber: 2.1 Consensus size: 98
3136 CCTCATCTTC
3146 AGGGTATAAGATTCGCCATTGCGGCTTCAATATTTCCCTTCACATCTCTAAGGTATAAGGTTCAC
1 AGGGTATAAGATTCGCCATTGCGGCTTCAATATTTCCCTTCACATCTCTAAGGTATAAGGTTCAC
**
3211 CGTTGCAGCTTAAACCTTTCCCTCTGCATCTCT
66 CGTTGCAGCTTAAACCTTTCCCTCCACATCTCT
* * * * * * *
3244 AGGGTATAAGATTCGCTATTGTGGCTTCAATCTTTCCGTTCATATCTTTAGGGTATAAGGTTCAC
1 AGGGTATAAGATTCGCCATTGCGGCTTCAATATTTCCCTTCACATCTCTAAGGTATAAGGTTCAC
* * *
3309 CGTTGCGGCTTCAACCTTTCCCTCCACATGTCT
66 CGTTGCAGCTTAAACCTTTCCCTCCACATCTCT
3342 AGGGTATAAG
1 AGGGTATAAG
3352 GAGCACCGTT
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (98 bp):
AGGGTATAAGATTCGCCATTGCGGCTTCAATATTTCCCTTCACATCTCTAAGGTATAAGGTTCAC
CGTTGCAGCTTAAACCTTTCCCTCCACATCTCT
Found at i:3370 original size:98 final size:97
Alignment explanation
Indices: 3146--3436 Score: 287
Period size: 98 Copynumber: 3.0 Consensus size: 97
3136 CCTCATCTTC
* * ** * * * *
3146 AGGGTATAAGATTCGCCATTGCGGCTTCAATATTTCCCTTCACATCTCTAAGGTATAAGGTTCAC
1 AGGGTATAAGATGCACCATTATGACTTCAATCTTT-CCTTCACATCTTTAGGGTATAAGGTTCAC
* **
3211 CGTTGCAGCTTAAACCTTTCCCTCTGCATCTCT
65 CGTTGCGGCTTAAACCTTTCCCTCCACATCTCT
* * * * * *
3244 AGGGTATAAGATTCGCTATTGTGGCTTCAATCTTTCCGTTCATATCTTTAGGGTATAAGGTTCAC
1 AGGGTATAAGATGCACCATTATGACTTCAATCTTTCC-TTCACATCTTTAGGGTATAAGGTTCAC
* *
3309 CGTTGCGGCTTCAACCTTTCCCTCCACATGTCT
65 CGTTGCGGCTTAAACCTTTCCCTCCACATCTCT
* * * *
3342 AGGGTATAAGGA-GCACCGTTATGACTTCAACCTTTCCCTCTACATCTTTAGGGTATAAGATTCA
1 AGGGTATAA-GATGCACCATTATGACTTCAATCTTTCCTTC-ACATCTTTAGGGTATAAGGTTCA
* * * * *
3406 CCATTGCGGCTTTAATCTTTCCTTTCACATC
64 CCGTTGCGGCTTAAACCTTTCCCTCCACATC
3437 GTTAGAGTAT
Statistics
Matches: 163, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
97 4 0.02
98 157 0.96
99 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (97 bp):
AGGGTATAAGATGCACCATTATGACTTCAATCTTTCCTTCACATCTTTAGGGTATAAGGTTCACC
GTTGCGGCTTAAACCTTTCCCTCCACATCTCT
Found at i:3374 original size:147 final size:147
Alignment explanation
Indices: 3139--3454 Score: 393
Period size: 147 Copynumber: 2.1 Consensus size: 147
3129 TGCTTCTCCT
* * * *
3139 CATCTTCAGGGTATAAGATTCGCCATTGCGGCTTCAATATTTCCCTTCACATCTCTAAGGTATAA
1 CATCTTTAGGGTATAAGATTCACCATTGCGGCTTCAACATTTCCCTCCACATCTCTAAGGTATAA
** * * * *
3204 GGTTCACCGTTGCAGCTTAAACCTTTCCCTCTGCATCTCTAGGGTATAAGATTCGCTATTGTGGC
66 GGAGCACCGTTGCAGCTTAAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCATTGCGGC
3269 TTCAATCTTTCCGTTCA
131 TTCAATCTTTCCGTTCA
* * * * * *
3286 TATCTTTAGGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCACATGTCTAGGGTATAA
1 CATCTTTAGGGTATAAGATTCACCATTGCGGCTTCAACATTTCCCTCCACATCTCTAAGGTATAA
* *
3351 GGAGCACCGTT--ATGACTTCAACCTTTCCCTCTACATCTTTAGGGTATAAGATTCACCATTGCG
66 GGAGCACCGTTGCA-G-CTTAAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCATTGCG
* *
3414 GCTTTAATCTTTCCTTTCA
129 GCTTCAATCTTTCCGTTCA
* * *
3433 CATCGTTAGAGTATAGGATTCA
1 CATCTTTAGGGTATAAGATTCA
3455 ATATTTCCTT
Statistics
Matches: 142, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
145 1 0.01
146 1 0.01
147 140 0.99
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (147 bp):
CATCTTTAGGGTATAAGATTCACCATTGCGGCTTCAACATTTCCCTCCACATCTCTAAGGTATAA
GGAGCACCGTTGCAGCTTAAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCATTGCGGC
TTCAATCTTTCCGTTCA
Found at i:4051 original size:113 final size:116
Alignment explanation
Indices: 3881--4092 Score: 286
Period size: 113 Copynumber: 1.9 Consensus size: 116
3871 CCTTATATTG
* * * *
3881 TTAGACCATTAACTATTATTTCAAATGCAAAAAATGGTTGAATCAAAGTTGTAAGGTGAATGAAA
1 TTAGACCACTAACCATTATTTCAAATGCAAAAAATGCTTGAATCAAAGTTGTAAGGTGAATAAAA
*
3946 TTGAATTTGATTGGAGGCAAAGATCGCATAAATGAAAAGATTAAAAAAAAA
66 TTGAATTTGATTAGAGGCAAAGATCGCATAAATGAAAAGATTAAAAAAAAA
* ** * *
3997 TTAGTCCACTAACCATTATTTC-AATGC-AAAAATGCTTGAA-CATGGTTGTGAGGTGGATAAAA
1 TTAGACCACTAACCATTATTTCAAATGCAAAAAATGCTTGAATCAAAGTTGTAAGGTGAATAAAA
* * *
4059 TTGAATTTTATTAGAGGCAAAGCTCGCATGAATG
66 TTGAATTTGATTAGAGGCAAAGATCGCATAAATG
4093 CAATATCAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
113 47 0.57
114 12 0.14
115 5 0.06
116 19 0.23
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (116 bp):
TTAGACCACTAACCATTATTTCAAATGCAAAAAATGCTTGAATCAAAGTTGTAAGGTGAATAAAA
TTGAATTTGATTAGAGGCAAAGATCGCATAAATGAAAAGATTAAAAAAAAA
Found at i:4326 original size:96 final size:96
Alignment explanation
Indices: 4197--4471 Score: 327
Period size: 96 Copynumber: 2.9 Consensus size: 96
4187 CACCATTCTA
* * * * * * * *
4197 AGCTTAACGTCCTTGAGGATACAGTGGACTGGAGTTAGACTTGAAATATCATATTCTTGGTGAGG
1 AGCTCAACGTCCTTGAGGATACAGTAGAGTGGAGTGAAACTTCAAATATCATATTCCTGGTAAGG
*
4262 TACAGAGAAGTGGGTCAAAATAACGAAGCAG
66 TACAAAGAAGTGGGTCAAAATAACGAAGCAG
* * *
4293 AGCTCAACGTCCTTGAGGATACAGTAGAGTGGAGTGAAACTTCAATTCTCATTTTCCTGGTAAGG
1 AGCTCAACGTCCTTGAGGATACAGTAGAGTGGAGTGAAACTTCAAATATCATATTCCTGGTAAGG
* *
4358 TATAAAGAAGTGGGTCAAAATAATGAAGCAG
66 TACAAAGAAGTGGGTCAAAATAACGAAGCAG
* * * * * * * *
4389 AGCTCAACGTCCCTGAGGTTATAGTAGAGTGAAGTGAAACTTCAAAT-CCTGTCTTCCTAGTAAG
1 AGCTCAACGTCCTTGAGGATACAGTAGAGTGGAGTGAAACTTCAAATATC-ATATTCCTGGTAAG
*
4453 GTACAGAGAAGTGGGTCAA
65 GTACAAAGAAGTGGGTCAA
4472 TGTAGTGTGC
Statistics
Matches: 153, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
95 1 0.01
96 152 0.99
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (96 bp):
AGCTCAACGTCCTTGAGGATACAGTAGAGTGGAGTGAAACTTCAAATATCATATTCCTGGTAAGG
TACAAAGAAGTGGGTCAAAATAACGAAGCAG
Found at i:4574 original size:109 final size:108
Alignment explanation
Indices: 4416--4904 Score: 324
Period size: 109 Copynumber: 4.5 Consensus size: 108
4406 GTTATAGTAG
* * * * * **
4416 AGTGAAGTGAAACTTCAAATCCTGTCTTCCTAGTAAGGTACAGAGAAGTGGGTCAATGTAGTGTG
1 AGTGGAGTGAGACTTCAAATCCTATCTTCCTAGTGAGGTATAGAGAAGTGGGTCAAAATAGTGTG
* *
4481 CTGAATCAAAACAACGAAGCCGAGCTCAACGTCCCTAAGGATAC
66 CTGAATCAAAA-AACGAAGCAGAGCTCAACGTCCCTAACGATAC
* * **
4525 AGTGGAGTGAGACTCCAAATCCTATCTT-CTCGGTGAGGTATAGAGAAGTGCATCAAAATAGTGT
1 AGTGGAGTGAGACTTCAAATCCTATCTTCCT-AGTGAGGTATAGAGAAGTGGGTCAAAATAGTGT
* * * * *
4589 GTTGAATCAAAAAATGAAGCAGAGCTCAACGTCCTTGACGTTAC
65 GCTGAATCAAAAAACGAAGCAGAGCTCAACGTCCCTAACGATAC
*
4633 AGTGGAGTAGAGTGAGTCTTCAAAT-CTATCTTCCTAGTGAGGTATAGAAAAGTGGGTCAAAATA
1 AGTGGAGT-GA--GA--CTTCAAATCCTATCTTCCTAGTGAGGTATAGAGAAGTGGGTCAAAATA
* * * *** ** **** ** *
4697 -----ATGAAGCAGAGCTC-AA-C---G-TCCCCGAGGAT-ACATTAG
61 GTGTGCTGAATCAAAAAACGAAGCAGAGCTCAACGTCCCTAACGATAC
* * *
4733 AGTGGAGTGAGACTTTAAATCCTATCTTCCTGGTGAGGTATAAAGAAGTGGGTCAAAATAGTGTG
1 AGTGGAGTGAGACTTCAAATCCTATCTTCCTAGTGAGGTATAGAGAAGTGGGTCAAAATAGTGTG
* * * * *
4798 TTGAATCAAAACAACGAAGCTGAGC-CTAATGTCCCTCAGGATAC
66 CTGAATCAAAA-AACGAAGCAGAGCTC-AACGTCCCTAACGATAC
* * * * *
4842 AGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAAAAGTGGGTTAAAA
1 -----AGTGGAGTGAGACTTCAAATCCTATCTTCCTAGTGAGGTATAGAGAAGTGGGTCAAAA
4905 CAAATAGCGA
Statistics
Matches: 288, Mismatches: 65, Indels: 49
0.72 0.16 0.12
Matches are distributed among these distances:
95 7 0.02
96 36 0.12
97 2 0.01
99 2 0.01
100 13 0.05
101 12 0.04
102 2 0.01
103 2 0.01
104 1 0.00
105 1 0.00
106 2 0.01
107 9 0.03
108 38 0.13
109 66 0.23
111 2 0.01
112 32 0.11
113 9 0.03
114 52 0.18
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (108 bp):
AGTGGAGTGAGACTTCAAATCCTATCTTCCTAGTGAGGTATAGAGAAGTGGGTCAAAATAGTGTG
CTGAATCAAAAAACGAAGCAGAGCTCAACGTCCCTAACGATAC
Found at i:4741 original size:95 final size:96
Alignment explanation
Indices: 4595--4792 Score: 276
Period size: 95 Copynumber: 2.1 Consensus size: 96
4585 GTGTGTTGAA
** * * *
4595 TCAAAA-AATGAAGCAGAGCTCAACGTCCTTGACGTTACAGTGGAGTAGAGTGAGTCTTCAAAT-
1 TCAAAATAATGAAGCAGAGCTCAACGTCCCCGACGATACAGTAGAGTAGAGTGAGACTTCAAATC
4658 CTATCTTCCTAGTGAGGTATAGAA-AAGTGGG
66 CTATCTTCCTAGTGAGGTATA-AAGAAGTGGG
* * * *
4689 TCAAAATAATGAAGCAGAGCTCAACGTCCCCGAGGATACATTAGAGTGGAGTGAGACTTTAAATC
1 TCAAAATAATGAAGCAGAGCTCAACGTCCCCGACGATACAGTAGAGTAGAGTGAGACTTCAAATC
*
4754 CTATCTTCCTGGTGAGGTATAAAGAAGTGGG
66 CTATCTTCCTAGTGAGGTATAAAGAAGTGGG
4785 TCAAAATA
1 TCAAAATA
4793 GTGTGTTGAA
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
94 6 0.07
95 50 0.55
96 35 0.38
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (96 bp):
TCAAAATAATGAAGCAGAGCTCAACGTCCCCGACGATACAGTAGAGTAGAGTGAGACTTCAAATC
CTATCTTCCTAGTGAGGTATAAAGAAGTGGG
Found at i:4756 original size:208 final size:210
Alignment explanation
Indices: 4525--4904 Score: 552
Period size: 208 Copynumber: 1.8 Consensus size: 210
4515 CTAAGGATAC
*
4525 AGTGGAGTGAGACTCCAAATCCTATCTT-CTCGGTGAGGTATAGAGAAGTGCATCAAAATAGTGT
1 AGTGGAGTGAGACTCCAAATCCTATCTTCCT-GGTGAGGTATAAAGAAGTGCATCAAAATAGTGT
* * * * *
4589 GTTGAATCAAAA-AATGAAGCAGAG-CTCAACGTCCTTGACGTTACAGTGGAGTAGAGTGAGTCT
65 GTTGAATCAAAACAACGAAGCAGAGCCT-AACGTCCCTCACGATACAGTGGAGTAGAGTGAGACT
* *
4652 TCAAAT-CTATCTTCCTAGTGAGGTATAGAAAAGTGGGTCAAAATAATGAAGCAGAGCTCAACGT
129 TCAAATCCCATCTTCCTAGTGAGGTACAGAAAAGTGGGTCAAAATAATGAAGCAGAGCTCAACGT
4716 CCCCGAGGATACATTAG
194 CCCCGAGGATACATTAG
** **
4733 AGTGGAGTGAGACTTTAAATCCTATCTTCCTGGTGAGGTATAAAGAAGTGGGTCAAAATAGTGTG
1 AGTGGAGTGAGACTCCAAATCCTATCTTCCTGGTGAGGTATAAAGAAGTGCATCAAAATAGTGTG
* * * *
4798 TTGAATCAAAACAACGAAGCTGAGCCTAATGTCCCTCAGGATACAGTGGAGTGGAGTGAGACTTC
66 TTGAATCAAAACAACGAAGCAGAGCCTAACGTCCCTCACGATACAGTGGAGTAGAGTGAGACTTC
* *
4863 AAATCCCATCTTCCTGGTGAGGTACAGAAAAGTGGGTTAAAA
131 AAATCCCATCTTCCTAGTGAGGTACAGAAAAGTGGGTCAAAA
4905 CAAATAGCGA
Statistics
Matches: 150, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
208 68 0.45
209 47 0.31
210 35 0.23
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (210 bp):
AGTGGAGTGAGACTCCAAATCCTATCTTCCTGGTGAGGTATAAAGAAGTGCATCAAAATAGTGTG
TTGAATCAAAACAACGAAGCAGAGCCTAACGTCCCTCACGATACAGTGGAGTAGAGTGAGACTTC
AAATCCCATCTTCCTAGTGAGGTACAGAAAAGTGGGTCAAAATAATGAAGCAGAGCTCAACGTCC
CCGAGGATACATTAG
Found at i:6804 original size:27 final size:26
Alignment explanation
Indices: 6764--6842 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 26
6754 TGAATTTTTA
6764 TTTTATTTTT-AATTTATTCCTTTCATG
1 TTTT-TTTTTAAATTTA-TCCTTTCATG
*
6791 TTTTTTTTTAAATTCATCCATTATTC-TG
1 TTTTTTTTTAAATTTATCC--T-TTCATG
*
6819 TTTTTTTTTAAATTAATCCTTTCA
1 TTTTTTTTTAAATTTATCCTTTCA
6843 ATTACTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 9 0.20
28 21 0.47
29 3 0.07
ACGTcount: A:0.22, C:0.13, G:0.03, T:0.63
Consensus pattern (26 bp):
TTTTTTTTTAAATTTATCCTTTCATG
Found at i:17761 original size:147 final size:147
Alignment explanation
Indices: 17494--17788 Score: 536
Period size: 147 Copynumber: 2.0 Consensus size: 147
17484 AGTACAAAAG
* *
17494 ACAACTTCACCCTAGTACATGTCATATAACCAAGTGATGAGAAACTACCAAACGAGCTCTACAAT
1 ACAACTTCAACCTAGTACATGCCATATAACCAAGTGATGAGAAACTACCAAACGAGCTCTACAAT
*
17559 AACGTGACTTCTTTGAGATGATCCGATCCTCAAGCAGTAAGATAATATACAAAACAACAATAACG
66 AACGTGACTTCTTTGAGATGATCCGATCCTCAAGCAATAAGATAATATACAAAACAACAATAACG
*
17624 TCTTTGGTAAGCTTCAT
131 TCTTTGGTAAACTTCAT
* *
17641 ACAACTTCAATCTAGTACATGCCATATAACCAAGTGATGAGAAACTACCAAACGAGCTCTGCAAT
1 ACAACTTCAACCTAGTACATGCCATATAACCAAGTGATGAGAAACTACCAAACGAGCTCTACAAT
17706 AACGTGACTTCTTTGAGATGATCCGATCCTCAAGCAATAAGATAATATACAAAACAACAATAACG
66 AACGTGACTTCTTTGAGATGATCCGATCCTCAAGCAATAAGATAATATACAAAACAACAATAACG
17771 TCTTTGGTAAACTTCAT
131 TCTTTGGTAAACTTCAT
17788 A
1 A
17789 GCTTAGTAAG
Statistics
Matches: 142, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 142 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (147 bp):
ACAACTTCAACCTAGTACATGCCATATAACCAAGTGATGAGAAACTACCAAACGAGCTCTACAAT
AACGTGACTTCTTTGAGATGATCCGATCCTCAAGCAATAAGATAATATACAAAACAACAATAACG
TCTTTGGTAAACTTCAT
Found at i:30467 original size:19 final size:18
Alignment explanation
Indices: 30430--30483 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
30420 GAACTTCTTC
* *
30430 ATATAATTTCTTGTATTT
1 ATATAATTTTTTATATTT
30448 ATATAATTTTTTAATATTT
1 ATATAATTTTTT-ATATTT
30467 A-ATAAGTTTTATTATAT
1 ATATAA-TTTT-TTATAT
30484 AGATATCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 15 0.48
19 14 0.45
20 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (18 bp):
ATATAATTTTTTATATTT
Found at i:37705 original size:49 final size:49
Alignment explanation
Indices: 37649--37746 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
37639 TTATAAGAAG
37649 GATAATTGATTTATAAAAAGGCAAAACACGATTACTATATGATTCATGA
1 GATAATTGATTTATAAAAAGGCAAAACACGATTACTATATGATTCATGA
*
37698 GATAATTGATTTATAAAAAGGCAGAACACGATTACTATATGATTCATGA
1 GATAATTGATTTATAAAAAGGCAAAACACGATTACTATATGATTCATGA
37747 ACAGGAACAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (49 bp):
GATAATTGATTTATAAAAAGGCAAAACACGATTACTATATGATTCATGA
Found at i:38377 original size:12 final size:13
Alignment explanation
Indices: 38355--38386 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
38345 TTTTTAAATG
38355 ATAAAAA-AATTA
1 ATAAAAATAATTA
38367 A-AAAAATAATTA
1 ATAAAAATAATTA
38379 ATAAAAAT
1 ATAAAAAT
38387 TATATTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 7 0.39
13 6 0.33
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAAAATAATTA
Found at i:38496 original size:17 final size:18
Alignment explanation
Indices: 38467--38523 Score: 80
Period size: 17 Copynumber: 3.2 Consensus size: 18
38457 CTAGATGAGT
*
38467 TAAAAAGTATAAAAATT-
1 TAAAAATTATAAAAATTA
*
38484 TAGAAATTATAAAAATTA
1 TAAAAATTATAAAAATTA
38502 TAAAAATTATAATAAATTA
1 TAAAAATTATAA-AAATTA
38521 TAA
1 TAA
38524 TAGATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
17 15 0.43
18 11 0.31
19 9 0.26
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
TAAAAATTATAAAAATTA
Found at i:38496 original size:26 final size:28
Alignment explanation
Indices: 38467--38523 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
38457 CTAGATGAGT
38467 TAAAAAGTATAAAAATT-T-AGAAATTA
1 TAAAAAGTATAAAAATTATAAGAAATTA
* *
38493 TAAAAATTATAAAAATTATAATAAATTA
1 TAAAAAGTATAAAAATTATAAGAAATTA
38521 TAA
1 TAA
38524 TAGATTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 16 0.59
27 1 0.04
28 10 0.37
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (28 bp):
TAAAAAGTATAAAAATTATAAGAAATTA
Found at i:38525 original size:10 final size:9
Alignment explanation
Indices: 38467--38523 Score: 80
Period size: 9 Copynumber: 6.3 Consensus size: 9
38457 CTAGATGAGT
*
38467 TAAAAAGTA
1 TAAAAATTA
38476 TAAAAATT-
1 TAAAAATTA
*
38484 TAGAAATTA
1 TAAAAATTA
38493 TAAAAATTA
1 TAAAAATTA
38502 TAAAAATTA
1 TAAAAATTA
38511 TAATAAATTA
1 TAA-AAATTA
38521 TAA
1 TAA
38524 TAGATTGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.16
9 27 0.63
10 9 0.21
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:38684 original size:13 final size:12
Alignment explanation
Indices: 38653--38700 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
38643 GAATTTTGTA
*
38653 TATATAAATTAT
1 TATAAAAATTAT
38665 TATAAAAATTAT
1 TATAAAAATTAT
38677 TAATAAAAATTA-
1 T-ATAAAAATTAT
38689 TATACAAAATTA
1 TATA-AAAATTA
38701 GAAACTAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
11 3 0.09
12 20 0.61
13 10 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
TATAAAAATTAT
Found at i:39173 original size:21 final size:20
Alignment explanation
Indices: 39126--39177 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
39116 GGTGTTTTTG
39126 TTTT-AATTAGGATTAGAGT
1 TTTTAAATTAGGATTAGAGT
*
39145 TTTTAAATTAGGATTTA-TGT
1 TTTTAAATTAGGA-TTAGAGT
39165 TTTTAAAATTAGG
1 TTTT-AAATTAGG
39178 GTTTTAGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTTAAATTAGGATTAGAGT
Found at i:39190 original size:21 final size:21
Alignment explanation
Indices: 39149--39190 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
39139 TAGAGTTTTT
*
39149 AAATTAGGATTTATGTTTTTA
1 AAATTAGGATTTATGTATTTA
*
39170 AAATTAGGGTTT-TAGTATTTA
1 AAATTAGGATTTAT-GTATTTA
39191 TTTTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (21 bp):
AAATTAGGATTTATGTATTTA
Found at i:44324 original size:20 final size:20
Alignment explanation
Indices: 44301--44339 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
44291 AATTAAATTA
44301 TAAA-ATTATTATAAAATAAG
1 TAAATATTATTA-AAAATAAG
44321 TAAATATTATTAAAAATAA
1 TAAATATTATTAAAAATAA
44340 TATAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAATATTATTAAAAATAAG
Found at i:44353 original size:20 final size:20
Alignment explanation
Indices: 44302--44355 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
44292 ATTAAATTAT
*
44302 AAAATTATTATAAAATAAGTA
1 AAAATTATTA-AAAATAAATA
*
44323 AATATTATTAAAAATAATATA
1 AAAATTATTAAAAATAA-ATA
44344 AAAATT-TTAAAA
1 AAAATTATTAAAA
44356 TTAACTCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATTATTAAAAATAAATA
Found at i:44514 original size:23 final size:23
Alignment explanation
Indices: 44471--44516 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
44461 TTGAGAGCTG
* *
44471 TAGAGAGAAATTTGTGTAAAATT
1 TAGAGAGAAATTTGGGGAAAATT
44494 TAGAGAGAAA-TTGGGAGAAAATT
1 TAGAGAGAAATTTGGG-GAAAATT
44517 AGTGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (23 bp):
TAGAGAGAAATTTGGGGAAAATT
Found at i:45321 original size:31 final size:31
Alignment explanation
Indices: 45283--45353 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
45273 TTTGAGAAAT
* *
45283 CTTATTTGAGCTCTTTTGAAAAA-GTCTA-ACC
1 CTTATTTGAGCAC-TTTCAAAAATGT-TAGACC
45314 CTTATTTGAGCACTTTCAAAAATGTTAGACC
1 CTTATTTGAGCACTTTCAAAAATGTTAGACC
45345 CTTATTTGA
1 CTTATTTGA
45354 CTATTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (31 bp):
CTTATTTGAGCACTTTCAAAAATGTTAGACC
Found at i:45533 original size:13 final size:13
Alignment explanation
Indices: 45515--45567 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
45505 AATCTTGTAT
*
45515 ATAATTTCTATTA
1 ATAATTTCTAATA
*
45528 ATAATTTTTAATA
1 ATAATTTCTAATA
*
45541 ATAATTTATATATA
1 ATAATTTCTA-ATA
* *
45555 AAAAATTCTAATA
1 ATAATTTCTAATA
45568 TAAAAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAATTTCTAATA
Found at i:45570 original size:26 final size:25
Alignment explanation
Indices: 45513--45570 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
45503 GTAATCTTGT
* * * *
45513 ATATAATTTCTATTAATAATTTTTA
1 ATATAATTTATATTAAAAAATTCTA
45538 ATAATAATTTATATATAAAAAATTCTA
1 AT-ATAATTTATAT-TAAAAAATTCTA
45565 ATATAA
1 ATATAA
45571 AAATTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 2 0.07
26 14 0.52
27 11 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATAATTTATATTAAAAAATTCTA
Found at i:45690 original size:9 final size:9
Alignment explanation
Indices: 45676--45750 Score: 55
Period size: 9 Copynumber: 8.1 Consensus size: 9
45666 TTTCAATCTA
45676 TTATAATTT
1 TTATAATTT
45685 TTATAATTTT
1 TTATAA-TTT
45695 TTATAATTT
1 TTATAATTT
*
45704 TTAAATAATTA
1 TT--ATAATTT
*
45715 TT-GAATTT
1 TTATAATTT
45723 TTCATAATTT
1 TT-ATAATTT
* *
45733 CT-TAACTT
1 TTATAATTT
*
45741 TTATACTTT
1 TTATAATTT
45750 T
1 T
45751 GAACTCATCT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
8 12 0.24
9 16 0.31
10 15 0.29
11 8 0.16
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (9 bp):
TTATAATTT
Found at i:45697 original size:10 final size:10
Alignment explanation
Indices: 45676--45705 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
45666 TTTCAATCTA
45676 TTATAA-TTT
1 TTATAATTTT
45685 TTATAATTTT
1 TTATAATTTT
45695 TTATAATTTT
1 TTATAATTTT
45705 T
1 T
45706 AAATAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATAATTTT
Found at i:46456 original size:27 final size:25
Alignment explanation
Indices: 46397--46456 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
46387 TATTATTGTG
46397 GTTTTGTCCACAAATTTTTGATTTT
1 GTTTTGTCCACAAATTTTTGATTTT
* ** *
46422 ATTTTGTCCACATTTTTTATAGTTTTT
1 GTTTTGTCCACAAATTTT-T-GATTTT
46449 GTTTTGTC
1 GTTTTGTC
46457 TACTTTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 15 0.54
26 1 0.04
27 12 0.43
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.60
Consensus pattern (25 bp):
GTTTTGTCCACAAATTTTTGATTTT
Found at i:53972 original size:86 final size:82
Alignment explanation
Indices: 53829--54047 Score: 237
Period size: 86 Copynumber: 2.6 Consensus size: 82
53819 TTTAAGTCTT
* * * *
53829 TTTTTTTCACTTAATTGAGTATTTGAACTTTTAAAATGTATCAAAAAGACCCCCAAACATTTAAA
1 TTTTTTTCACTTAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACTCCCAAAC--TT-AA
* *
53894 AAAAATCAATTAAGCCTC-TG-C
63 AAAAA--AATTAAACC-CAAGAC
* * * **
53915 TTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGACTGTCAAACTTAAAAA
1 TTTTTTTCACTTAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACTCCCAAACTTAAAAA
*
53980 AAAATTAAACCCAAGAT
66 AAAATTAAACCCAAGAC
*
53997 TTTTTTTGCACTTAATTGAGTACTTGAACTGTC-AAATGCATCAAAAAGACT
1 TTTTTTT-CACTTAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACT
54048 TTTTGACTGT
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
80 1 0.01
81 9 0.08
82 24 0.21
83 29 0.25
84 2 0.02
86 49 0.43
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (82 bp):
TTTTTTTCACTTAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACTCCCAAACTTAAAAA
AAAATTAAACCCAAGAC
Found at i:54188 original size:19 final size:19
Alignment explanation
Indices: 54166--54215 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
54156 TAAAAAATTG
54166 AAAATTAATAAAAGT-TATA
1 AAAATT-ATAAAAGTCTATA
* *
54185 AAAATTGTAAAATTCTATA
1 AAAATTATAAAAGTCTATA
*
54204 AAAATCATAAAA
1 AAAATTATAAAA
54216 AATATAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAATTATAAAAGTCTATA
Found at i:54231 original size:27 final size:26
Alignment explanation
Indices: 54148--54234 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
54138 ACATGTGACA
*
54148 AAAAATTATAAAAAATTGAAAATTAAT
1 AAAAATTATAAAAAATT-AAAATTCAT
* *
54175 AAAAGTTATAAAAATTGTAAAATTCTAT
1 AAAAATTATAAAAAAT-TAAAATTC-AT
* *
54203 AAAAATCATAAAAAATATAAAATGCAT
1 AAAAATTATAAAAAAT-TAAAATTCAT
54230 AAAAA
1 AAAAA
54235 AGATCATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 27 0.54
28 23 0.46
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (26 bp):
AAAAATTATAAAAAATTAAAATTCAT
Found at i:54367 original size:9 final size:9
Alignment explanation
Indices: 54317--54368 Score: 52
Period size: 10 Copynumber: 5.4 Consensus size: 9
54307 ACATATAACG
54317 AAAAATGATA
1 AAAAAT-ATA
54327 AAAAA-ATA
1 AAAAATATA
*
54335 AAAATTAATA
1 AAAAAT-ATA
54345 AAAAATATAA
1 AAAAATAT-A
54355 AAAAACTATA
1 AAAAA-TATA
54365 AAAA
1 AAAA
54369 TGCTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 2 0.06
10 24 0.67
11 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAAAATATA
Found at i:54367 original size:19 final size:19
Alignment explanation
Indices: 54324--54369 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
54314 ACGAAAAATG
*
54324 ATAAAAAAATAAAAATTAAT
1 ATAAAAATATAAAAA-TAAT
54344 A-AAAAATATAAAAA-AACT
1 ATAAAAATATAAAAATAA-T
54362 ATAAAAAT
1 ATAAAAAT
54370 GCTTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 18 0.78
20 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
ATAAAAATATAAAAATAAT
Found at i:54408 original size:21 final size:21
Alignment explanation
Indices: 54383--54446 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
54373 TTTTTTAGTA
*
54383 TTACAATTTTTATAATTTTTT
1 TTACAATTTTTATAATTTTCT
*
54404 TTACAAATTTTAT-A-TTTCT
1 TTACAATTTTTATAATTTTCT
*
54423 TTACATTTTTTTTATAATTTTCT
1 TTACA--ATTTTTATAATTTTCT
54446 T
1 T
54447 ATGATTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 9 0.26
20 1 0.03
21 18 0.51
22 1 0.03
23 6 0.17
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.66
Consensus pattern (21 bp):
TTACAATTTTTATAATTTTCT
Found at i:54443 original size:10 final size:10
Alignment explanation
Indices: 54389--54532 Score: 73
Period size: 10 Copynumber: 14.4 Consensus size: 10
54379 AGTATTACAA
54389 TTTTTATAAT
1 TTTTTATAAT
* *
54399 TTTTTTTACAA
1 TTTTTATA-AT
*
54410 ATTTTAT-AT
1 TTTTTATAAT
* *
54419 TTCTTTACATTT
1 TT-TTTATA-AT
54431 TTTTTATAAT
1 TTTTTATAAT
*
54441 TTTCTTATGA-
1 TTT-TTATAAT
*
54451 -TTTTATAAA
1 TTTTTATAAT
*
54460 ATTTTATAAT
1 TTTTTATAAT
*
54470 TTTTTCT-AT
1 TTTTTATAAT
*
54479 ATTTCTAT-AT
1 -TTTTTATAAT
* *
54489 ATTTTATAGT
1 TTTTTATAAT
*
54499 TTTTTACAAT
1 TTTTTATAAT
*
54509 TTTTTATATT
1 TTTTTATAAT
*
54519 TTTTTCTAAT
1 TTTTTATAAT
54529 TTTT
1 TTTT
54533 AATATTTCCT
Statistics
Matches: 98, Mismatches: 27, Indels: 18
0.69 0.19 0.13
Matches are distributed among these distances:
8 5 0.05
9 11 0.11
10 63 0.64
11 16 0.16
12 3 0.03
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:54482 original size:29 final size:29
Alignment explanation
Indices: 54432--54503 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
54422 TTTACATTTT
*
54432 TTTTATAATTTTCTTATGATTT-TATAAAA
1 TTTTATAATTTTTTTATGATTTCTAT-AAA
*
54461 TTTTATAATTTTTTCTAT-ATTTCTATATA
1 TTTTATAATTTTTT-TATGATTTCTATAAA
*
54490 TTTTATAGTTTTTT
1 TTTTATAATTTTTT
54504 ACAATTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 32 0.84
30 6 0.16
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTTATAATTTTTTTATGATTTCTATAAA
Found at i:54504 original size:39 final size:39
Alignment explanation
Indices: 54410--54513 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 39
54400 TTTTTTACAA
* *
54410 ATTTTATATTTCTTTACATTTTTTTTATAATTTTCTTATG
1 ATTTTATATTT-TTTAAATTTTTTCTATAATTTTCTTATG
**
54450 ATTTTATAAAATTTTATAATTTTTTCTAT-A-TTTCTATAT-
1 ATTTTAT-ATTTTTTA-AATTTTTTCTATAATTTTCT-TATG
54489 ATTTTATAGTTTTTTACAATTTTTT
1 ATTTTATA-TTTTTTA-AATTTTTT
54514 ATATTTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
38 1 0.02
39 25 0.47
40 15 0.28
41 12 0.23
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (39 bp):
ATTTTATATTTTTTAAATTTTTTCTATAATTTTCTTATG
Found at i:54516 original size:29 final size:29
Alignment explanation
Indices: 54451--54539 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
54441 TTTCTTATGA
* *
54451 TTTTATAAAATTTTATAATTTTTTCTATAT
1 TTTTAT-ATATTTTATAATTTTTTCAATAT
* *
54481 TTCTATATATTTTATAGTTTTTTACAAT-T
1 TTTTATATATTTTATAATTTTTT-CAATAT
* *
54510 TTTTATATTTTTTTCTAA-TTTTT-AATAT
1 TTTTATA-TATTTTATAATTTTTTCAATAT
54538 TT
1 TT
54540 CCTACTTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
27 3 0.06
28 3 0.06
29 27 0.56
30 15 0.31
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (29 bp):
TTTTATATATTTTATAATTTTTTCAATAT
Found at i:55255 original size:29 final size:29
Alignment explanation
Indices: 55193--55266 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
55183 AGTTTATATT
* * *
55193 TTTTTATAATTTTAAAGAATTAAATCGAA
1 TTTTTATTATTTTAAAAAATTAAATAGAA
*
55222 TTTTTATTATTTTAAAAAATTAAAATATAA
1 TTTTTATTATTTTAAAAAATT-AAATAGAA
55252 -TTTTATTATTATTAA
1 TTTTTATTATT-TTAA
55267 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 29 0.74
30 10 0.26
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTTTATTATTTTAAAAAATTAAATAGAA
Found at i:55281 original size:16 final size:17
Alignment explanation
Indices: 55260--55291 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55250 AATTTTATTA
55260 TTATTAATT-TAAAATT
1 TTATTAATTATAAAATT
55276 TTATTAATTATAAAAT
1 TTATTAATTATAAAAT
55292 ACTTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTAATTATAAAATT
Found at i:56021 original size:25 final size:26
Alignment explanation
Indices: 55987--56039 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
55977 ATTTGCATTA
*
55987 TATTTTTA-TTATTGAAA-ATAGTTTT
1 TATTTATATTTATT-AAACATAGTTTT
*
56012 TATTTATATTTATTAAACATATTTTT
1 TATTTATATTTATTAAACATAGTTTT
56038 TA
1 TA
56040 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (26 bp):
TATTTATATTTATTAAACATAGTTTT
Found at i:56207 original size:19 final size:19
Alignment explanation
Indices: 56183--56230 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
56173 ATTTATTTTG
56183 AAATTATAAAAAACCATAA
1 AAATTATAAAAAACCATAA
* **
56202 AAATTATTAAAAATTATAA
1 AAATTATAAAAAACCATAA
56221 AAA-TATAAAA
1 AAATTATAAAA
56231 TTAACTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATTATAAAAAACCATAA
Found at i:56212 original size:10 final size:9
Alignment explanation
Indices: 56183--56249 Score: 57
Period size: 9 Copynumber: 7.2 Consensus size: 9
56173 ATTTATTTTG
56183 AAATTATAAA
1 AAATTAT-AA
**
56193 AAACCATAA
1 AAATTATAA
56202 AAATTATTAA
1 AAATTA-TAA
56212 AAATTATAA
1 AAATTATAA
56221 AAA-TAT-A
1 AAATTATAA
56228 AAATTAACTAA
1 AAATT-A-TAA
*
56239 AAACTATAA
1 AAATTATAA
56248 AA
1 AA
56250 TATACTAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.09
8 4 0.09
9 18 0.38
10 16 0.34
11 5 0.11
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATTATAA
Found at i:56230 original size:27 final size:28
Alignment explanation
Indices: 56183--56253 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
56173 ATTTATTTTG
* *
56183 AAATTATAAAAAACCATAAAAATT-ATTAA
1 AAATTAT-AAAAA-TATAAAAATTAACTAA
56212 AAATTATAAAAATAT-AAAATTAACTAA
1 AAATTATAAAAATATAAAAATTAACTAA
*
56239 AAACTAT-AAAATATA
1 AAATTATAAAAATATA
56254 CTAAAGCCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 13 0.35
27 12 0.32
28 5 0.14
29 7 0.19
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (28 bp):
AAATTATAAAAATATAAAAATTAACTAA
Found at i:56722 original size:24 final size:24
Alignment explanation
Indices: 56689--56736 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
56679 GTAAAAGGCT
*
56689 GATGTTAACTAATGGTCAATGACC
1 GATGTCAACTAATGGTCAATGACC
** *
56713 GATGTCAACTGGTGGTCGATGACC
1 GATGTCAACTAATGGTCAATGACC
56737 AAAAAATAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (24 bp):
GATGTCAACTAATGGTCAATGACC
Found at i:56900 original size:24 final size:25
Alignment explanation
Indices: 56853--56902 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
56843 GTCTAACAAA
56853 CTAACTACTCTAACAAATCTTTAACTG
1 CTAACTACTCTAACAAA--TTTAACTG
*
56880 CTAACTACTTTAACAAA-TTAACT
1 CTAACTACTCTAACAAATTTAACT
56903 TAGGTAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
27 16 0.73
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (25 bp):
CTAACTACTCTAACAAATTTAACTG
Found at i:57708 original size:24 final size:24
Alignment explanation
Indices: 57680--57742 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
57670 AGAAATAATC
57680 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
** *
57704 TTTCAAATAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
57728 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
57743 TATTAGTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:63309 original size:23 final size:23
Alignment explanation
Indices: 63259--63309 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
63249 ATCATTCAGA
* **
63259 GTTTATTCTTCGTTAATCTTTAT
1 GTTTATTCTTAGTTAATCAATAT
* *
63282 TTTTATTCTTAGTTATTCAATAT
1 GTTTATTCTTAGTTAATCAATAT
63305 GTTTA
1 GTTTA
63310 CAAATTTTCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.61
Consensus pattern (23 bp):
GTTTATTCTTAGTTAATCAATAT
Found at i:72180 original size:15 final size:16
Alignment explanation
Indices: 72148--72181 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
72138 TATTCATCTC
*
72148 ATTTGCATTTAGGTTA
1 ATTTGCATCTAGGTTA
72164 ATTTGCATCTA-GTTA
1 ATTTGCATCTAGGTTA
72179 ATT
1 ATT
72182 AATTTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (16 bp):
ATTTGCATCTAGGTTA
Found at i:73696 original size:24 final size:24
Alignment explanation
Indices: 73659--73719 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
73649 TTAGACTAAT
*
73659 AAGAGTTTGATTGAAACAAATAAA
1 AAGAGTTTAATTGAAACAAATAAA
* *
73683 TAGATTTTAATTGAAACAAATAAA
1 AAGAGTTTAATTGAAACAAATAAA
73707 AAGAGTTTAATTG
1 AAGAGTTTAATTG
73720 GAAGATTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (24 bp):
AAGAGTTTAATTGAAACAAATAAA
Found at i:77090 original size:15 final size:15
Alignment explanation
Indices: 77057--77101 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
77047 CACGAAAAAG
* *
77057 TCTTCCTCTTTCTCA
1 TCTTCTTCTTTCTCT
77072 TCTTC--CTTTCT-T
1 TCTTCTTCTTTCTCT
77084 TCTTCTTCTTTCTCT
1 TCTTCTTCTTTCTCT
77099 TCT
1 TCT
77102 GCCTTCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.19
13 6 0.23
14 6 0.23
15 9 0.35
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTCTTCTTTCTCT
Found at i:96639 original size:18 final size:15
Alignment explanation
Indices: 96616--96655 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
96606 ACACATGAGT
96616 AGAAGAAGTGGAAGAAGA
1 AGAAGAAG-GGAA-AA-A
96634 AGAAGAAGGGAAAAA
1 AGAAGAAGGGAAAAA
96649 AGAAGAA
1 AGAAGAA
96656 AGAGAGGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 2 0.09
17 4 0.18
18 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (15 bp):
AGAAGAAGGGAAAAA
Found at i:96665 original size:24 final size:20
Alignment explanation
Indices: 96627--96670 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 20
96617 GAAGAAGTGG
96627 AAGAAGAAGAAGAAGGGAAAA
1 AAGAAGAAGAAGAA-GGAAAA
96648 AAGAAGAAAGAGAGGAAGGAAAA
1 AAGAAG-AAGA-A-GAAGGAAAA
96671 GAAGTCGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 7 0.35
24 3 0.15
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AAGAAGAAGAAGAAGGAAAA
Found at i:97158 original size:17 final size:17
Alignment explanation
Indices: 97122--97166 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
97112 TGCATTTTTA
* *
97122 ATTGTCACTGCATGTGC
1 ATTGTCATTGCATGTCC
*
97139 ATTGTCATTGCATTTCC
1 ATTGTCATTGCATGTCC
97156 ATTTGTCATTG
1 A-TTGTCATTG
97167 TAAATTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (17 bp):
ATTGTCATTGCATGTCC
Found at i:97163 original size:18 final size:18
Alignment explanation
Indices: 97104--97166 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
97094 CCACATTCAC
* **
97104 TTTGTGATTGCATTTTTA
1 TTTGTCATTGCATTTCCA
* * * *
97122 ATTGTCACTGCATGTGCA
1 TTTGTCATTGCATTTCCA
97140 -TTGTCATTGCATTTCCA
1 TTTGTCATTGCATTTCCA
97157 TTTGTCATTG
1 TTTGTCATTG
97167 TAAATTAATG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.49
Consensus pattern (18 bp):
TTTGTCATTGCATTTCCA
Found at i:101328 original size:15 final size:14
Alignment explanation
Indices: 101291--101329 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
101281 TTTGATGGAA
101291 AATTCAAAATTTTTT
1 AATT-AAAATTTTTT
101306 AA-TAAAATTTGTTT
1 AATTAAAATTT-TTT
101320 AATTAAAATT
1 AATTAAAATT
101330 AATACTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (14 bp):
AATTAAAATTTTTT
Found at i:101457 original size:49 final size:50
Alignment explanation
Indices: 101404--101507 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 50
101394 ATTTAAATAC
* *
101404 ATTAAATTAAAATCTCTTTAATTAAAATTAATGTT-TTTTATTTGGTTTG
1 ATTAAATTAAAATCTCTTTAATTAAAATTAATGTTGATTGATTTGGTTTG
*
101453 ATTAATTTAAAATCTCTTTAATTAAAATTAATGTTGATTGATTTGGTTTG
1 ATTAAATTAAAATCTCTTTAATTAAAATTAATGTTGATTGATTTGGTTTG
101503 ATTAA
1 ATTAA
101508 TAAATATACA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
49 34 0.67
50 17 0.33
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.51
Consensus pattern (50 bp):
ATTAAATTAAAATCTCTTTAATTAAAATTAATGTTGATTGATTTGGTTTG
Found at i:104150 original size:20 final size:20
Alignment explanation
Indices: 104125--104165 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
104115 AACTTAACTA
104125 ACATTAGAGTTACATAATGC
1 ACATTAGAGTTACATAATGC
104145 ACATTAGAGTTACATAATGC
1 ACATTAGAGTTACATAATGC
104165 A
1 A
104166 TGTCATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
ACATTAGAGTTACATAATGC
Found at i:107082 original size:183 final size:183
Alignment explanation
Indices: 106774--107144 Score: 607
Period size: 183 Copynumber: 2.0 Consensus size: 183
106764 TCATGTATAG
* *
106774 TTGAAAAGGCATGTCTCTTCACTTGTTGATTACTTAATGTTCCCTTAATGTGTTGTTTGGTATCC
1 TTGAAAAGGCATGTCTCTTCACTTGTTGATGACTTAATGTTCCCTTAATGTGTTGTTCGGTATCC
* * * *
106839 CTCTATCTTCCTTAAAATCGAACGTCAAAAGACTTGGTTTAGACATCTTAAAATGGCGTCATAAT
66 CTCTATCTTCCTTAAAATCGAACATCAAAAGAATTCGCTTAGACATCTTAAAATGGCGTCATAAT
* *
106904 GACCATTGAAGGCACCAAAACCCATCAGATTTGAAAAGTCTTCCTTGATCCAT
131 GACCATTGAAGCCACCAAAACCAATCAGATTTGAAAAGTCTTCCTTGATCCAT
106957 TTGAAAAGGCATGTCTCTTCACTTGTTGATGACTTAATGTTCCCTTAATGTGTTGTTCGGTATCC
1 TTGAAAAGGCATGTCTCTTCACTTGTTGATGACTTAATGTTCCCTTAATGTGTTGTTCGGTATCC
* * * *
107022 CTTTATCTTCCTTAAAATTGAATATCAAAAGAATTCGCTTAGACCTCTTAAAATGGCGTCATAAT
66 CTCTATCTTCCTTAAAATCGAACATCAAAAGAATTCGCTTAGACATCTTAAAATGGCGTCATAAT
* * *
107087 GACCATTGAAGCCACCAAAACCAATCAGTTTTGAAAAGTCTTCTTTGTTCCAT
131 GACCATTGAAGCCACCAAAACCAATCAGATTTGAAAAGTCTTCCTTGATCCAT
107140 TTGAA
1 TTGAA
107145 CAGCCACCAT
Statistics
Matches: 173, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
183 173 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (183 bp):
TTGAAAAGGCATGTCTCTTCACTTGTTGATGACTTAATGTTCCCTTAATGTGTTGTTCGGTATCC
CTCTATCTTCCTTAAAATCGAACATCAAAAGAATTCGCTTAGACATCTTAAAATGGCGTCATAAT
GACCATTGAAGCCACCAAAACCAATCAGATTTGAAAAGTCTTCCTTGATCCAT
Found at i:108308 original size:50 final size:50
Alignment explanation
Indices: 108233--108336 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
108223 TTGAGTATAT
* * *
108233 TAATTTTAAATCTCTTTAATTAAAATTAATGCTCT-TTGGTTTGGTTTGAC
1 TAATTTAAAATCTCTTTAATTAAAATTAATGCT-TATTGATTTGGTTTGAA
108283 TAATTTAAAATCTCTTTAATTAAAATTAATGCTTATTGATTTGGTTTGAA
1 TAATTTAAAATCTCTTTAATTAAAATTAATGCTTATTGATTTGGTTTGAA
108333 TAAT
1 TAAT
108337 AATTATACAG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
49 1 0.02
50 49 0.98
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.49
Consensus pattern (50 bp):
TAATTTAAAATCTCTTTAATTAAAATTAATGCTTATTGATTTGGTTTGAA
Found at i:108609 original size:16 final size:17
Alignment explanation
Indices: 108588--108624 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
108578 ATGATAAGTC
*
108588 TTTTGTTTCT-TTTTTT
1 TTTTGTTACTGTTTTTT
108604 TTTTGTTACTGTTTTTT
1 TTTTGTTACTGTTTTTT
108621 TTTT
1 TTTT
108625 TGCTTTCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.84
Consensus pattern (17 bp):
TTTTGTTACTGTTTTTT
Found at i:109825 original size:12 final size:13
Alignment explanation
Indices: 109793--109817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109783 AGTTTGATTC
109793 GATTTAAAATTTG
1 GATTTAAAATTTG
109806 GATTTAAAATTT
1 GATTTAAAATTT
109818 TGTTTAAATT
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
GATTTAAAATTTG
Found at i:114219 original size:29 final size:29
Alignment explanation
Indices: 114169--114225 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
114159 CTCATGGGCA
* ** *
114169 AAAGCGCTTCCATATGGGCGCTTTTTTGT
1 AAAGCGCTTCCACATCAGCGCTCTTTTGT
*
114198 AAAGCGCTTCCACATCATCGCTCTTTTG
1 AAAGCGCTTCCACATCAGCGCTCTTTTG
114226 CCTGACACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (29 bp):
AAAGCGCTTCCACATCAGCGCTCTTTTGT
Found at i:123035 original size:22 final size:24
Alignment explanation
Indices: 122991--123035 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
122981 ATTTAGTAGT
**
122991 ATAATATATTTAACATTTTTTAGC
1 ATAATATATTTAACATTGATTAGC
123015 ATAAT-TATTT-ACATTGATTAG
1 ATAATATATTTAACATTGATTAG
123036 AATTAGGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (24 bp):
ATAATATATTTAACATTGATTAGC
Found at i:127566 original size:25 final size:23
Alignment explanation
Indices: 127488--127660 Score: 147
Period size: 23 Copynumber: 7.4 Consensus size: 23
127478 TATACGGAAC
* *
127488 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
127510 -AACAGAGAGCACATAAA-TACT
1 AAACAGAGAGCACACAAAGTGCT
* * *
127531 GGGCAACAGAGAGAACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
127557 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
127580 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
127603 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
127626 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
127651 AAACAGAGAG
1 AAACAGAGAG
127661 AGCGCTAGTG
Statistics
Matches: 126, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
21 15 0.12
22 3 0.02
23 71 0.56
24 2 0.02
25 31 0.25
26 4 0.03
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:127587 original size:46 final size:47
Alignment explanation
Indices: 127536--127660 Score: 164
Period size: 46 Copynumber: 2.7 Consensus size: 47
127526 ATACTGGGCA
* *
127536 ACAGAGAGAACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * *
127583 -CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
*
127629 AACAGAGAGCACGAGAC-GTGCTAAACAGAGAG
1 -ACAGAGAGCAC-ACACAGTGCTAAACAGAGAG
127661 AGCGCTAGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 41 0.61
48 24 0.36
49 2 0.03
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (47 bp):
ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:127610 original size:69 final size:67
Alignment explanation
Indices: 127488--127637 Score: 178
Period size: 69 Copynumber: 2.1 Consensus size: 67
127478 TATACGGAAC
* *
127488 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAATACTGGGCAACAGAGAGAACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAATACT--G-AACAGAGAGAACACAAAG
127553 TGCT-
63 TGCTA
* *
127557 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACAAA-TACTGAA-CAGAGAGAACACAAA
127621 GTGCTA
62 GTGCTA
127627 ATAACAGAGAG
1 A-AACAGAGAG
127638 CACGAGACGT
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
68 2 0.03
69 31 0.44
70 12 0.17
71 23 0.32
72 3 0.04
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAATACTGAACAGAGAGAACACAAAGTGC
TA
Done.