Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 94 of 132
Found at i:28947033 original size:39 final size:39
Alignment explanation
Indices: 28946979--28947055 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
28946969 AAGATTGGAT
* *
28946979 GATGGTTGCAATTTGCCCCATGATCGGGGTAAGAGATTG
1 GATGGCTGCAATTTGCCCCATGATCGGAGTAAGAGATTG
28947018 GATGGCTGCAATTTGCCCCATGATCGGAGTAAGAGATT
1 GATGGCTGCAATTTGCCCCATGATCGGAGTAAGAGATT
28947056 AGGGTAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (39 bp):
GATGGCTGCAATTTGCCCCATGATCGGAGTAAGAGATTG
Found at i:28947074 original size:91 final size:91
Alignment explanation
Indices: 28946979--28947145 Score: 199
Period size: 91 Copynumber: 1.8 Consensus size: 91
28946969 AAGATTGGAT
* * * * * * * * * *
28946979 GATGGTTGCAATTTGCCCCATGATCGGGGTAAGAGATTGGATGGCTGCAATTTGCCCCATGATCG
1 GATGGCTGCAATCTGCCCCAAGATCAGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGATCG
28947044 GAGTAAGAGATTAGGGTAAAAGATCA
66 GAGTAAGAGATTAGGGTAAAAGATCA
* * * *
28947070 GATGGCTGTAATCTGCCCCAAGCTCAGGGTAAAAGATCGAATGGTTGCAATCTACCCCAGGCTCG
1 GATGGCTGCAATCTGCCCCAAGATCAGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGATCG
*
28947135 GGGTAAGAGAT
66 GAGTAAGAGAT
28947146 CGATTGATGG
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
91 61 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (91 bp):
GATGGCTGCAATCTGCCCCAAGATCAGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGATCG
GAGTAAGAGATTAGGGTAAAAGATCA
Found at i:28947122 original size:39 final size:39
Alignment explanation
Indices: 28947057--28947613 Score: 375
Period size: 39 Copynumber: 14.3 Consensus size: 39
28947047 TAAGAGATTA
* *
28947057 GGGTAAAAGATC-AGATGGCTGTAATCTGCCCCAAGCTCA
1 GGGTAAAAGATCGA-ATGGTTGTAATCTGCCCCAAGCTCG
* * *
28947096 GGGTAAAAGATCGAATGGTTGCAATCTACCCCAGGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * * * * *
28947135 GGGTAAGAGATCGATTGATGGTGATCTGCCCCAAACTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * * *
28947174 GGGTAAAAGATAGGATGGTTGCAATCTGTCCCAAGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * * * *
28947213 GGGTAAGAGATTGGCTAATGG-TG--ATCTGTCCTAGGCTCG
1 GGGTAAAAGA-T--CGAATGGTTGTAATCTGCCCCAAGCTCG
* * *
28947252 GGGTAAAAGATCGGATGGCTGTAATCTGCCTCAAGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* ** * * * * *
28947291 GGGTAAAAGATTGGCTGATGGTGATTTGCCCCAAGCTTG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * * * * *
28947330 GGGTAAAAGATTGGATGGCTGCAATTTTCCCCAAGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * * * * *
28947369 GGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * * * *
28947408 GGGTAAAAGATCGAATGGCTGTAATTTACCCTAGGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * * * * * *
28947447 GGGTAAGAGATTGATTGATGGTGATCTGCCTCAAGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * ** * *
28947486 GGGTAAGAGATCGGATGGTTAAAATCTGCCCTAGGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * ** * * * * * *
28947525 GGGTAAGAGATTGGCTGATGGTGATCTGTCTCAAGCTTG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
* * *
28947564 GGATAAAAGATCGAATGGCTGTAATCTGCCTCAAGCTCG
1 GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
*
28947603 GGGTAAGAGAT
1 GGGTAAAAGAT
28947614 TAGCTGATAG
Statistics
Matches: 388, Mismatches: 123, Indels: 14
0.74 0.23 0.03
Matches are distributed among these distances:
36 5 0.01
37 2 0.01
38 1 0.00
39 372 0.96
40 2 0.01
41 2 0.01
42 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (39 bp):
GGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCG
Found at i:28947192 original size:78 final size:78
Alignment explanation
Indices: 28947080--28947687 Score: 662
Period size: 78 Copynumber: 7.8 Consensus size: 78
28947070 GATGGCTGTA
* * * * *
28947080 ATCTGCCCCAAGCTCAGGGTAAAAGATCGAATGGTTGCAATCTACCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
* *
28947145 TCGATTGATGGTG
66 TTGACTGATGGTG
* * * *
28947158 ATCTGCCCCAAACTCGGGGTAAAAGATAGGATGGTTGCAATCTGTCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
* *
28947223 TTGGCTAATGGTG
66 TTGACTGATGGTG
* * * * * *
28947236 ATCTGTCCTAGGCTCGGGGTAAAAGATCGGATGGCTGTAATCTGCCTCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
*
28947301 TTGGCTGATGGTG
66 TTGACTGATGGTG
* * * * *
28947314 ATTTGCCCCAAGCTTGGGGTAAAAGATTGGATGGCTGCAATTTTCCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
28947379 TTGACTGATGGTG
66 TTGACTGATGGTG
* * * * * *
28947392 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTGTAATTTACCCTAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
*
28947457 TTGATTGATGGTG
66 TTGACTGATGGTG
* * * ** * *
28947470 ATCTGCCTCAAGCTCGGGGTAAGAGATCGGATGGTTAAAATCTGCCCTAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
*
28947535 TTGGCTGATGGTG
66 TTGACTGATGGTG
* * * * * * *
28947548 ATCTGTCTCAAGCTTGGGATAAAAGATCGAATGGCTGTAATCTGCCTCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
*
28947613 TT-AGCTGATAGTG
66 TTGA-CTGATGGTG
* * * * ** * * * * *
28947626 ATCTG-CCTAGGTTCAGGGTAAAAGATCAAACGACTGTAATCTGCCCCACGCTCAGGGTAAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGA
28947688 AATCGGACGG
Statistics
Matches: 450, Mismatches: 79, Indels: 3
0.85 0.15 0.01
Matches are distributed among these distances:
77 44 0.10
78 406 0.90
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (78 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
TTGACTGATGGTG
Found at i:28948668 original size:16 final size:17
Alignment explanation
Indices: 28948647--28948680 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28948637 TCGACCTCTC
28948647 TTTTTCT-TTTTCCATT
1 TTTTTCTATTTTCCATT
*
28948663 TTTTTCTATTTTCTATT
1 TTTTTCTATTTTCCATT
28948680 T
1 T
28948681 CCTTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTATTTTCCATT
Found at i:28948681 original size:23 final size:22
Alignment explanation
Indices: 28948643--28948701 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
28948633 CACCTCGACC
*
28948643 TCTCTTTTTCTTTTTCCATTTTT
1 TCTCTTTTTCTATTTCC-TTTTT
28948666 T-TCTATTTTCTATTTCCTTTTT
1 TCTCT-TTTTCTATTTCCTTTTT
28948688 TCTCTTTTT-TATTT
1 TCTCTTTTTCTATTT
28948702 TTTTCCCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.15
22 13 0.39
23 15 0.45
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.75
Consensus pattern (22 bp):
TCTCTTTTTCTATTTCCTTTTT
Found at i:28948705 original size:17 final size:16
Alignment explanation
Indices: 28948683--28948742 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
28948673 TTCTATTTCC
*
28948683 TTTTTTCTCTTTTTTA
1 TTTTTTTTCTTTTTTA
* *
28948699 TTTTTTTCCCTCTTTT-
1 TTTTTTT-TCTTTTTTA
*
28948715 TTTCTTTTCTTTTTTA
1 TTTTTTTTCTTTTTTA
28948731 TTTATTTTTCTT
1 TTT-TTTTTCTT
28948743 CATCGAATCT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 6 0.18
16 15 0.44
17 13 0.38
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTA
Found at i:28949644 original size:5 final size:5
Alignment explanation
Indices: 28949595--28949643 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
28949585 TTCATCTTGA
28949595 TTTTC TTTT- TTCTTCC TTTTC TTTTC TTCTT- TTTTC TTTTC TTTT-
1 TTTTC TTTTC TT-TT-C TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC
28949640 TTTT
1 TTTT
28949644 TGATAACATG
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
4 8 0.21
5 25 0.64
6 4 0.10
7 2 0.05
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:28949644 original size:15 final size:15
Alignment explanation
Indices: 28949595--28949643 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
28949585 TTCATCTTGA
28949595 TTTTCTTTT-TTCTT
1 TTTTCTTTTCTTCTT
28949609 CCTTTTCTTTTCTTCTT
1 --TTTTCTTTTCTTCTT
28949626 TTTTCTTTTCTT-TT
1 TTTTCTTTTCTTCTT
28949640 TTTT
1 TTTT
28949644 TGATAACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.19
15 12 0.38
16 9 0.28
17 5 0.16
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTCTTCTT
Found at i:28954726 original size:30 final size:30
Alignment explanation
Indices: 28954661--28954758 Score: 137
Period size: 29 Copynumber: 3.3 Consensus size: 30
28954651 GGCAAAATCA
* *
28954661 TAATTTTGGAGAAGTTTGA-GGTCAAAATG
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATG
** *
28954690 GGATTTTAGAAAAGTTTGAGGGTTAAAATG
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATG
28954720 TAATTTTAGAAAAGTTT-AGGGTCAAAATG
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATG
28954749 TAATTTTAGA
1 TAATTTTAGA
28954759 GAAAAATAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 36 0.60
30 24 0.40
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
TAATTTTAGAAAAGTTTGAGGGTCAAAATG
Found at i:28955834 original size:2 final size:2
Alignment explanation
Indices: 28955827--28955851 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28955817 TTATGTATTA
28955827 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 A
28955852 ACATTCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28960946 original size:2 final size:2
Alignment explanation
Indices: 28960941--28960972 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28960931 ATACACACAC
28960941 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
28960973 TGAAATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28964951 original size:5 final size:5
Alignment explanation
Indices: 28964941--28964967 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28964931 TGACCCCCCA
28964941 CCATC CCATC CCATC CCATC CCATC CC
1 CCATC CCATC CCATC CCATC CCATC CC
28964968 TGCCGTCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.63, G:0.00, T:0.19
Consensus pattern (5 bp):
CCATC
Found at i:28974103 original size:22 final size:23
Alignment explanation
Indices: 28974058--28974110 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
28974048 ACTCGTATTT
28974058 ATATTTTTTATTCATATTTTTTA
1 ATATTTTTTATTCATATTTTTTA
28974081 A-ATTTTTTATT-AT-TTTTAATTA
1 ATATTTTTTATTCATATTTT--TTA
28974103 ATATTTTT
1 ATATTTTT
28974111 AACATATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.15
21 2 0.07
22 14 0.52
23 7 0.26
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
ATATTTTTTATTCATATTTTTTA
Found at i:28974908 original size:5 final size:5
Alignment explanation
Indices: 28974898--28974931 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
28974888 ATATTATTTA
*
28974898 AAAAT AAAAT AAAAT AAAAC AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
28974932 GTACAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:28978346 original size:42 final size:42
Alignment explanation
Indices: 28978286--28978385 Score: 130
Period size: 42 Copynumber: 2.3 Consensus size: 42
28978276 GTGGCTAGTC
* *
28978286 CACACGACTGTGTGTCTACCCGTGTAACTCACTGACTTGGTT
1 CACACGACTGTGTCTCTACCCGTGTAACTCACTGACTTGGGT
* *
28978328 CACAC-ACTCGTGTCTCTACCCGTGTAACTTATTGACTTGGGT
1 CACACGACT-GTGTCTCTACCCGTGTAACTCACTGACTTGGGT
28978370 CACACGATCATGTGTC
1 CACACGA-C-TGTGTC
28978386 AGCCCGTGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 3 0.06
42 39 0.78
43 1 0.02
44 6 0.12
45 1 0.02
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (42 bp):
CACACGACTGTGTCTCTACCCGTGTAACTCACTGACTTGGGT
Found at i:28981003 original size:10 final size:11
Alignment explanation
Indices: 28980982--28981016 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
28980972 TTCTGAATTT
28980982 GAAAAATCATA
1 GAAAAATCATA
28980993 GAAAAAT-ATA
1 GAAAAATCATA
28981003 GAAAAATCACTA
1 GAAAAATCA-TA
28981015 GA
1 GA
28981017 GGCTGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 8 0.36
12 4 0.18
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (11 bp):
GAAAAATCATA
Found at i:28981534 original size:23 final size:22
Alignment explanation
Indices: 28981498--28981666 Score: 128
Period size: 23 Copynumber: 7.5 Consensus size: 22
28981488 ACGCTAGCGC
*
28981498 GCTTACT-TTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTGTGTGT
*
28981520 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTGTGTGT
* *
28981543 GCTTATTGTTTCGCACCT-CGTGT
1 GCTTACTGTTT-GCA-CTGTGTGT
* ** * *
28981566 GCCTACTGATTTGTGCTATGTGC
1 GCTTACTG-TTTGCACTGTGTGT
*
28981589 G-TCTACTGATTGCACTGTGTGT
1 GCT-TACTGTTTGCACTGTGTGT
* *
28981611 GCCTACTGGATTGCACTGTGTGT
1 GCTTACT-GTTTGCACTGTGTGT
*
28981634 GCTTACTGGATTGCACTGTGTGT
1 GCTTACT-GTTTGCACTGTGTGT
28981657 GCTTACTGTT
1 GCTTACTGTT
28981667 AAGTACTTCA
Statistics
Matches: 123, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
22 25 0.20
23 93 0.76
24 5 0.04
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (22 bp):
GCTTACTGTTTGCACTGTGTGT
Found at i:28981613 original size:45 final size:45
Alignment explanation
Indices: 28981562--28981664 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
28981552 TTCGCACCTC
**
28981562 GTGTGCCTACTGATTTGTGCTATGTGCG-TCTACT-GATTGCACTGT
1 GTGTGCCTACTGA-TTGCACTATGTGCGCT-TACTGGATTGCACTGT
* *
28981607 GTGTGCCTACTGGATTGCACTGTGTGTGCTTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTATGTGCGCTTACTGGATTGCACTGT
*
28981653 GTGTGCTTACTG
1 GTGTGCCTACTG
28981665 TTAAGTACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
45 26 0.52
46 24 0.48
ACGTcount: A:0.13, C:0.19, G:0.29, T:0.39
Consensus pattern (45 bp):
GTGTGCCTACTGATTGCACTATGTGCGCTTACTGGATTGCACTGT
Found at i:28984889 original size:34 final size:34
Alignment explanation
Indices: 28984795--28984947 Score: 191
Period size: 34 Copynumber: 4.5 Consensus size: 34
28984785 ACACGGTTAA
* *
28984795 CCATCTAGCACACGAAATGCTCGTATGAGCCAAT
1 CCATCTAGCACACCAAATGCTCGTATGAGCTAAT
* * * * *
28984829 -CATCCAACACAGCAAATGCTCATATGAGCTAGT
1 CCATCTAGCACACCAAATGCTCGTATGAGCTAAT
*
28984862 CCATCTAGCACACCAAGTGCTCGTATGAGCTAAT
1 CCATCTAGCACACCAAATGCTCGTATGAGCTAAT
* *
28984896 CCATCTAGCACACCAAATGCTCGTATAAGCTACT
1 CCATCTAGCACACCAAATGCTCGTATGAGCTAAT
* *
28984930 CCATCCAACACACCAAAT
1 CCATCTAGCACACCAAAT
28984948 AACACTGTAA
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
33 26 0.26
34 74 0.74
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (34 bp):
CCATCTAGCACACCAAATGCTCGTATGAGCTAAT
Found at i:28990156 original size:16 final size:16
Alignment explanation
Indices: 28990135--28990165 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28990125 TTCAATACTC
28990135 ATAAAAATAATATAAA
1 ATAAAAATAATATAAA
*
28990151 ATAAAATTAATATAA
1 ATAAAAATAATATAA
28990166 CTAGTCATAG
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAATATAAA
Found at i:28992868 original size:21 final size:20
Alignment explanation
Indices: 28992818--28992868 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
28992808 AGAGTTTTTA
28992818 GTATCGGTAGAAGTAAGACTT
1 GTATCGGTAGAAG-AAGACTT
* *
28992839 GTTTTGGTAGAAG-AGTCACTT
1 GTATCGGTAGAAGAAG--ACTT
28992860 GTATCGGTA
1 GTATCGGTA
28992869 AAAGTCTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
21 22 0.92
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.33
Consensus pattern (20 bp):
GTATCGGTAGAAGAAGACTT
Found at i:28993331 original size:20 final size:20
Alignment explanation
Indices: 28993303--28993351 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
28993293 CTACCTTGAG
*
28993303 ACTTCTACCGGTAGAACTTC
1 ACTTCTACCGATAGAACTTC
* *
28993323 ACTTTTACCGATATAACTTC
1 ACTTCTACCGATAGAACTTC
*
28993343 AGTTCTACC
1 ACTTCTACC
28993352 AATACAAGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.35
Consensus pattern (20 bp):
ACTTCTACCGATAGAACTTC
Found at i:28994398 original size:27 final size:27
Alignment explanation
Indices: 28994367--28994419 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28994357 ATTCTGAATA
* *
28994367 AAATACTAATATTTTAAAT-AAAATATT
1 AAATAATAATAATTT-AATGAAAATATT
28994394 AAATAATAATAATTTAATGAAAATAT
1 AAATAATAATAATTTAATGAAAATAT
28994420 CATTTAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
AAATAATAATAATTTAATGAAAATATT
Found at i:29002857 original size:2 final size:2
Alignment explanation
Indices: 29002850--29002888 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29002840 AAGCTTCTTC
29002850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29002889 TTTGAAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29003640 original size:76 final size:74
Alignment explanation
Indices: 29003508--29003677 Score: 261
Period size: 76 Copynumber: 2.3 Consensus size: 74
29003498 TTAGTAATTT
* * *
29003508 TATATACATTTTTTTACATTGTATATTTTATACATTTTTTTCAATATATACAATTTTATACTTAT
1 TATACACATTTTTTTACATTATATATATTATACATTTTTTTCAATATATACAATTTTATACTTAT
29003573 ACAATGTTA
66 ACAATGTTA
*
29003582 TATACACATTTTTTT-CTATATATATATATTATACATATTTTTTCAATATATACGATTTTATACT
1 TATACACATTTTTTTAC-AT-TATATATATTATACAT-TTTTTTCAATATATACAATTTTATACT
29003646 TATACAATGTTA
63 TATACAATGTTA
29003658 TATACACATTTTTTATACAT
1 TATACACATTTTTT-TACAT
29003678 ATCTACATAT
Statistics
Matches: 87, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
73 1 0.01
74 16 0.18
75 14 0.16
76 52 0.60
77 3 0.03
78 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (74 bp):
TATACACATTTTTTTACATTATATATATTATACATTTTTTTCAATATATACAATTTTATACTTAT
ACAATGTTA
Found at i:29003642 original size:29 final size:27
Alignment explanation
Indices: 29003587--29003644 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
29003577 TGTTATATAC
* *
29003587 ACATTTTTTTCTATATATATATATTAT
1 ACATTTTTTTCAATATATAGATATTAT
*
29003614 ACATATTTTTTCAATATATACGATTTTAT
1 ACAT-TTTTTTCAATATATA-GATATTAT
29003643 AC
1 AC
29003645 TTATACAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 14 0.54
29 8 0.31
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.53
Consensus pattern (27 bp):
ACATTTTTTTCAATATATAGATATTAT
Found at i:29003708 original size:76 final size:74
Alignment explanation
Indices: 29003551--29003708 Score: 203
Period size: 76 Copynumber: 2.1 Consensus size: 74
29003541 ATTTTTTTCA
*
29003551 ATATATACAATTTTATACTTATACAATGTTATATACACATTTTTTTCTATATATATATATTATAC
1 ATATATACAATTTTATACTTATACAATGTTATATACACATTTTTTTCTATATACATATATTATAC
*
29003616 ATATTTTTT
66 ATATTTATT
* *
29003625 CAATATATACGATTTTATACTTATACAATGTTATATACACATTTTTTATACATATCTACATATA-
1 --ATATATACAATTTTATACTTATACAATGTTATATACACATTTTTT-T-C-TATATACATATAT
*
29003689 TATATATATATTATT
61 TATACATAT-TTATT
29003704 -TATAT
1 ATATAT
29003709 TTACATATAT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
76 49 0.67
77 1 0.01
78 9 0.12
79 14 0.19
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (74 bp):
ATATATACAATTTTATACTTATACAATGTTATATACACATTTTTTTCTATATACATATATTATAC
ATATTTATT
Found at i:29011672 original size:11 final size:11
Alignment explanation
Indices: 29011656--29011687 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
29011646 ATAAAATTAG
29011656 ATATTGTAATA
1 ATATTGTAATA
29011667 ATATTGTAATA
1 ATATTGTAATA
29011678 ATATTGTAAT
1 ATATTGTAAT
29011688 GTAAGATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (11 bp):
ATATTGTAATA
Found at i:29011857 original size:51 final size:51
Alignment explanation
Indices: 29011800--29011897 Score: 187
Period size: 51 Copynumber: 1.9 Consensus size: 51
29011790 CATTTGCTTT
29011800 CCTATATATAATCAAAATCTCCATATACAACTCAGAGAAAAAAAAAAAAAC
1 CCTATATATAATCAAAATCTCCATATACAACTCAGAGAAAAAAAAAAAAAC
*
29011851 CCTATATATAATCAAAATCTCCATATACAACTCATAGAAAAAAAAAA
1 CCTATATATAATCAAAATCTCCATATACAACTCAGAGAAAAAAAAAA
29011898 CCCCCCGAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.21
Consensus pattern (51 bp):
CCTATATATAATCAAAATCTCCATATACAACTCAGAGAAAAAAAAAAAAAC
Found at i:29014984 original size:21 final size:22
Alignment explanation
Indices: 29014948--29014998 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
29014938 TTTTTAAATA
29014948 ATATTTATATAATTTTATTTTT
1 ATATTTATATAATTTTATTTTT
*
29014970 ATATTTA-ATAGTTTTATTTTT
1 ATATTTATATAATTTTATTTTT
*
29014991 TTATTTAT
1 ATATTTAT
29014999 TGAACTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
ATATTTATATAATTTTATTTTT
Found at i:29017272 original size:25 final size:25
Alignment explanation
Indices: 29017219--29017264 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
29017209 GTTGGATCCA
29017219 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
29017244 AATTAAA-TCTAAAAA-ATAATT
1 AATTAAATTCTAAAAAGATAATT
29017265 CCCTAATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:29032556 original size:17 final size:16
Alignment explanation
Indices: 29032534--29032579 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
29032524 AAAAAATCAC
29032534 AAAAAGAAAGAACAAGA
1 AAAAAGAAAGAA-AAGA
29032551 AAAAAG-AAGAAAAGA
1 AAAAAGAAAGAAAAGA
*
29032566 GAAAAGAAAAGAAA
1 AAAAAG-AAAGAAA
29032580 TATATTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 9 0.35
16 5 0.19
17 12 0.46
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAGA
Found at i:29037137 original size:21 final size:21
Alignment explanation
Indices: 29037111--29037166 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
29037101 GCACACTCTA
29037111 ATGCATCCACAACAAAGCCAG
1 ATGCATCCACAACAAAGCCAG
* * *
29037132 ATGCATCCACACCAGAGTCAG
1 ATGCATCCACAACAAAGCCAG
*
29037153 ATGCAGCCACAACA
1 ATGCATCCACAACA
29037167 CTCTTCAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.34, G:0.16, T:0.11
Consensus pattern (21 bp):
ATGCATCCACAACAAAGCCAG
Found at i:29040069 original size:53 final size:53
Alignment explanation
Indices: 29039921--29040188 Score: 380
Period size: 53 Copynumber: 5.1 Consensus size: 53
29039911 GTAAATGCAA
29039921 AAAGGTCTGATGACTCTATGTCAGT-GTGAGTTATATGAATCCTATTACGGATT
1 AAAGGTCTGATGACTCTATGTCA-TCGTGAGTTATATGAATCCTATTACGGATT
* *
29039974 AACGGTCTGATGACTC--TGTCATCGTGAGTTATATGAATCCTATTATGGATT
1 AAAGGTCTGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTACGGATT
*
29040025 AAAGGTCTGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTATGGATT
1 AAAGGTCTGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTACGGATT
* * * *
29040078 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAAATCCTATTCCAGATT
1 AAAGGTCTGATGACTCTATGTCATCGTGAGTTATATG-AATCCTATTACGGATT
* ** * * *
29040132 ACAGGTCCAATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
1 AAAGGTCTGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTACGGATT
29040185 AAAG
1 AAAG
29040189 TTCGATTACA
Statistics
Matches: 198, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
50 1 0.01
51 47 0.24
53 103 0.52
54 47 0.24
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (53 bp):
AAAGGTCTGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTACGGATT
Found at i:29040165 original size:107 final size:104
Alignment explanation
Indices: 29039933--29040188 Score: 361
Period size: 107 Copynumber: 2.4 Consensus size: 104
29039923 AGGTCTGATG
* *
29039933 ACTCTATGTCAGT-GTGAGTTATATGAATCCTATTACGGATTAACGGTCTGATGACTCTGTCATC
1 ACTCTATGTCA-TCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTCATC
** ** *
29039997 GTGAGTTATATGAATCCTATTATGGATTAAAGGTCTGATG
65 GTGAGTTATATGAATCCTATTACAGATTAAAGGTCCAATA
*
29040037 ACTCTATGTCATCGTGAGTTATATGAATCCTATTATGGATTAAAGGTCCGATGACTCTGTGTCAT
1 ACTCTATGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCCGATGACTC--TGTCAT
* *
29040102 CGTGAGTTATATGAAATCCTATTCCAGATTACAGGTCCAATA
64 CGTGAGTTATATG-AATCCTATTACAGATTAAAGGTCCAATA
* *
29040144 ACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATTAAAG
1 ACTCTATGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAG
29040189 TTCGATTACA
Statistics
Matches: 135, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
103 1 0.01
104 52 0.39
106 19 0.14
107 63 0.47
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (104 bp):
ACTCTATGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTCATCG
TGAGTTATATGAATCCTATTACAGATTAAAGGTCCAATA
Found at i:29042018 original size:15 final size:15
Alignment explanation
Indices: 29042000--29042033 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29041990 GATGCCAAGG
29042000 AAGAAGATGCAGAGA
1 AAGAAGATGCAGAGA
* *
29042015 AAGAAGGTGCTGAGA
1 AAGAAGATGCAGAGA
29042030 AAGA
1 AAGA
29042034 TTCAACTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.35, T:0.09
Consensus pattern (15 bp):
AAGAAGATGCAGAGA
Found at i:29042328 original size:21 final size:20
Alignment explanation
Indices: 29042302--29042341 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29042292 CTCTAAAGAC
*
29042302 AAAAAGCGCAGGAAGGAGGAG
1 AAAAAGAGCAGGAA-GAGGAG
*
29042323 AAAAAGAGGAGGAAGAGGA
1 AAAAAGAGCAGGAAGAGGA
29042342 AGCATCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.53, C:0.05, G:0.42, T:0.00
Consensus pattern (20 bp):
AAAAAGAGCAGGAAGAGGAG
Found at i:29045744 original size:29 final size:30
Alignment explanation
Indices: 29045680--29045738 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29045670 ATGCTAGGGG
29045680 TGAATT-TAAAATTTTTAAGAGGGTCAAAAT
1 TGAATTAT-AAATTTTTAAGAGGGTCAAAAT
* *
29045710 TGAATTATAAATTTTTTAGA-TGTCAAAAT
1 TGAATTATAAATTTTTAAGAGGGTCAAAAT
29045739 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 8 0.31
30 17 0.65
31 1 0.04
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (30 bp):
TGAATTATAAATTTTTAAGAGGGTCAAAAT
Found at i:29048957 original size:24 final size:24
Alignment explanation
Indices: 29048883--29049075 Score: 140
Period size: 24 Copynumber: 8.1 Consensus size: 24
29048873 GTTCGTTACA
* **
29048883 TTTACGCTCGTCAGCTTCCACATA
1 TTTACGCTCGTCAGCTTGCACACG
* ** * *
29048907 TTT-TGCTCGTCAGCTTATATACA
1 TTTACGCTCGTCAGCTTGCACACG
* * *
29048930 TTTACACTCGTCAACTTGCACATG
1 TTTACGCTCGTCAGCTTGCACACG
* *
29048954 TTTACAG-TCGTTATCTTGCACACG
1 TTTAC-GCTCGTCAGCTTGCACACG
** * *
29048978 TTTACGCTCGTCAGCTTATATATG
1 TTTACGCTCGTCAGCTTGCACACG
29049002 TTTACGCTCGTCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTGCACACG
** * *
29049026 TTTACGCTCG-CAGCTTATATACT
1 TTTACGCTCGTCAGCTTGCACACG
* * *
29049049 TTTATGCTAGTCAGCTTGCACATG
1 TTTACGCTCGTCAGCTTGCACACG
29049073 TTT
1 TTT
29049076 GTGCTTGTAA
Statistics
Matches: 127, Mismatches: 38, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
23 36 0.28
24 91 0.72
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.38
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTGCACACG
Found at i:29049062 original size:47 final size:48
Alignment explanation
Indices: 29048968--29049075 Score: 166
Period size: 47 Copynumber: 2.3 Consensus size: 48
29048958 CAGTCGTTAT
*
29048968 CTTGCACACGTTTACGCTCGTCAGCTTATATATGTTTACGCTCGTCAG
1 CTTGCACACGTTTACGCTCGTCAGCTTATATATGTTTACGCTAGTCAG
*
29049016 CTTGCACACGTTTACGCTCG-CAGCTTATATACT-TTTATGCTAGTCAG
1 CTTGCACACGTTTACGCTCGTCAGCTTATATA-TGTTTACGCTAGTCAG
*
29049063 CTTGCACATGTTT
1 CTTGCACACGTTT
29049076 GTGCTTGTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 35 0.62
48 21 0.38
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (48 bp):
CTTGCACACGTTTACGCTCGTCAGCTTATATATGTTTACGCTAGTCAG
Found at i:29062208 original size:2 final size:2
Alignment explanation
Indices: 29062201--29062227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29062191 TTAAAGAGAA
29062201 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
29062228 AAGACTTTAA
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:29063380 original size:13 final size:13
Alignment explanation
Indices: 29063362--29063429 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
29063352 CTACAATTAC
29063362 TTCATATAATCAT
1 TTCATATAATCAT
29063375 TTCATAT-ATCAAT
1 TTCATATAATC-AT
*
29063388 TTCCATATAA-GAT
1 TT-CATATAATCAT
**
29063401 TTTGTATAATCAT
1 TTCATATAATCAT
*
29063414 TTAACACATAATCAT
1 TT--CATATAATCAT
29063429 T
1 T
29063430 ATGTATAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 8 0.19
13 19 0.45
14 5 0.12
15 10 0.24
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (13 bp):
TTCATATAATCAT
Found at i:29064868 original size:2 final size:2
Alignment explanation
Indices: 29064861--29064914 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
29064851 AAAGTACTTT
29064861 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
29064903 CA CA CA CA CA CA
1 CA CA CA CA CA CA
29064915 TATATATATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:29066765 original size:43 final size:43
Alignment explanation
Indices: 29066704--29066789 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
29066694 AAAAGTTCAT
* *
29066704 TACATTTACGCTCGTCAACATGAATATGTTTACGCTTGTCAGC
1 TACATTTACGCTCGTCAACATGAACATGTTTACGCTCGTCAGC
* * * *
29066747 TACATTTATGTTCGTCAACTTGCACATGTTTACGCTCGTCAGC
1 TACATTTACGCTCGTCAACATGAACATGTTTACGCTCGTCAGC
29066790 ATGAATATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (43 bp):
TACATTTACGCTCGTCAACATGAACATGTTTACGCTCGTCAGC
Found at i:29066785 original size:24 final size:22
Alignment explanation
Indices: 29066708--29066787 Score: 58
Period size: 24 Copynumber: 3.6 Consensus size: 22
29066698 GTTCATTACA
*
29066708 TTTACGCTCGTCAACATGAATATG
1 TTTACGCTCGTCAAC-TG-ACATG
* *
29066732 TTTACGCTTGTCAGCT-ACA--
1 TTTACGCTCGTCAACTGACATG
* *
29066751 TTTATGTTCGTCAACTTGCACATG
1 TTTACGCTCGTCAAC-TG-ACATG
29066775 TTTACGCTCGTCA
1 TTTACGCTCGTCA
29066788 GCATGAATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
19 11 0.26
20 1 0.02
21 2 0.05
22 3 0.07
23 1 0.02
24 24 0.57
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.38
Consensus pattern (22 bp):
TTTACGCTCGTCAACTGACATG
Found at i:29067924 original size:14 final size:15
Alignment explanation
Indices: 29067905--29067933 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29067895 CGAGAAAATG
29067905 ACCAATTT-AAGCTT
1 ACCAATTTGAAGCTT
29067919 ACCAATTTGAAGCTT
1 ACCAATTTGAAGCTT
29067934 GAACCTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (15 bp):
ACCAATTTGAAGCTT
Found at i:29069476 original size:13 final size:13
Alignment explanation
Indices: 29069458--29069525 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
29069448 CTACAATTAC
29069458 TTCATATAATCAT
1 TTCATATAATCAT
29069471 TTCATAT-ATCTAT
1 TTCATATAATC-AT
*
29069484 TTCCATATAA-GAT
1 TT-CATATAATCAT
**
29069497 TTTGTATAATCAT
1 TTCATATAATCAT
*
29069510 TTAACACATAATCAT
1 TT--CATATAATCAT
29069525 T
1 T
29069526 ATGTATAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 8 0.19
13 19 0.45
14 5 0.12
15 10 0.24
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.46
Consensus pattern (13 bp):
TTCATATAATCAT
Found at i:29070233 original size:23 final size:23
Alignment explanation
Indices: 29070207--29070251 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29070197 TAAAGAAAAA
29070207 AGAACACCATCC-AAGCAGATAAC
1 AGAACACCA-CCGAAGCAGATAAC
*
29070230 AGAACACCACCGAAGCGGATAA
1 AGAACACCACCGAAGCAGATAA
29070252 ATAGAGAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.47, C:0.29, G:0.18, T:0.07
Consensus pattern (23 bp):
AGAACACCACCGAAGCAGATAAC
Found at i:29071769 original size:21 final size:21
Alignment explanation
Indices: 29071743--29071797 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
29071733 TATAGATTTG
**
29071743 TACCGATACAAGTGACAGTTC
1 TACCGATACAAGTGACACCTC
*
29071764 TACCGATACAAGTGACTCCTC
1 TACCGATACAAGTGACACCTC
29071785 TACCGATACAAGT
1 TACCGATACAAGT
29071798 CTTACTTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (21 bp):
TACCGATACAAGTGACACCTC
Found at i:29071807 original size:21 final size:20
Alignment explanation
Indices: 29071743--29071814 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
29071733 TATAGATTTG
*
29071743 TACCGATACAAGTGAC-AGTTC
1 TACCGATACAAGT--CTACTTC
*
29071764 TACCGATACAAGTGACT-CCTC
1 TACCGATACAAGT--CTACTTC
29071785 TACCGATACAAGTCTTACTTC
1 TACCGATACAAGTC-TACTTC
*
29071806 TATCGATAC
1 TACCGATAC
29071815 TAAAAACTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 42 0.95
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (20 bp):
TACCGATACAAGTCTACTTC
Found at i:29072006 original size:135 final size:136
Alignment explanation
Indices: 29071783--29072066 Score: 525
Period size: 135 Copynumber: 2.1 Consensus size: 136
29071773 AAGTGACTCC
* * *
29071783 TCTACCGATACAAGTCTTACTTCTATCGATACTAAAAACTCCAAATAGCTAAAAATCTTACCCTG
1 TCTACCGATACAAGTCTTACCTCTATCGATACTAAAAACTCCAAATAGCTAAAAATCATACCCTA
*
29071848 CTACTTCTATCGATACAAGTATGCAAACTACCGATACTTCTAAACACATGACTACCGATACTTTT
66 CTACTTCTACCGATACAAGTATGCAAACTACCGATACTTCTAAACACATGACTACCGATACTTTT
29071913 TATTCA
131 TATTCA
29071919 TCTACCGATACAAGTCTTACCTCTATCGATACT-AAAACTCCAAATAGCTAAAAATCATACCCTA
1 TCTACCGATACAAGTCTTACCTCTATCGATACTAAAAACTCCAAATAGCTAAAAATCATACCCTA
29071983 CTACTTCTACCGATACAAGTATGCAAACTACCGATACTTCTAAACACATGACTACCGATACTTTT
66 CTACTTCTACCGATACAAGTATGCAAACTACCGATACTTCTAAACACATGACTACCGATACTTTT
29072048 TATTCA
131 TATTCA
29072054 TCTACCGATACAA
1 TCTACCGATACAA
29072067 CCCAAGTCAG
Statistics
Matches: 144, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
135 112 0.78
136 32 0.22
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.30
Consensus pattern (136 bp):
TCTACCGATACAAGTCTTACCTCTATCGATACTAAAAACTCCAAATAGCTAAAAATCATACCCTA
CTACTTCTACCGATACAAGTATGCAAACTACCGATACTTCTAAACACATGACTACCGATACTTTT
TATTCA
Found at i:29075136 original size:24 final size:24
Alignment explanation
Indices: 29075102--29075354 Score: 290
Period size: 24 Copynumber: 10.5 Consensus size: 24
29075092 CAAGTTCATT
* * *
29075102 ACGTTTACGCTCGTCAGCATGTAT
1 ACGTTTACGCTCGTCAGCTTGCAC
* ** *
29075126 ATGTTTACGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTGCAC
* * ** *
29075150 ATGTTTATGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTGCAC
*
29075174 ACGTTTACGCTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
**
29075198 ACGTTTACGCTCGTCAGCTTATAC
1 ACGTTTACGCTCGTCAGCTTGCAC
* *
29075222 ACGTTTACGCTCATTAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
* *
29075246 ATGTTTACGCTCGTCAGCATGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
29075270 ACGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
29075294 ACGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
* * * *
29075318 ACCTTTACGCTCGTCAGCATGAAT
1 ACGTTTACGCTCGTCAGCTTGCAC
*
29075342 ACGTTTATGCTCG
1 ACGTTTACGCTCG
29075355 CTCGTCAGCA
Statistics
Matches: 200, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 200 1.00
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.34
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAGCTTGCAC
Found at i:29075189 original size:72 final size:72
Alignment explanation
Indices: 29075102--29075354 Score: 326
Period size: 72 Copynumber: 3.5 Consensus size: 72
29075092 CAAGTTCATT
* * * * * *
29075102 ACGTTTACGCTCGTCAGCATGTATATGTTTACGCTCGTCAGCTTATATATGTTTATGCTCGTCAG
1 ACGTTTACGCTCGTCAGCATGCACACGTTTACGCTCGTCAGCTTATACACGTTTACGCTCGTCAG
** *
29075167 CTTATAT
66 CTTGCAC
* * * *
29075174 ACGTTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATACACGTTTACGCTCATTAG
1 ACGTTTACGCTCGTCAGCATGCACACGTTTACGCTCGTCAGCTTATACACGTTTACGCTCGTCAG
29075239 CTTGCAC
66 CTTGCAC
* **
29075246 ATGTTTACGCTCGTCAGCATGCACACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAG
1 ACGTTTACGCTCGTCAGCATGCACACGTTTACGCTCGTCAGCTTATACACGTTTACGCTCGTCAG
29075311 CTTGCAC
66 CTTGCAC
* * * *
29075318 ACCTTTACGCTCGTCAGCATGAATACGTTTATGCTCG
1 ACGTTTACGCTCGTCAGCATGCACACGTTTACGCTCG
29075355 CTCGTCAGCA
Statistics
Matches: 156, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 156 1.00
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.34
Consensus pattern (72 bp):
ACGTTTACGCTCGTCAGCATGCACACGTTTACGCTCGTCAGCTTATACACGTTTACGCTCGTCAG
CTTGCAC
Found at i:29075774 original size:17 final size:17
Alignment explanation
Indices: 29075752--29075795 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 17
29075742 TGTCCTACCC
29075752 TTCAATTATAATTCCAT
1 TTCAATTATAATTCCAT
29075769 TTCAATTAT-A--CCAT
1 TTCAATTATAATTCCAT
29075783 TTCAATTATAATT
1 TTCAATTATAATT
29075796 TTCAAATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 13 0.54
15 1 0.04
16 1 0.04
17 9 0.38
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (17 bp):
TTCAATTATAATTCCAT
Found at i:29076705 original size:24 final size:25
Alignment explanation
Indices: 29076668--29076714 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
29076658 TTTTCTTTTT
*
29076668 CTAGTCAAATTCTGATTA-TTTATC
1 CTAGTCAAACTCTGATTAGTTTATC
* *
29076692 CTAGTCGAACTCTGTTTAGTTTA
1 CTAGTCAAACTCTGATTAGTTTA
29076715 GATTATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (25 bp):
CTAGTCAAACTCTGATTAGTTTATC
Found at i:29083888 original size:15 final size:15
Alignment explanation
Indices: 29083870--29083899 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29083860 TTCACTATTA
*
29083870 TGTCTTTCGTATTTT
1 TGTCTTTCATATTTT
29083885 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
29083900 GCATGAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:29091666 original size:17 final size:19
Alignment explanation
Indices: 29091620--29091668 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
29091610 AGTATTTTAT
29091620 TAATTTAATATTAAAGTGA
1 TAATTTAATATTAAAGTGA
*
29091639 TTATCTTAATATTAAA-T-A
1 TAAT-TTAATATTAAAGTGA
29091657 TAATTTAATATT
1 TAATTTAATATT
29091669 TATCTACAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.30
18 4 0.15
19 4 0.15
20 11 0.41
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TAATTTAATATTAAAGTGA
Found at i:29093614 original size:31 final size:31
Alignment explanation
Indices: 29093563--29093621 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
29093553 AACCTAAAAC
*
29093563 TTAAATAAAAATTTTTAAATAGTTCAATGAT
1 TTAAATAAAAATTTTCAAATAGTTCAATGAT
*
29093594 TTAAATGAAAAA-TTTCAAATATTTCAAT
1 TTAAAT-AAAAATTTTCAAATAGTTCAAT
29093622 AACTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (31 bp):
TTAAATAAAAATTTTCAAATAGTTCAATGAT
Found at i:29094787 original size:30 final size:30
Alignment explanation
Indices: 29094750--29094852 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 30
29094740 TTAATATAAC
*
29094750 ATTTGATACTTGTAA-TTAACACTTTTTTTA
1 ATTTGATACTT-AAACTTAACACTTTTTTTA
* *
29094780 GTTTGATACTTAAACTTAACATTTTTTTTA
1 ATTTGATACTTAAACTTAACACTTTTTTTA
* * * *
29094810 ATTTGGTACCTAAATTTAACACTTTTTTAA
1 ATTTGATACTTAAACTTAACACTTTTTTTA
*
29094840 AGTTG-TACTTAAA
1 ATTTGATACTTAAA
29094853 TTTTTTGGGG
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 9 0.15
30 52 0.85
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (30 bp):
ATTTGATACTTAAACTTAACACTTTTTTTA
Found at i:29095130 original size:32 final size:31
Alignment explanation
Indices: 29095094--29095193 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 31
29095084 ATCTTAGGTG
29095094 CCAAATTAGAAAAAAAATACCAAGTTCAAGTA
1 CCAAATTAGAAAAAAAATA-CAAGTTCAAGTA
** * *
29095126 CCAAATT-GAGTCAAAAA-A-AAGTTTAGGTA
1 CCAAATTAGA-AAAAAAATACAAGTTCAAGTA
* * * *
29095155 CCAAATTAGGAAAAAAGTGTCAAATTCAAGTA
1 CCAAATTAGAAAAAAAAT-ACAAGTTCAAGTA
29095187 CCAAATT
1 CCAAATT
29095194 GGGTCAAAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
29 20 0.39
30 1 0.02
31 3 0.06
32 27 0.53
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (31 bp):
CCAAATTAGAAAAAAAATACAAGTTCAAGTA
Found at i:29095170 original size:29 final size:28
Alignment explanation
Indices: 29095057--29095170 Score: 70
Period size: 29 Copynumber: 3.8 Consensus size: 28
29095047 ATTTAATAAA
*
29095057 TTTAGGTATCAAATT-GAATATAAAAAAA-
1 TTTAGGTACCAAATTGGAA-A-AAAAAAAG
* *
29095085 TCTTAGGTGCCAAATTAGAAAAAAAATACCAAG
1 T-TTAGGTACCAAATT-GGAAAAAAA-A--AAG
* * **
29095118 TTCAAGTACCAAATTGAGTCAAAAAAAAG
1 TTTAGGTACCAAATTG-GAAAAAAAAAAG
29095147 TTTAGGTACCAAATTAGGAAAAAA
1 TTTAGGTACCAAATT-GGAAAAAA
29095171 GTGTCAAATT
Statistics
Matches: 64, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
28 1 0.02
29 37 0.58
30 3 0.05
31 4 0.06
32 18 0.28
33 1 0.02
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.25
Consensus pattern (28 bp):
TTTAGGTACCAAATTGGAAAAAAAAAAG
Found at i:29095211 original size:60 final size:61
Alignment explanation
Indices: 29095078--29095251 Score: 228
Period size: 61 Copynumber: 2.9 Consensus size: 61
29095068 AATTGAATAT
* * * *
29095078 AAAAAAA-TCTTAGGTGCCAAATTAGAAAAAAAATACCAAGTTCAAGTACCAAATTGAGTCA
1 AAAAAAAGT-TTAGGTACCAAATTAGGAAAAAAGTATCAAGTTCAAGTACCAAATTGAGTCA
* * *
29095139 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAGTGTCAAATTCAAGTACCAAATTGGGTC-
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAGTATCAAGTTCAAGTACCAAATTGAGTCA
* * *
29095199 AAAAAAAGTTTAGTTATCAAATTAAG-AAAAAGTATCAAGTTCAAGTACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAGTATCAAGTTCAAGTACCAAAT
29095252 GTTATATTAA
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
59 25 0.25
60 23 0.23
61 51 0.51
62 1 0.01
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (61 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAGTATCAAGTTCAAGTACCAAATTGAGTCA
Found at i:29096627 original size:14 final size:14
Alignment explanation
Indices: 29096605--29096636 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
29096595 CAATTTGAAA
*
29096605 TTTTCTTTTTATTT
1 TTTTATTTTTATTT
29096619 TTTTATTTTTATTT
1 TTTTATTTTTATTT
29096633 TTTT
1 TTTT
29096637 CTTCCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:29097509 original size:20 final size:20
Alignment explanation
Indices: 29097486--29097530 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
29097476 TTAAATTTCC
*
29097486 TTTATTTCATTTTCATTTTA
1 TTTATTTCATTTTCACTTTA
*
29097506 TTTATTTCATTTTCCCTTTA
1 TTTATTTCATTTTCACTTTA
29097526 TTTAT
1 TTTAT
29097531 GTTTCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTCATTTTCACTTTA
Found at i:29097513 original size:14 final size:16
Alignment explanation
Indices: 29097486--29097518 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
29097476 TTAAATTTCC
29097486 TTTATTTCATTTTCAT
1 TTTATTTCATTTTCAT
29097502 TTTATTT-A-TTTCAT
1 TTTATTTCATTTTCAT
29097516 TTT
1 TTT
29097519 CCCTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTTCATTTTCAT
Found at i:29097545 original size:22 final size:22
Alignment explanation
Indices: 29097486--29097560 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 22
29097476 TTAAATTTCC
**
29097486 TTTA-TTTC-ATTTTCATTTTA
1 TTTATTTTCTATTTTCCCTTTA
29097506 TTTA-TTTC-ATTTTCCCTTTA
1 TTTATTTTCTATTTTCCCTTTA
*
29097526 TTTATGTTTCTATTTT-CCTTTG
1 TTTAT-TTTCTATTTTCCCTTTA
29097548 TTTCATTTTCTAT
1 TTT-ATTTTCTAT
29097561 GTTCTTCGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
20 22 0.46
22 19 0.40
23 7 0.15
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTATTTTCTATTTTCCCTTTA
Found at i:29113264 original size:14 final size:15
Alignment explanation
Indices: 29113229--29113266 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
29113219 ATTAATGTTA
29113229 TATGGAATTTTGAAT
1 TATGGAATTTTGAAT
29113244 TGA-GGAATTTT-AAT
1 T-ATGGAATTTTGAAT
29113258 TATGGAATT
1 TATGGAATT
29113267 AAAAGTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 10 0.48
15 9 0.43
16 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
TATGGAATTTTGAAT
Found at i:29127911 original size:85 final size:85
Alignment explanation
Indices: 29127768--29127938 Score: 297
Period size: 85 Copynumber: 2.0 Consensus size: 85
29127758 ATGTATTGTG
*
29127768 AGTGTTAAAGGCAAATATGATAGTTGGTTTATATACCAAATGTGTTTTCCATGAGTAAGTTTAAT
1 AGTGTTAAAGGAAAATATGATAGTTGGTTTATATACCAAATGTGTTTTCCATGAGTAAGTTTAAT
* *
29127833 ATTAGGATAAAATTATATGT
66 ATCAGGATAAAATTAAATGT
* *
29127853 AGTGTTAAAGGAAAATATGATGGTTGGTTTATATATCAAATGTGTTTTCCATGAGTAAGTTTAAT
1 AGTGTTAAAGGAAAATATGATAGTTGGTTTATATACCAAATGTGTTTTCCATGAGTAAGTTTAAT
29127918 ATCAGGATAAAATTAAATGT
66 ATCAGGATAAAATTAAATGT
29127938 A
1 A
29127939 CTACATATGA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (85 bp):
AGTGTTAAAGGAAAATATGATAGTTGGTTTATATACCAAATGTGTTTTCCATGAGTAAGTTTAAT
ATCAGGATAAAATTAAATGT
Found at i:29131672 original size:46 final size:46
Alignment explanation
Indices: 29131588--29131676 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
29131578 ACTGTGCCGT
* *
29131588 TTGAGCAATTGGCAACACTCCTTCCTTATCACTGATGATTGAACGC
1 TTGAGCAATTGGCAACACTCCTTCCCTATCACTAATGATTGAACGC
* *
29131634 TTGAGCAATTGGCAGCACTCCTTCCCTGTCA-TCAATGATTGAA
1 TTGAGCAATTGGCAACACTCCTTCCCTATCACT-AATGATTGAA
29131677 GCAATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (46 bp):
TTGAGCAATTGGCAACACTCCTTCCCTATCACTAATGATTGAACGC
Found at i:29133966 original size:26 final size:26
Alignment explanation
Indices: 29133923--29134112 Score: 165
Period size: 26 Copynumber: 7.5 Consensus size: 26
29133913 TTTTAGATTG
*
29133923 TGGCTCGT-GGAGCGAAATATCTATC
1 TGGCTCGTAAGAGCGAAATATCTATC
* * *
29133948 TGGCTTGTAAGAGTGAAATATCTGTC
1 TGGCTCGTAAGAGCGAAATATCTATC
* *
29133974 TGGCTCGTAAGAGCAAAATATCTATT
1 TGGCTCGTAAGAGCGAAATATCTATC
* * * *
29134000 TGGCTCGTAAGAACGATAT-TCTGTA
1 TGGCTCGTAAGAGCGAAATATCTATC
* *
29134025 TGGCTCGTAAGAGCAAAATATCTATT
1 TGGCTCGTAAGAGCGAAATATCTATC
* * *
29134051 TGGCTCGTAAAAGC--AATATTCTGTA
1 TGGCTCGTAAGAGCGAAATA-TCTATC
* * * *
29134076 TGGCTCATAAAAGCGATAT-TCTGTC
1 TGGCTCGTAAGAGCGAAATATCTATC
29134101 TGGCTCGTAAGA
1 TGGCTCGTAAGA
29134113 ACGATACTTT
Statistics
Matches: 133, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
24 4 0.03
25 59 0.44
26 68 0.51
27 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (26 bp):
TGGCTCGTAAGAGCGAAATATCTATC
Found at i:29134029 original size:51 final size:51
Alignment explanation
Indices: 29133923--29134141 Score: 230
Period size: 51 Copynumber: 4.3 Consensus size: 51
29133913 TTTTAGATTG
* * * ** * *
29133923 TGGCTCGT-GGAGCGAAATATCTATCTGGCTTGTAAGAGTGAAATATCTGTC
1 TGGCTCGTAAGAGCAAAATATCTATCTGGCTCGTAAGAACGATAT-TCTGTA
*
29133974 TGGCTCGTAAGAGCAAAATATCTATTTGGCTCGTAAGAACGATATTCTGTA
1 TGGCTCGTAAGAGCAAAATATCTATCTGGCTCGTAAGAACGATATTCTGTA
* *
29134025 TGGCTCGTAAGAGCAAAATATCTATTTGGCTCGTAA-AAGCAATATTCTGTA
1 TGGCTCGTAAGAGCAAAATATCTATCTGGCTCGTAAGAA-CGATATTCTGTA
* * * * * *
29134076 TGGCTCATAAAAGCGATAT-TCTGTCTGGCTCGTAAGAACGATACTT-TGTC
1 TGGCTCGTAAGAGCAAAATATCTATCTGGCTCGTAAGAACGATA-TTCTGTA
*
29134126 TAGCTCGTAAGAGCAA
1 TGGCTCGTAAGAGCAA
29134142 TAATCTGACT
Statistics
Matches: 143, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
50 35 0.24
51 79 0.55
52 29 0.20
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (51 bp):
TGGCTCGTAAGAGCAAAATATCTATCTGGCTCGTAAGAACGATATTCTGTA
Found at i:29134117 original size:25 final size:25
Alignment explanation
Indices: 29133964--29134148 Score: 144
Period size: 25 Copynumber: 7.4 Consensus size: 25
29133954 GTAAGAGTGA
*
29133964 AATA-TCTGTCTGGCTCGTAAGAGC
1 AATATTCTGTCTGGCTCGTAAGAAC
* * *
29133988 AAAATATCTATTTGGCTCGTAAGAAC
1 AATAT-TCTGTCTGGCTCGTAAGAAC
* * *
29134014 GATATTCTGTATGGCTCGTAAGAGC
1 AATATTCTGTCTGGCTCGTAAGAAC
* * *
29134039 AAAATATCTATTTGGCTCGTAA-AAGC
1 AATAT-TCTGTCTGGCTCGTAAGAA-C
* *
29134065 AATATTCTGTATGGCTCATAA-AAGC
1 AATATTCTGTCTGGCTCGTAAGAA-C
*
29134090 GATATTCTGTCTGGCTCGTAAGAAC
1 AATATTCTGTCTGGCTCGTAAGAAC
* * *
29134115 GATACTT-TGTCTAGCTCGTAAGAGC
1 AATA-TTCTGTCTGGCTCGTAAGAAC
*
29134140 AATAATCTG
1 AATATTCTG
29134149 ACTAGGTTCG
Statistics
Matches: 129, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
24 4 0.03
25 82 0.64
26 43 0.33
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (25 bp):
AATATTCTGTCTGGCTCGTAAGAAC
Found at i:29138839 original size:26 final size:26
Alignment explanation
Indices: 29138805--29138929 Score: 92
Period size: 26 Copynumber: 4.9 Consensus size: 26
29138795 CTAGCTCGTG
* *
29138805 GAGCAAAATATCTATTTGGCTCGCAA
1 GAGCAAAATATCTGTCTGGCTCGCAA
* * *
29138831 GAGCGAAATATCTGTCTCGCTCGGAA
1 GAGCAAAATATCTGTCTGGCTCGCAA
* * *
29138857 AAGCAAAATATCTGCCTGGCTCGTAA
1 GAGCAAAATATCTGTCTGGCTCGCAA
* * * **
29138883 GAGCGATAT-TCTGTCTAGCTCATAA
1 GAGCAAAATATCTGTCTGGCTCGCAA
** *
29138908 GAGTGATAT-TCTGTCTGGCTCG
1 GAGCAAAATATCTGTCTGGCTCG
29138930 TAAAAGCGAC
Statistics
Matches: 80, Mismatches: 19, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
25 32 0.40
26 48 0.60
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (26 bp):
GAGCAAAATATCTGTCTGGCTCGCAA
Found at i:29138877 original size:52 final size:51
Alignment explanation
Indices: 29138806--29138903 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 51
29138796 TAGCTCGTGG
** *
29138806 AGCAAAATATCTATTTGGCTCGCAAGAGCGAAATATCTGTCTCGCTCGGAAA
1 AGCAAAATATCTACCTGGCTCGCAAGAGCGAAAT-TCTGTCTAGCTCGGAAA
* * *
29138858 AGCAAAATATCTGCCTGGCTCGTAAGAGCGATATTCTGTCTAGCTC
1 AGCAAAATATCTACCTGGCTCGCAAGAGCGAAATTCTGTCTAGCTC
29138904 ATAAGAGTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 11 0.28
52 29 0.73
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (51 bp):
AGCAAAATATCTACCTGGCTCGCAAGAGCGAAATTCTGTCTAGCTCGGAAA
Found at i:29138903 original size:25 final size:25
Alignment explanation
Indices: 29138821--29138965 Score: 137
Period size: 25 Copynumber: 5.7 Consensus size: 25
29138811 AATATCTATT
* *
29138821 TGGCTCGCAAGAGCGAAATATCTGTC
1 TGGCTCGTAAGAGCGATAT-TCTGTC
* * * * * *
29138847 TCGCTCGGAAAAGCAAAATATCTGCC
1 TGGCTCGTAAGAGCGATAT-TCTGTC
29138873 TGGCTCGTAAGAGCGATATTCTGTC
1 TGGCTCGTAAGAGCGATATTCTGTC
* * *
29138898 TAGCTCATAAGAGTGATATTCTGTC
1 TGGCTCGTAAGAGCGATATTCTGTC
* * *
29138923 TGGCTCGTAAAAGCGACACTCTGTC
1 TGGCTCGTAAGAGCGATATTCTGTC
*
29138948 TTGCTCGTAAGAGCGATA
1 TGGCTCGTAAGAGCGATA
29138966 ATTTGACTCG
Statistics
Matches: 96, Mismatches: 23, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
25 61 0.64
26 35 0.36
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (25 bp):
TGGCTCGTAAGAGCGATATTCTGTC
Found at i:29144986 original size:13 final size:13
Alignment explanation
Indices: 29144968--29144992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29144958 ATTAACTCCG
29144968 AAAATATTTAAGA
1 AAAATATTTAAGA
29144981 AAAATATTTAAG
1 AAAATATTTAAG
29144993 GACTCTGTTT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
AAAATATTTAAGA
Found at i:29146593 original size:25 final size:25
Alignment explanation
Indices: 29146565--29146619 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29146555 TGCATATCAA
*
29146565 AGAGCACTAACGGGCTAATATTCGG
1 AGAGCACTAACGGGCTAATAATCGG
* * *
29146590 AGAGTACTAACGTGCTAATAATCTG
1 AGAGCACTAACGGGCTAATAATCGG
29146615 AGAGC
1 AGAGC
29146620 GTGCTAAGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (25 bp):
AGAGCACTAACGGGCTAATAATCGG
Found at i:29149221 original size:83 final size:83
Alignment explanation
Indices: 29149076--29149242 Score: 246
Period size: 83 Copynumber: 2.0 Consensus size: 83
29149066 AGTATTTAAT
* * * *
29149076 ACATAAGTCCAAAACGTTTACGCTCGTCAGCTAATCAGAATCAGAATGATCATGTTAGGTTATCC
1 ACATAAGTCCAAAACATTTACGCTCGTAAGCTAATCAGAATCAGAATGATCATGTCAAGTTATCC
29149141 TTTCGGATTTAACCAATG
66 TTTCGGATTTAACCAATG
* * *
29149159 ACATAAGTCCAGAACATTTATGCTCGTAAG-TAAATCAGTATCAGAATGATCATGTCAAGTTATC
1 ACATAAGTCCAAAACATTTACGCTCGTAAGCT-AATCAGAATCAGAATGATCATGTCAAGTTATC
*
29149223 CTTTTGGATTTAACCAATG
65 CTTTCGGATTTAACCAATG
29149242 A
1 A
29149243 TCGCTCATAG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
82 1 0.01
83 74 0.99
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (83 bp):
ACATAAGTCCAAAACATTTACGCTCGTAAGCTAATCAGAATCAGAATGATCATGTCAAGTTATCC
TTTCGGATTTAACCAATG
Found at i:29163943 original size:54 final size:54
Alignment explanation
Indices: 29163833--29164111 Score: 427
Period size: 54 Copynumber: 5.2 Consensus size: 54
29163823 TAAGAGCTCC
* * *
29163833 GTCATCGGACCTTTAATCCATAATAGGA-TTCATATAAGTCATGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
*
29163886 GTCATCGGATCTTTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
* *
29163940 GTCATCAGACCTTTAATCCGTAATAGGA-TTCATATAACTCACGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
*
29163993 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
* * * * *
29164047 GACATTGGAACTTTAATCCATAATAGGATTTCATATAGCTCAAGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
*
29164101 GTTATCGGACC
1 GTCATCGGACC
29164112 GTTTTGCATT
Statistics
Matches: 206, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
53 77 0.37
54 129 0.63
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (54 bp):
GTCATCGGACCTTTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
Found at i:29164019 original size:107 final size:107
Alignment explanation
Indices: 29163833--29164111 Score: 441
Period size: 107 Copynumber: 2.6 Consensus size: 107
29163823 TAAGAGCTCC
* * *
29163833 GTCATCGGACCTTTAATCCATAATAGGATTCATATAAGTCATGATGACACAGAGTCATCGGATCT
1 GTCATCGGACCTTTAATCCATAATAGGATTCATATAACTCAAGATGACACAGAGTCATCGGACCT
29163898 TTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
66 TTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
* * *
29163940 GTCATCAGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGAGTCATCGGACCT
1 GTCATCGGACCTTTAATCCATAATAGGATTCATATAACTCAAGATGACACAGAGTCATCGGACCT
*
29164005 TTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGA
66 TTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
* * * * *
29164047 GACATTGGAACTTTAATCCATAATAGGATTTCATATAGCTCAAGATGACACAGAGTTATCGGACC
1 GTCATCGGACCTTTAATCCATAATAGGA-TTCATATAACTCAAGATGACACAGAGTCATCGGACC
29164112 GTTTTGCATT
Statistics
Matches: 157, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 124 0.79
108 33 0.21
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (107 bp):
GTCATCGGACCTTTAATCCATAATAGGATTCATATAACTCAAGATGACACAGAGTCATCGGACCT
TTAATCCGTAATAGGATTTCATATAACTCAAGATGACACAGA
Found at i:29167789 original size:17 final size:18
Alignment explanation
Indices: 29167761--29167794 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29167751 GCAAAAAAAT
*
29167761 TTAAAGTTAAAACATAAA
1 TTAAAGTTAAAAAATAAA
29167779 TTAAA-TTAAAAAATAA
1 TTAAAGTTAAAAAATAA
29167795 TAAAATTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TTAAAGTTAAAAAATAAA
Found at i:29167925 original size:18 final size:18
Alignment explanation
Indices: 29167890--29167927 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29167880 CTCCTTCTCT
*
29167890 CATTCCCATCCCCATTCC
1 CATTCCCATCCACATTCC
29167908 CATTCCCCATCCAC-TTCC
1 CATT-CCCATCCACATTCC
29167926 CA
1 CA
29167928 CACTCAGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.55, G:0.00, T:0.26
Consensus pattern (18 bp):
CATTCCCATCCACATTCC
Found at i:29168615 original size:19 final size:19
Alignment explanation
Indices: 29168586--29168626 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
29168576 GGGTAAATAT
29168586 TTTATTGTTTTTTAATTTAA
1 TTTATTG-TTTTTAATTTAA
*
29168606 TTTA-TGTTTTTACTTTAA
1 TTTATTGTTTTTAATTTAA
29168624 TTT
1 TTT
29168627 TTTTGCTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 2 0.10
20 4 0.20
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTATTGTTTTTAATTTAA
Found at i:29173351 original size:33 final size:33
Alignment explanation
Indices: 29173309--29173372 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
29173299 GAATGTGAAT
*
29173309 CCCATTTCGATATCTACACAAATAATTAAAAAA
1 CCCATTTCGATATCTACACAAACAATTAAAAAA
* * *
29173342 CCCATTTCGATATTTGCACAAGCAATTAAAA
1 CCCATTTCGATATCTACACAAACAATTAAAA
29173373 TTTTAATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (33 bp):
CCCATTTCGATATCTACACAAACAATTAAAAAA
Found at i:29176454 original size:94 final size:95
Alignment explanation
Indices: 29176214--29176541 Score: 518
Period size: 96 Copynumber: 3.5 Consensus size: 95
29176204 ATATGGCACT
* * *
29176214 ACCACTTTAATTAAATGAATTTTTTTACACGATTTATTATTTATATTTTTAAAATAAATTAAAAT
1 ACCACTTTAATTAAATAAATTTTTTTAAACGATTTATTATTTATATTTTTAAAATAAATTTAAA-
29176279 TTTTTTTGGTGGTGCCATATTAAATGGCGCC
65 TTTTTTTGGTGGTGCCATATTAAATGGCGCC
* *
29176310 ACCATTTTAATTAAATAAATTTTTTTAAACGATTTATTATTTATATTTTTAAAAAAAAATTTAAA
1 ACCACTTTAATTAAATAAATTTTTTTAAACGATTTATTATTTATATTTTT-AAAATAAATTTAAA
29176375 TTTTTTTGGTGGTGCCATATTAAATGGCGCC
65 TTTTTTTGGTGGTGCCATATTAAATGGCGCC
* *
29176406 ACCACTTTAATT-AA-AATTTTTTTTAAATGATTTATTATTTATATTTTTAAAATAAATTTAAAT
1 ACCACTTTAATTAAATAAATTTTTTTAAACGATTTATTATTTATATTTTTAAAATAAATTTAAAT
* * *
29176469 TTTTTT-GTGGTGTCATATTAAATGGTGCT
66 TTTTTTGGTGGTGCCATATTAAATGGCGCC
*
29176498 ACCACTTTAATTAAATAAATTTTTTTAAACGATTTTTTATTTAT
1 ACCACTTTAATTAAATAAATTTTTTTAAACGATTTATTATTTAT
29176542 TATATAATAT
Statistics
Matches: 214, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
92 32 0.15
93 22 0.10
94 57 0.27
95 2 0.01
96 89 0.42
97 12 0.06
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (95 bp):
ACCACTTTAATTAAATAAATTTTTTTAAACGATTTATTATTTATATTTTTAAAATAAATTTAAAT
TTTTTTGGTGGTGCCATATTAAATGGCGCC
Found at i:29176571 original size:18 final size:18
Alignment explanation
Indices: 29176550--29176585 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29176540 ATTATATAAT
29176550 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
*
29176568 ATTTAAATATATATTTTA
1 ATTTAAATATATAGTTTA
29176586 TTTTTGGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:29180028 original size:22 final size:22
Alignment explanation
Indices: 29180000--29180050 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
29179990 ATATATTTAG
*
29180000 TGAAATTATATTACATAACACT
1 TGAAATTATATGACATAACACT
29180022 TGAAATTATATGACATAACACT
1 TGAAATTATATGACATAACACT
*
29180044 TAAAATT
1 TGAAATT
29180051 GAAATGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (22 bp):
TGAAATTATATGACATAACACT
Found at i:29182391 original size:23 final size:23
Alignment explanation
Indices: 29182364--29182411 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
29182354 TATTTTAAAA
* *
29182364 TAAAATCAAAATTAGAAGGA-AAT
1 TAAAATAAAAATGA-AAGGAGAAT
29182387 TAAAATAAAAATGAAAGGAGAAT
1 TAAAATAAAAATGAAAGGAGAAT
29182410 TA
1 TA
29182412 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (23 bp):
TAAAATAAAAATGAAAGGAGAAT
Found at i:29182436 original size:17 final size:19
Alignment explanation
Indices: 29182414--29182451 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29182404 GAGAATTATA
29182414 AAAATAA-AAA-AATAATG
1 AAAATAACAAACAATAATG
*
29182431 AAAATAACAAACATTAATG
1 AAAATAACAAACAATAATG
29182450 AA
1 AA
29182452 TAACAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAATAACAAACAATAATG
Found at i:29184410 original size:13 final size:13
Alignment explanation
Indices: 29184368--29184423 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
29184358 TTAAAGTTTA
*
29184368 AAAATTAAATACT
1 AAAATTAAATAAT
* ** *
29184381 AATATTTTATTAT
1 AAAATTAAATAAT
29184394 AAAA-TATAATAAT
1 AAAATTA-AATAAT
29184407 AAAATTAAATAAT
1 AAAATTAAATAAT
29184420 AAAA
1 AAAA
29184424 AAGAAAAAGC
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
12 1 0.03
13 29 0.91
14 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAAATAAT
Found at i:29184707 original size:29 final size:29
Alignment explanation
Indices: 29184659--29184716 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
29184649 CTATAGATTT
* * *
29184659 TAGGTTATTTTCGTATTTAATCAAAAAAA
1 TAGGTTATTTACCTAATTAATCAAAAAAA
*
29184688 TAGGTTATTTACCTAATTAATTAAAAAAA
1 TAGGTTATTTACCTAATTAATCAAAAAAA
29184717 GGGGTTACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.40
Consensus pattern (29 bp):
TAGGTTATTTACCTAATTAATCAAAAAAA
Found at i:29184722 original size:29 final size:29
Alignment explanation
Indices: 29184660--29184723 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
29184650 TATAGATTTT
* * * *
29184660 AGGTTATTTTCGTATTTAATCAAAAAAAT
1 AGGTTATTTACCTAATTAATCAAAAAAAG
*
29184689 AGGTTATTTACCTAATTAATTAAAAAAAG
1 AGGTTATTTACCTAATTAATCAAAAAAAG
*
29184718 GGGTTA
1 AGGTTA
29184724 CTTTTATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (29 bp):
AGGTTATTTACCTAATTAATCAAAAAAAG
Found at i:29190769 original size:24 final size:24
Alignment explanation
Indices: 29190737--29190783 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
29190727 AGTTTTGTTG
29190737 TCTTAATCTTGAATAGAAAAGTAC
1 TCTTAATCTTGAATAGAAAAGTAC
29190761 TCTTAATCTTGAATAGAAAAGTA
1 TCTTAATCTTGAATAGAAAAGTA
29190784 TGTTGTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (24 bp):
TCTTAATCTTGAATAGAAAAGTAC
Found at i:29194051 original size:58 final size:58
Alignment explanation
Indices: 29193963--29194108 Score: 156
Period size: 58 Copynumber: 2.5 Consensus size: 58
29193953 ATATATTATA
* * * *
29193963 ATTTTTACT-AATTCATATTTTAAAAATAATTATATTAAAA-AT-ATT-ATTAACTTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
29194020 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
*
29194080 ATTTTTATTCAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
29194109 CATTAAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
57 1 0.01
58 46 0.61
59 11 0.15
60 10 0.13
61 7 0.09
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:29194251 original size:39 final size:44
Alignment explanation
Indices: 29194192--29194296 Score: 105
Period size: 46 Copynumber: 2.5 Consensus size: 44
29194182 TTTCTTATGC
* *
29194192 TATTACAGCATC-ATTTCATT-CAACCAA-ACACAA-GAA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTACT
*
29194231 TATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAA-CAAACAA-TGAATTACT
*
29194277 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
29194297 ACAGTTCTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
38 2 0.04
39 16 0.30
40 6 0.11
42 5 0.09
44 3 0.06
45 2 0.04
46 20 0.37
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (44 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTACT
Found at i:29194299 original size:16 final size:16
Alignment explanation
Indices: 29194278--29194333 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
29194268 TGAATTACTG
29194278 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
29194294 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
29194310 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
29194326 ATTACAGC
1 ATTACAGC
29194334 GAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:29199802 original size:14 final size:14
Alignment explanation
Indices: 29199783--29199809 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29199773 AATTCGAATT
29199783 TCGAATTATTCGAA
1 TCGAATTATTCGAA
29199797 TCGAATTATTCGA
1 TCGAATTATTCGA
29199810 GTTAAACGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TCGAATTATTCGAA
Found at i:29207899 original size:33 final size:34
Alignment explanation
Indices: 29207862--29207925 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
29207852 GGGCAAAATA
* *
29207862 AAGGACGAAACTTACTTATTAACAA-ATTAAGAG
1 AAGGAAGAAACTTACCTATTAACAATATTAAGAG
29207895 AAGGAAGAAACTTACCTATTAACAATATTAA
1 AAGGAAGAAACTTACCTATTAACAATATTAA
29207926 TTAAATATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (34 bp):
AAGGAAGAAACTTACCTATTAACAATATTAAGAG
Found at i:29208809 original size:24 final size:24
Alignment explanation
Indices: 29208781--29208843 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
29208771 AGAAATAATC
*
29208781 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTA
*
29208805 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAGTTAAACTCTGTTTATTTA
* *
29208829 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
29208844 TATTACTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTA
Found at i:29210279 original size:14 final size:14
Alignment explanation
Indices: 29210260--29210287 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29210250 GAATCTCATC
29210260 TCCTTAAGTATTTT
1 TCCTTAAGTATTTT
29210274 TCCTTAAGTATTTT
1 TCCTTAAGTATTTT
29210288 AGACTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
TCCTTAAGTATTTT
Found at i:29210813 original size:24 final size:24
Alignment explanation
Indices: 29210785--29210847 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
29210775 AGAAATAATC
*
29210785 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTA
*
29210809 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAGTTAAACTCTGTTTATTTA
* *
29210833 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
29210848 TATTACTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTA
Found at i:29213690 original size:30 final size:31
Alignment explanation
Indices: 29213621--29213696 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 31
29213611 TTTAATATTT
* *
29213621 TTTTATTTATTTATTTTTAGGGTTTTCTTAGG
1 TTTTATTTATTTA-TTTAAGGGTTTTCTTAGA
*
29213653 GTTTATTTATTTATTTAAGGGTTTT-TTAGA
1 TTTTATTTATTTATTTAAGGGTTTTCTTAGA
29213683 TTTTATTTATTTAT
1 TTTTATTTATTTAT
29213697 AAAATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 17 0.43
31 11 0.28
32 12 0.30
ACGTcount: A:0.20, C:0.01, G:0.13, T:0.66
Consensus pattern (31 bp):
TTTTATTTATTTATTTAAGGGTTTTCTTAGA
Found at i:29216062 original size:18 final size:18
Alignment explanation
Indices: 29216039--29216077 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29216029 AATTAAATAT
* *
29216039 TTAAATTTATTGGAATGA
1 TTAAATTGATGGGAATGA
*
29216057 TTAAATTGATGGGAATTA
1 TTAAATTGATGGGAATGA
29216075 TTA
1 TTA
29216078 TTTAGATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
TTAAATTGATGGGAATGA
Found at i:29216825 original size:2 final size:2
Alignment explanation
Indices: 29216820--29216852 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29216810 AAAAATCAAG
29216820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29216853 GAAAAATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29217324 original size:196 final size:196
Alignment explanation
Indices: 29216987--29217341 Score: 525
Period size: 196 Copynumber: 1.8 Consensus size: 196
29216977 TAGGGGTTAT
* * *
29216987 TTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCG
1 TTACAGGTTATATGAGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGGTCCTGCATTGGTTGCG
* ** * *
29217052 GATTCTCCACAGCTCATGTGAGCAGCATCATGTAGTCTAACATCTCGACCCACAGCTCATGTGAG
66 GATTCTCCACAACTCATGTGAGCAGCATCACATAGCCTAACATCTCAACCCACAGCTCATGTGAG
* *
29217117 CAGATCCATTTCACAGCTTGTATGAGCATATATGATTACATGATACAGTTACAGCTCGTGTGAGC
131 CAGACCCATTTCACAGCTCGTATGAGCATATATGATTACATGATACAGTTACAGCTCGTGTGAGC
29217182 A
196 A
* *
29217183 TTACAGGTTATATGAGTGTTGGTCTT-GAATGTCTTACCT-ATGGCTGAGGTCCTGCATTGGTTG
1 TTACAGGTTATATGAGTGCTGGTCTTAG-ATGTCCTA-CTGATGGCTGAGGTCCTGCATTGGTTG
* * *
29217246 CGGATTCTCCACAACTCGTGTGAGCAGCATCGCATAGCCTAACATCTCAACCCACAGCTCGTGTG
64 CGGATTCTCCACAACTCATGTGAGCAGCATCACATAGCCTAACATCTCAACCCACAGCTCATGTG
* *
29217311 AGCAGGCCCATTTCACAGCTCGTGTGAGCAT
129 AGCAGACCCATTTCACAGCTCGTATGAGCAT
29217342 TATAGGTTAT
Statistics
Matches: 140, Mismatches: 17, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
195 1 0.01
196 137 0.98
197 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (196 bp):
TTACAGGTTATATGAGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGGTCCTGCATTGGTTGCG
GATTCTCCACAACTCATGTGAGCAGCATCACATAGCCTAACATCTCAACCCACAGCTCATGTGAG
CAGACCCATTTCACAGCTCGTATGAGCATATATGATTACATGATACAGTTACAGCTCGTGTGAGC
A
Found at i:29217458 original size:158 final size:158
Alignment explanation
Indices: 29217167--29217505 Score: 475
Period size: 158 Copynumber: 2.1 Consensus size: 158
29217157 TGATACAGTT
* * *
29217167 ACAGCTCGTGTGAGCATTACAGGTTATATGAGTGTTGGTCTTGAATGTCTTACCTATGGCTGAGG
1 ACAGCTCGTGTGAGCATTATAGGTTATATGAGTGCTGGTCTTGAATGTCTTACCGATGGCTGAGG
* * * *
29217232 TCCTGCATTGGTTGCGGATTCTCCACAACTCGTGTGAGCAGCATCGCATAGCCTAACATCTCAAC
66 TCCTGCATTGATTGCGGATTCTCCACAACTCATGTGAGCAACATCGCATAGCCCAACATCTCAAC
*
29217297 CCACAGCTCGTGTGAGCAGGCCCATTTC
131 CCACAGCTCGTGTGAGCAGACCCATTTC
*
29217325 ACAGCTCGTGTGAGCATTATAGGTTATATGGGTGCTGGTCTT-AGATGTCTTACCGATGGCTGAG
1 ACAGCTCGTGTGAGCATTATAGGTTATATGAGTGCTGGTCTTGA-ATGTCTTACCGATGGCTGAG
* * ** * *
29217389 GTCC-GACATTTATTGCGGATTCTCCACAGCTCATGTGAGCAACATCGTGTAGCCCCACATCTCG
65 GTCCTG-CATTGATTGCGGATTCTCCACAACTCATGTGAGCAACATCGCATAGCCCAACATCTCA
*
29217453 GCCCACAGCTCGTGTGAGCAGACCCATTTC
129 ACCCACAGCTCGTGTGAGCAGACCCATTTC
* *
29217483 ATAGCTTGTGTGAGCATATATAG
1 ACAGCTCGTGTGAGCAT-TATAG
29217506 TTACATGTAT
Statistics
Matches: 160, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
157 2 0.01
158 153 0.96
159 5 0.03
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (158 bp):
ACAGCTCGTGTGAGCATTATAGGTTATATGAGTGCTGGTCTTGAATGTCTTACCGATGGCTGAGG
TCCTGCATTGATTGCGGATTCTCCACAACTCATGTGAGCAACATCGCATAGCCCAACATCTCAAC
CCACAGCTCGTGTGAGCAGACCCATTTC
Found at i:29219436 original size:39 final size:39
Alignment explanation
Indices: 29219252--29219419 Score: 228
Period size: 39 Copynumber: 4.3 Consensus size: 39
29219242 ACATCGAAAG
* * *
29219252 TATACTGAACTGACAGTGACACTATAAACACTACAATGA
1 TATACTGAACTGGCAGTGACACTGTAAACACTACAATGC
* * * *
29219291 TATGCTAAACTGGCAATGACACTGTAAACACTACAATGT
1 TATACTGAACTGGCAGTGACACTGTAAACACTACAATGC
* *
29219330 TATACTGAACTGGTAGTGACACTATAAACACTACAATGC
1 TATACTGAACTGGCAGTGACACTGTAAACACTACAATGC
* *
29219369 TATACTGAATTGGCAGTGACACTGTAAACACTGCAATGC
1 TATACTGAACTGGCAGTGACACTGTAAACACTACAATGC
*
29219408 TATACTAAACTG
1 TATACTGAACTG
29219420 ATGGTGACAA
Statistics
Matches: 111, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (39 bp):
TATACTGAACTGGCAGTGACACTGTAAACACTACAATGC
Found at i:29219436 original size:78 final size:78
Alignment explanation
Indices: 29219252--29219428 Score: 255
Period size: 78 Copynumber: 2.3 Consensus size: 78
29219242 ACATCGAAAG
* *
29219252 TATACTGAACTGACAGTGACACTATAAACACTACAATGATATGCTAAACTGGCAATGACACTGTA
1 TATACTGAACTGATAGTGACACTATAAACACTACAATGATATACTAAACTGGCAATGACACTGTA
*
29219317 AACACTACAATGT
66 AACACTACAATGC
* * * * *
29219330 TATACTGAACTGGTAGTGACACTATAAACACTACAATGCTATACTGAATTGGCAGTGACACTGTA
1 TATACTGAACTGATAGTGACACTATAAACACTACAATGATATACTAAACTGGCAATGACACTGTA
*
29219395 AACACTGCAATGC
66 AACACTACAATGC
* *
29219408 TATACTAAACTGATGGTGACA
1 TATACTGAACTGATAGTGACA
29219429 ATGTAAACGA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 87 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (78 bp):
TATACTGAACTGATAGTGACACTATAAACACTACAATGATATACTAAACTGGCAATGACACTGTA
AACACTACAATGC
Found at i:29219463 original size:117 final size:116
Alignment explanation
Indices: 29219252--29219477 Score: 267
Period size: 117 Copynumber: 1.9 Consensus size: 116
29219242 ACATCGAAAG
* * *
29219252 TATACTGAACTGACAGTGACACTATAAACACTACAATGATATGCTAAACTGGCAATGACACTGTA
1 TATACTGAACTGACAGTGACACTATAAACACTACAATGATATACTAAACTGACAATGACAATGTA
*
29219317 AACACTACAATGTTATACTGAACTGGTAGTGACACTATAAACACTACAATGC
66 AACACTA-AATGTTATACTGAACTAGTAGTGACACTATAAACACTACAATGC
* * * * * ***
29219369 TATACTGAATTGGCAGTGACACTGTAAACACTGCAATGCTATACTAAACTGATGGTGACAATGTA
1 TATACTGAACTGACAGTGACACTATAAACACTACAATGATATACTAAACTGACAATGACAATGTA
* * *
29219434 AACGACGT-AATTTTATACTGAGGC-AGTAGTGACACTTTAAACAC
66 AAC-AC-TAAATGTTATACTGA-ACTAGTAGTGACACTATAAACAC
29219478 CGCAATATTA
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
117 87 0.96
118 3 0.03
119 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (116 bp):
TATACTGAACTGACAGTGACACTATAAACACTACAATGATATACTAAACTGACAATGACAATGTA
AACACTAAATGTTATACTGAACTAGTAGTGACACTATAAACACTACAATGC
Found at i:29219466 original size:39 final size:39
Alignment explanation
Indices: 29219423--29219516 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
29219413 TAAACTGATG
* *
29219423 GTGACAATGTAAACGA-CGTAATTTTATACTGAGGCAGTA
1 GTGACAATGTAAAC-ACCGCAATATTATACTGAGGCAGTA
* * *
29219462 GTGACACTTTAAACACCGCAATATTATACTGAGGTAGTA
1 GTGACAATGTAAACACCGCAATATTATACTGAGGCAGTA
*
29219501 GTGGA-ATTGTAAACAC
1 GT-GACAATGTAAACAC
29219517 TACTAGACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.02
39 43 0.93
40 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (39 bp):
GTGACAATGTAAACACCGCAATATTATACTGAGGCAGTA
Found at i:29228847 original size:24 final size:24
Alignment explanation
Indices: 29228816--29228873 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
29228806 ATTTAGCTCA
*
29228816 TACGAGCCC-AGATAGGTTAACTCT
1 TACGAGCCCAAAAT-GGTTAACTCT
* *
29228840 TACTAGCCCAAAATGGTTAGCTCT
1 TACGAGCCCAAAATGGTTAACTCT
29228864 TACGAGCCCA
1 TACGAGCCCA
29228874 TAATTAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (24 bp):
TACGAGCCCAAAATGGTTAACTCT
Found at i:29228918 original size:27 final size:27
Alignment explanation
Indices: 29228859--29228962 Score: 145
Period size: 27 Copynumber: 3.8 Consensus size: 27
29228849 AAAATGGTTA
* * * *
29228859 GCTCTTACGAGCCCATAATTAGAATAAT
1 GCTCTTTCGAG-CCAGAATCAGAATAAC
29228887 GCTCTTTCGAGCCAGAATCAGAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
*
29228914 ACTCTTTCGAGCCAGAATCAGAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
*
29228941 GCTCTTTCAAGCCAGAATCAGA
1 GCTCTTTCGAGCCAGAATCAGA
29228963 TTACTCCTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
27 59 0.86
28 10 0.14
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (27 bp):
GCTCTTTCGAGCCAGAATCAGAATAAC
Found at i:29234422 original size:72 final size:72
Alignment explanation
Indices: 29234343--29234501 Score: 203
Period size: 72 Copynumber: 2.2 Consensus size: 72
29234333 ATGCCCACAG
* * * * * *
29234343 TCGTGTGTGCATATTGTTTTGTGTGTATACTGGCTTGAGATACACAGGTTAGACACACGGGCGTG
1 TCGTGTGTGCATACTGTTTTCTGTGTATACTGACTTGAGACACACAGGCTAGACACACGCGCGTG
*
29234408 CATT-ATA
66 C-TTCAAA
* * *
29234415 TCGTGTGTGCATACTGTTTTCTGTGTATATTGACTTGAGACACACGGGCTGGACACACGCGCGTG
1 TCGTGTGTGCATACTGTTTTCTGTGTATACTGACTTGAGACACACAGGCTAGACACACGCGCGTG
29234480 CTTCAAA
66 CTTCAAA
*
29234487 TCATGTGTGCATACT
1 TCGTGTGTGCATACT
29234502 AACTTGGTAC
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
71 2 0.03
72 73 0.97
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (72 bp):
TCGTGTGTGCATACTGTTTTCTGTGTATACTGACTTGAGACACACAGGCTAGACACACGCGCGTG
CTTCAAA
Found at i:29234899 original size:39 final size:39
Alignment explanation
Indices: 29234850--29235022 Score: 199
Period size: 39 Copynumber: 4.5 Consensus size: 39
29234840 ACTGGCAGTG
**
29234850 ACACT-CAATGATATGTTGAACTGGCAGTGACATTGTAA
1 ACACTACAATGATATACTGAACTGGCAGTGACATTGTAA
* *
29234888 ACACTATAATGATATACTGAACTGGCAGTGACATTATAA
1 ACACTACAATGATATACTGAACTGGCAGTGACATTGTAA
* * *
29234927 ACACTACAATGGTATACTTAACTGGCAGTAACATTGTAA
1 ACACTACAATGATATACTGAACTGGCAGTGACATTGTAA
* * * *
29234966 ATACTACAATGCTATACTGAAC-GGACGGTGACACTGTAA
1 ACACTACAATGATATACTGAACTGG-CAGTGACATTGTAA
*
29235005 ACA-TCACAATGCTATACT
1 ACACT-ACAATGATATACT
29235023 AAGGCAGTAG
Statistics
Matches: 116, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
38 8 0.07
39 108 0.93
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (39 bp):
ACACTACAATGATATACTGAACTGGCAGTGACATTGTAA
Found at i:29235043 original size:78 final size:80
Alignment explanation
Indices: 29234875--29235047 Score: 198
Period size: 78 Copynumber: 2.2 Consensus size: 80
29234865 TTGAACTGGC
* * *
29234875 AGTGACATTGTAAACACTATAATGATATACTGAACTGGCAGTGACATTATAAACACTACAATGGT
1 AGTGACATTGTAAACACTACAATGATATACTGAACTGGCAGTGACACTATAAACACTACAATGCT
29234940 ATACTTAACTGGCAGT
66 ATACTTAAC-GGCAGT
* * * *
29234956 A---ACATTGTAAATACTACAATGCTATACTGAAC-GGACGGTGACACTGTAAACA-TCACAATG
1 AGTGACATTGTAAACACTACAATGATATACTGAACTGG-CAGTGACACTATAAACACT-ACAATG
29235016 CTATAC-TAA-GGCAGT
64 CTATACTTAACGGCAGT
*
29235031 AGTGACACTGTAAACAC
1 AGTGACATTGTAAACAC
29235048 CACTAGACTA
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
75 7 0.09
77 6 0.08
78 64 0.82
81 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (80 bp):
AGTGACATTGTAAACACTACAATGATATACTGAACTGGCAGTGACACTATAAACACTACAATGCT
ATACTTAACGGCAGT
Found at i:29237459 original size:18 final size:18
Alignment explanation
Indices: 29237436--29237473 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29237426 TAATATAGTC
*
29237436 TTATTCGATTTATTCAAA
1 TTATTCGAGTTATTCAAA
*
29237454 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCAAA
29237472 TT
1 TT
29237474 CGAAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCAAA
Found at i:29237561 original size:23 final size:23
Alignment explanation
Indices: 29237517--29237562 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29237507 AAAAAAAATT
**
29237517 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCGAATAACTCGAA
*
29237540 TAACTCGATTCGAATAATTCGAA
1 TAACTCGATTCGAATAACTCGAA
29237563 ATTAGAATTT
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:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTCGAA
Found at i:29240394 original size:30 final size:30
Alignment explanation
Indices: 29240319--29240637 Score: 199
Period size: 30 Copynumber: 10.7 Consensus size: 30
29240309 TATTTTATTT
* * *
29240319 AAAAATTACATTTCGACCCCCAAACTTTTC
1 AAAAATTACATTTTGAACCCCAAACTTTCC
* * * * *
29240349 AAAACTTAGACTTTGAACCTCAAACTTTCT
1 AAAAATTACATTTTGAACCCCAAACTTTCC
* * *
29240379 AAAAATCAGATTTTG-ACCCCAAACTCTT-T
1 AAAAATTACATTTTGAACCCCAAACT-TTCC
* **
29240408 AAAAATTACATTTT-AACCTCTAATTTTTCC
1 AAAAATTACATTTTGAACC-CCAAACTTTCC
* * *
29240438 AAAAATCATATCTT-AACCCCTAAACTTTCC
1 AAAAATTACATTTTGAACCCC-AAACTTTCC
*
29240468 AAAAATTATATTTTG-ACCCCTAAACTTTCC
1 AAAAATTACATTTTGAACCCC-AAACTTTCC
* * *
29240498 AAAAATTAAAATTTGACCCCCAAACTTTCC
1 AAAAATTACATTTTGAACCCCAAACTTTCC
* ** * *
29240528 AAAACTTTGATTTTG-ACCCTTAAACTTTCT
1 AAAAATTACATTTTGAACCC-CAAACTTTCC
* ** *
29240558 AAAAATCACATTTTG-ACTTCGAACTCTT-C
1 AAAAATTACATTTTGAACCCCAAACT-TTCC
* *
29240587 AAAAATTTCATTTT-AACCCTTAAACTTTCC
1 AAAAATTACATTTTGAACCC-CAAACTTTCC
* *
29240617 -AAATTTACATTTTTAACCCCA
1 AAAAATTACATTTTGAACCCCA
29240638 TTTTTCTTAT
Statistics
Matches: 222, Mismatches: 54, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
29 63 0.28
30 155 0.70
31 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAAATTACATTTTGAACCCCAAACTTTCC
Found at i:29240552 original size:90 final size:89
Alignment explanation
Indices: 29240319--29240593 Score: 259
Period size: 90 Copynumber: 3.1 Consensus size: 89
29240309 TATTTTATTT
* * * * * *
29240319 AAAAATT-ACATTTCGACCCCCAAACTTTTCAAAACTTAGACTTTGAACCTCAAACTTTCTAAAA
1 AAAAATTAAAATTT-GACCCCCAAACTTTCCAAAACTTTGATTTTGACCCTTAAACTTTCTAAAA
* *
29240383 ATCAGATTTTGACCCCAAACTCTTT
65 ATCACATTTTGACCCCAAACTCTTC
* * * * * ** * * * * * *
29240408 AAAAATTACATTTTAACCTCTAATTTTTCCAAAAATCAT-ATCTTAACCCCTAAACTTTCCAAAA
1 AAAAATTAAAATTTGACCCCCAAACTTTCCAAAACT-TTGATTTTGACCCTTAAACTTTCTAAAA
* *
29240472 ATTATATTTTGACCCCTAAACT-TTCC
65 ATCACATTTTGACCCC-AAACTCTT-C
29240498 AAAAATTAAAATTTGACCCCCAAACTTTCCAAAACTTTGATTTTGACCCTTAAACTTTCTAAAAA
1 AAAAATTAAAATTTGACCCCCAAACTTTCCAAAACTTTGATTTTGACCCTTAAACTTTCTAAAAA
** *
29240563 TCACATTTTGACTTCGAACTCTTC
66 TCACATTTTGACCCCAAACTCTTC
29240587 AAAAATT
1 AAAAATT
29240594 TCATTTTAAC
Statistics
Matches: 140, Mismatches: 40, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
89 69 0.49
90 71 0.51
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (89 bp):
AAAAATTAAAATTTGACCCCCAAACTTTCCAAAACTTTGATTTTGACCCTTAAACTTTCTAAAAA
TCACATTTTGACCCCAAACTCTTC
Done.