Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012276.1 Kokia drynarioides strain JFW-HI SEQ_127277, 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: 679560
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:497086 original size:106 final size:106
Alignment explanation
Indices: 496944--497154 Score: 341
Period size: 106 Copynumber: 2.0 Consensus size: 106
496934 CTAGGCCTCT
*
496944 AAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGA
1 AAATGCAATGAAAAGTAAATAGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGA
*
497009 CCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGG
66 CCTCCACACATGGGCCTCTAAATGCAATGAAAAGTAAATGG
* * ** *
497050 AAATGCGATGAAAAGTAAATAGACCTCCACATCTGAGCCTCTAAATGTGATGAAAAGTAAATGGG
1 AAATGCAATGAAAAGTAAATAGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGA
* *
497115 CCTCCACACATGGGCCTCTAAGTGCGATGAAAAGTAAATG
66 CCTCCACACATGGGCCTCTAAATGCAATGAAAAGTAAATG
497155 AGCCTCCACA
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (106 bp):
AAATGCAATGAAAAGTAAATAGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGA
CCTCCACACATGGGCCTCTAAATGCAATGAAAAGTAAATGG
Found at i:497190 original size:190 final size:190
Alignment explanation
Indices: 496867--497240 Score: 536
Period size: 190 Copynumber: 2.0 Consensus size: 190
496857 TCTAAATGTA
* * * * * *
496867 ATGAAAAGTAAATGGACCTCAACACCTGGGTCTTTAAATGTAATGAAGAGTAAATGGACCTCCAT
1 ATGAAAAGTAAATAGACCTCAACACCTGAGCCTCTAAATGTAATGAAAAGTAAATGGACCTCCAC
* *
496932 GCCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGA
66 ACATAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGA
*
496997 AAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGGAAATGCG
131 AAAGTAAATGAACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGGAAATGCG
* * * *
497057 ATGAAAAGTAAATAGACCTCCACATCTGAGCCTCTAAATGTGATGAAAAGTAAATGGGCCTCCAC
1 ATGAAAAGTAAATAGACCTCAACACCTGAGCCTCTAAATGTAATGAAAAGTAAATGGACCTCCAC
* * * * *
497122 ACATGGGCCTCTAAGTGCGATGAAAAGTAAAT-GAGCCTCCACA-CTTAGACCTCTAAATGCGAT
66 ACATAGGCCTCTAAATGCAATGAAAAGTAAATGGA-CCTCCACACCTGAG-CCTCTAAATGCAAT
**
497185 GAAAAGTAAATGAACCTCCACATTTGGGCCTCTAAATGCAATGAAAAGTAAATGGA
129 GAAAAGTAAATGAACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGGA
497241 CCTCCACACT
Statistics
Matches: 162, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
189 6 0.04
190 156 0.96
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (190 bp):
ATGAAAAGTAAATAGACCTCAACACCTGAGCCTCTAAATGTAATGAAAAGTAAATGGACCTCCAC
ACATAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGA
AAAGTAAATGAACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGGAAATGCG
Found at i:497224 original size:232 final size:232
Alignment explanation
Indices: 496818--497268 Score: 654
Period size: 232 Copynumber: 1.9 Consensus size: 232
496808 CTGGGCCTCT
* * *
496818 AAATGCGATGAAAAGTAAATGGACTTTCACACCTAGGCCTCTAAATGTAATGAAAAGTAAATGGA
1 AAATGCGATGAAAAGTAAATAGACCTCCACACCTAGGCCTCTAAATGTAATGAAAAGTAAATGGA
* * * * * ** *
496883 CCTCAACACCTGGGTCTTTAAATGTAATGAAGAGTAAATGGACCTCCATGCCTAGGCCTCTAAAT
66 CCTCAACACATGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGACCTCTAAAT
*
496948 GCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGACCTC
131 GCAATGAAAAGTAAATGAACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGACCTC
497013 CACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGG
196 CACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGG
* *
497050 AAATGCGATGAAAAGTAAATAGACCTCCACATCT-GAGCCTCTAAATGTGATGAAAAGTAAATGG
1 AAATGCGATGAAAAGTAAATAGACCTCCACACCTAG-GCCTCTAAATGTAATGAAAAGTAAATGG
* * * * *
497114 GCCTCCACACATGGGCCTCTAAGTGCGATGAAAAGTAAAT-GAGCCTCCACACTTAGACCTCTAA
65 ACCTCAACACATGGGCCTCTAAATGCAATGAAAAGTAAATGGA-CCTCCACACCTAGACCTCTAA
* ** *
497178 ATGCGATGAAAAGTAAATGAACCTCCACATTTGGGCCTCTAAATGCAATGAAAAGTAAATGGACC
129 ATGCAATGAAAAGTAAATGAACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGACC
*
497243 TCCACACTTGGGCCTCTAAATGCAAT
194 TCCACACCTGGGCCTCTAAATGCAAT
497269 TAATGCTTTC
Statistics
Matches: 193, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
231 3 0.02
232 190 0.98
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (232 bp):
AAATGCGATGAAAAGTAAATAGACCTCCACACCTAGGCCTCTAAATGTAATGAAAAGTAAATGGA
CCTCAACACATGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGACCTCTAAAT
GCAATGAAAAGTAAATGAACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGACCTC
CACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGG
Found at i:497268 original size:42 final size:42
Alignment explanation
Indices: 497050--497265 Score: 301
Period size: 42 Copynumber: 5.1 Consensus size: 42
497040 AAGTAAATGG
* *
497050 AAATGCGATGAAAAGTAAATAGACCTCCACA-TCTGAGCCTCT
1 AAATGCGATGAAAAGTAAATGGACCTCCACACT-TGGGCCTCT
* * *
497092 AAATGTGATGAAAAGTAAATGGGCCTCCACACATGGGCCTCT
1 AAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCTCT
* * *
497134 AAGTGCGATGAAAAGTAAAT-GAGCCTCCACACTTAGACCTCT
1 AAATGCGATGAAAAGTAAATGGA-CCTCCACACTTGGGCCTCT
* *
497176 AAATGCGATGAAAAGTAAATGAACCTCCACATTTGGGCCTCT
1 AAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCTCT
*
497218 AAATGCAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCT
1 AAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCTCT
497260 AAATGC
1 AAATGC
497266 AATTAATGCT
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 150 0.99
43 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
AAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCTCT
Found at i:497701 original size:21 final size:21
Alignment explanation
Indices: 497676--497750 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 21
497666 TCTCTCTCTA
497676 TTTTTTTCTTCTTTTTTGTTG
1 TTTTTTTCTTCTTTTTTGTTG
*
497697 TTTTTTTC-TCTTTTTCTGTTTT
1 TTTTTTTCTTCTTTTT-TG-TTG
497719 TCTTTTTTCTTCTTTTCTTG-TG
1 T-TTTTTTCTTCTTTT-TTGTTG
497741 TTTTTTTCTT
1 TTTTTTTCTT
497751 GATTTAAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.15
21 19 0.40
22 5 0.11
23 7 0.15
24 8 0.17
25 1 0.02
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTTTCTTCTTTTTTGTTG
Found at i:497705 original size:45 final size:44
Alignment explanation
Indices: 497651--497749 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
497641 CTTTAATATA
*
497651 GTTTCTTTCTCTTGCTCTCTCTCTAT-TTTTTTCTTCTTTT-TTGTT
1 GTTTTTTTCTCTT--TCTCTCTCTATCTTTTTTCTTCTTTTCTTG-T
* * * *
497696 GTTTTTTTCTCTTTTTCTGTTTTTCTTTTTTCTTCTTTTCTTGT
1 GTTTTTTTCTCTTTCTCTCTCTATCTTTTTTCTTCTTTTCTTGT
497740 GTTTTTTTCT
1 GTTTTTTTCT
497750 TGATTTAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 7 0.15
44 25 0.53
45 15 0.32
ACGTcount: A:0.01, C:0.18, G:0.07, T:0.74
Consensus pattern (44 bp):
GTTTTTTTCTCTTTCTCTCTCTATCTTTTTTCTTCTTTTCTTGT
Found at i:497725 original size:15 final size:14
Alignment explanation
Indices: 497677--497750 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
497667 CTCTCTCTAT
497677 TTTTTTCTTCTTTT-
1 TTTTTTCTT-TTTTC
*
497691 TTGTTGT-TTTTTTC
1 TT-TTTTCTTTTTTC
497705 TCTTTTTCTGTTTTTC
1 T-TTTTTCT-TTTTTC
497721 TTTTTTCTTCTTTTC
1 TTTTTTCTT-TTTTC
* *
497736 TTGTGT-TTTTTTC
1 TTTTTTCTTTTTTC
497749 TT
1 TT
497751 GATTTAAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
13 11 0.22
14 11 0.22
15 21 0.42
16 7 0.14
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTTTTTC
Found at i:497726 original size:26 final size:27
Alignment explanation
Indices: 497679--497745 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
497669 CTCTCTATTT
* *
497679 TTTTCTTCT-TTTTTGTTGTTTTTTTC
1 TTTTCTTCTGTTTTTCTTGTTTTCTTC
497705 TCTTT-TTCTGTTTTTCTT-TTTTCTTC
1 T-TTTCTTCTGTTTTTCTTGTTTTCTTC
*
497731 TTTTCTTGTGTTTTT
1 TTTTCTTCTGTTTTT
497746 TTCTTGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 3 0.09
26 22 0.63
27 10 0.29
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.79
Consensus pattern (27 bp):
TTTTCTTCTGTTTTTCTTGTTTTCTTC
Found at i:497735 original size:8 final size:7
Alignment explanation
Indices: 497677--497750 Score: 55
Period size: 8 Copynumber: 10.3 Consensus size: 7
497667 CTCTCTCTAT
497677 TTTTTTC
1 TTTTTTC
497684 TTCTTTT-
1 TT-TTTTC
*
497691 TTGTTGT-
1 TT-TTTTC
497698 TTTTTTC
1 TTTTTTC
497705 TCTTTTTC
1 T-TTTTTC
497713 TGTTTTTC
1 T-TTTTTC
497721 TTTTTTC
1 TTTTTTC
497728 TTCTTTTC
1 TT-TTTTC
* *
497736 TTGTGT-
1 TTTTTTC
497742 TTTTTTC
1 TTTTTTC
497749 TT
1 TT
497751 GATTTAAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
6 7 0.13
7 22 0.41
8 25 0.46
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:505289 original size:23 final size:20
Alignment explanation
Indices: 505245--505289 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 20
505235 ATTAGAAAAT
*
505245 TAAATAAATTAATGCACTAA
1 TAAATAAATTAATGCACAAA
505265 TAAATAAATCTAATATGCACAAA
1 TAAATAAAT-T-A-ATGCACAAA
505288 TA
1 TA
505290 CTAAAAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 1 0.05
22 1 0.05
23 10 0.48
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (20 bp):
TAAATAAATTAATGCACAAA
Found at i:506034 original size:41 final size:41
Alignment explanation
Indices: 505988--506073 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
505978 CTCATCGCCT
*
505988 AAAATTGGTATCTAATCGATTATTTAAAGTCTTATTTGTTC
1 AAAATTGGTACCTAATCGATTATTTAAAGTCTTATTTGTTC
*
506029 AAAATTGGTACCTAATCGATTATTTAAAGTCTTATTTGTTG
1 AAAATTGGTACCTAATCGATTATTTAAAGTCTTATTTGTTC
506070 AAAA
1 AAAA
506074 CTAAAAACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (41 bp):
AAAATTGGTACCTAATCGATTATTTAAAGTCTTATTTGTTC
Found at i:506608 original size:13 final size:13
Alignment explanation
Indices: 506587--506616 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
506577 ATTAATTAAG
*
506587 AATATAAATAGGA
1 AATAAAAATAGGA
506600 AATAAAAATAGGA
1 AATAAAAATAGGA
506613 AATA
1 AATA
506617 CAATAGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (13 bp):
AATAAAAATAGGA
Found at i:506756 original size:11 final size:11
Alignment explanation
Indices: 506742--506799 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
506732 AAAATAACAC
506742 ATAAATAAATA
1 ATAAATAAATA
*
506753 ATAAGT-AATA
1 ATAAATAAATA
506763 ATAAATTAAATA
1 ATAAA-TAAATA
506775 A-AAATTAAAT-
1 ATAAA-TAAATA
* *
506785 ATTAGTAAATA
1 ATAAATAAATA
506796 ATAA
1 ATAA
506800 TAGGATCATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 14 0.37
11 19 0.50
12 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:510694 original size:3 final size:3
Alignment explanation
Indices: 510686--510714 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
510676 TTTACATCAA
510686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
510715 GAAACGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:515476 original size:46 final size:46
Alignment explanation
Indices: 515424--515521 Score: 144
Period size: 46 Copynumber: 2.1 Consensus size: 46
515414 CTGTTTTTTT
515424 GTGCAAGTCATTTTTTCTGCACACT-TATTCTTTACCTACATTATTG
1 GTGCAAGTCATTTTTTCTGCAC-CTGTATTCTTTACCTACATTATTG
* * * *
515470 GTGCAAGTTATTTTTTCTGCACGTGTATTTTTTGCCTACATTATTG
1 GTGCAAGTCATTTTTTCTGCACCTGTATTCTTTACCTACATTATTG
515516 GTGCAA
1 GTGCAA
515522 ATAATGTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
45 1 0.02
46 46 0.98
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.46
Consensus pattern (46 bp):
GTGCAAGTCATTTTTTCTGCACCTGTATTCTTTACCTACATTATTG
Found at i:517280 original size:34 final size:34
Alignment explanation
Indices: 517242--517317 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
517232 AAACAAGAAC
517242 AAAAACTGTTTAAAGGATTAAATTGAAAGAAAAT
1 AAAAACTGTTTAAAGGATTAAATTGAAAGAAAAT
* *
517276 AAAAATTATTTAAAGGATTAAATTGAAAGAAAAT
1 AAAAACTGTTTAAAGGATTAAATTGAAAGAAAAT
517310 AAAAACTG
1 AAAAACTG
517318 AAATAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (34 bp):
AAAAACTGTTTAAAGGATTAAATTGAAAGAAAAT
Found at i:519655 original size:9 final size:9
Alignment explanation
Indices: 519640--519671 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
519630 GATAATGATT
519640 AAAATTTTA
1 AAAATTTTA
*
519649 CAAATTTTA
1 AAAATTTTA
519658 AAAATTTTA
1 AAAATTTTA
519667 AAAAT
1 AAAAT
519672 ATGAGACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:524124 original size:31 final size:31
Alignment explanation
Indices: 524089--524196 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 31
524079 ACTTCCAAAA
* * * *
524089 TAGTCCCTTTTATTTGTCGCGGGTTGCATTT
1 TAGTCACTTATATTTGTCACAGGTTGCATTT
* * * *
524120 TAGTCACTTATATTTG--AAATGTTACGTTT
1 TAGTCACTTATATTTGTCACAGGTTGCATTT
* * * *
524149 TAAGTCCCTTTTATTTGTCTCTGGTTGCATTT
1 T-AGTCACTTATATTTGTCACAGGTTGCATTT
524181 TAGTCACTTATATTTG
1 TAGTCACTTATATTTG
524197 AAATGTTACG
Statistics
Matches: 56, Mismatches: 18, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
29 8 0.14
30 13 0.23
31 27 0.48
32 8 0.14
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.50
Consensus pattern (31 bp):
TAGTCACTTATATTTGTCACAGGTTGCATTT
Found at i:524165 original size:30 final size:29
Alignment explanation
Indices: 524117--524224 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 29
524107 GCGGGTTGCA
524117 TTTTAGTCACTTATATTTGAAATGTTACG
1 TTTTAGTCACTTATATTTGAAATGTTACG
* * *** * *
524146 TTTTAAGTCCCTTTTATTTGTCTCTGGTTGCA
1 TTTT-AGTCACTTATATTTG-AAAT-GTTACG
524178 TTTTAGTCACTTATATTTGAAATGTTACG
1 TTTTAGTCACTTATATTTGAAATGTTACG
*
524207 TTTTAGTCACTTACATTT
1 TTTTAGTCACTTATATTT
524225 AAGGATATCA
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
29 25 0.41
30 14 0.23
31 14 0.23
32 8 0.13
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (29 bp):
TTTTAGTCACTTATATTTGAAATGTTACG
Found at i:524185 original size:61 final size:61
Alignment explanation
Indices: 524090--524211 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
524080 CTTCCAAAAT
524090 AGTCCCTTTTATTTGTCGCGGGTTGCATTTTAGTCACTTATATTTGAAATGTTACGTTTTA
1 AGTCCCTTTTATTTGTCGCGGGTTGCATTTTAGTCACTTATATTTGAAATGTTACGTTTTA
* *
524151 AGTCCCTTTTATTTGTCTCTGGTTGCATTTTAGTCACTTATATTTGAAATGTTACGTTTTA
1 AGTCCCTTTTATTTGTCGCGGGTTGCATTTTAGTCACTTATATTTGAAATGTTACGTTTTA
524212 GTCACTTACA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (61 bp):
AGTCCCTTTTATTTGTCGCGGGTTGCATTTTAGTCACTTATATTTGAAATGTTACGTTTTA
Found at i:527411 original size:19 final size:19
Alignment explanation
Indices: 527389--527579 Score: 105
Period size: 19 Copynumber: 10.1 Consensus size: 19
527379 TACTAAAAGT
*
527389 TTATAAAAACTTGTAAAAA-
1 TTATAAAAA-TTATAAAAAC
*
527408 TTATAAAACTTA-AAAAA-
1 TTATAAAAATTATAAAAAC
527425 TTATAAAAATTCATAAAAAC
1 TTATAAAAATT-ATAAAAAC
* *
527445 CTATAAATATTATAAAAAC
1 TTATAAAAATTATAAAAAC
*
527464 TTATAAAAAAATT-TAAATAC
1 TTAT--AAAAATTATAAAAAC
* *
527484 -TACAAATAGTTAT-AAAAC
1 TTATAAA-AATTATAAAAAC
527502 TTATAAAAATTCATAATAAGA-
1 TTATAAAAATT-ATAA-AA-AC
*
527523 TTA-AATAAATTAGAAAAA-
1 TTATAA-AAATTATAAAAAC
* * * *
527541 TTAT-AAATTTTTAATATC
1 TTATAAAAATTATAAAAAC
*
527559 ATTATAAAATTTATAAAAAC
1 -TTATAAAAATTATAAAAAC
527579 T
1 T
527580 CATTTATTGG
Statistics
Matches: 133, Mismatches: 22, Indels: 34
0.70 0.12 0.18
Matches are distributed among these distances:
17 25 0.19
18 18 0.14
19 41 0.31
20 32 0.24
21 16 0.12
22 1 0.01
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (19 bp):
TTATAAAAATTATAAAAAC
Found at i:527425 original size:17 final size:18
Alignment explanation
Indices: 527389--527432 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
527379 TACTAAAAGT
*
527389 TTATAAAAACTTGTAAAAA
1 TTAT-AAAACTTGAAAAAA
527408 TTATAAAACTT-AAAAAA
1 TTATAAAACTTGAAAAAA
527425 TTATAAAA
1 TTATAAAA
527433 ATTCATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 7 0.29
19 4 0.17
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (18 bp):
TTATAAAACTTGAAAAAA
Found at i:527462 original size:29 final size:27
Alignment explanation
Indices: 527392--527472 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 27
527382 TAAAAGTTTA
* * *
527392 TAAAAACTTGTAAAAATTAT-AAAACT
1 TAAAAAATTATAAAAATTATAAAAACC
527418 TAAAAAATTATAAAAATTCATAAAAACC
1 TAAAAAATTATAAAAATT-ATAAAAACC
*
527446 TATAAATATTATAAAAACTTATAAAAA
1 TA-AAAAATTATAAAAA-TTATAAAAA
527473 AATTTAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 16 0.34
27 2 0.04
28 7 0.15
29 20 0.43
30 2 0.04
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.30
Consensus pattern (27 bp):
TAAAAAATTATAAAAATTATAAAAACC
Found at i:527517 original size:10 final size:9
Alignment explanation
Indices: 527389--527547 Score: 108
Period size: 9 Copynumber: 16.8 Consensus size: 9
527379 TACTAAAAGT
527389 TTATAAAAA
1 TTATAAAAA
*
527398 CTTGTAAAAA
1 -TTATAAAAA
*
527408 TTATAAAAC
1 TTATAAAAA
527417 TTA-AAAAA
1 TTATAAAAA
527425 TTATAAAAA
1 TTATAAAAA
527434 TTCATAAAAA
1 TT-ATAAAAA
* *
527444 CCTATAAATA
1 -TTATAAAAA
527454 TTATAAAAA
1 TTATAAAAA
527463 CTTATAAAAAAA
1 -TTAT--AAAAA
*
527475 TT-TAAATA
1 TTATAAAAA
* * *
527483 CTACAAATAG
1 TTATAAA-AA
*
527493 TTATAAAAC
1 TTATAAAAA
527502 TTATAAAAA
1 TTATAAAAA
527511 TTCATAATAAGA
1 TT-ATAA-AA-A
527523 TTA-AATAAA
1 TTATAA-AAA
*
527532 TTAGAAAAA
1 TTATAAAAA
527541 TTATAAA
1 TTATAAA
527548 TTTTTAATAT
Statistics
Matches: 119, Mismatches: 18, Indels: 25
0.73 0.11 0.15
Matches are distributed among these distances:
8 12 0.10
9 51 0.43
10 42 0.35
11 6 0.05
12 8 0.07
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (9 bp):
TTATAAAAA
Found at i:528706 original size:2 final size:2
Alignment explanation
Indices: 528699--528723 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
528689 ATACAATTGC
528699 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
528724 CTCGATATCC
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:537119 original size:12 final size:12
Alignment explanation
Indices: 537102--537142 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
537092 TATAGAAGAC
537102 ATAAAATAAAAG
1 ATAAAATAAAAG
*
537114 ATAAAATAAAAT
1 ATAAAATAAAAG
537126 AGT-AAATAAAAG
1 A-TAAAATAAAAG
537138 A-AAAA
1 ATAAAA
537143 GCTTGAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 21 0.84
13 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:540663 original size:19 final size:19
Alignment explanation
Indices: 540639--540675 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
540629 GTGAATTTTA
*
540639 ATTTATTTTCAAGACTTGG
1 ATTTATTTTAAAGACTTGG
540658 ATTTATTTTAAAGACTTG
1 ATTTATTTTAAAGACTTG
540676 TAATTGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (19 bp):
ATTTATTTTAAAGACTTGG
Found at i:541272 original size:37 final size:37
Alignment explanation
Indices: 541227--541309 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
541217 CCCAAGACTG
* *
541227 TCGCTGCATAAATATTCTTCAATTGCATCCAGAACTA
1 TCGCTGCATAAATATTCTTCAATTGCACCCAGAAATA
* * *
541264 TCGTTGCATAAGTATTCTTCAATTGCACCCCGAAATA
1 TCGCTGCATAAATATTCTTCAATTGCACCCAGAAATA
541301 TCGCTGCAT
1 TCGCTGCAT
541310 GAACATGTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (37 bp):
TCGCTGCATAAATATTCTTCAATTGCACCCAGAAATA
Found at i:541332 original size:26 final size:25
Alignment explanation
Indices: 541297--541350 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 25
541287 TGCACCCCGA
541297 AATATCGCTGCATGAACATGTCCAG
1 AATATCGCTGCATGAACATGTCCAG
*
541322 AATAGTCGCTGCATGAACGTGTCCAG
1 AATA-TCGCTGCATGAACATGTCCAG
541348 AAT
1 AAT
541351 TACGCCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (25 bp):
AATATCGCTGCATGAACATGTCCAG
Found at i:543547 original size:17 final size:17
Alignment explanation
Indices: 543527--543574 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
543517 CACATTTCCT
*
543527 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTGAA
* * *
543544 TTGTCACTACATTTGCA
1 TTGTCATTGCATTTGAA
*
543561 TTATCATTGCATTT
1 TTGTCATTGCATTT
543575 ACATTTCTCA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:543548 original size:34 final size:34
Alignment explanation
Indices: 543505--543574 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
543495 GTAGCTATAA
* *
543505 TTTAATTGTCACCACATTTCCTTTGTCATTGCAT
1 TTTAATTGTCACCACATTTCCATTATCATTGCAT
* *
543539 TTTAATTGTCACTACATTTGCATTATCATTGCAT
1 TTTAATTGTCACCACATTTCCATTATCATTGCAT
543573 TT
1 TT
543575 ACATTTCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (34 bp):
TTTAATTGTCACCACATTTCCATTATCATTGCAT
Found at i:544843 original size:37 final size:37
Alignment explanation
Indices: 544746--544855 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 37
544736 CACTTCCAGA
* * * **
544746 TTGCACCCAAAACTGTCGCTGCATGAATATTTCTGGA-
1 TTGCACCCAAAACTATCACTGCATAAATA-TTCTTCAG
* * * *
544783 ATGCACCCAAGACTGTCATTGCATAAATATTCTTCAG
1 TTGCACCCAAAACTATCACTGCATAAATATTCTTCAG
* *
544820 TTGCATCCAAAACTATCACTGCATAAGTATTCTTCA
1 TTGCACCCAAAACTATCACTGCATAAATATTCTTCA
544856 ATTAAACCCA
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
36 5 0.08
37 54 0.92
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (37 bp):
TTGCACCCAAAACTATCACTGCATAAATATTCTTCAG
Found at i:544899 original size:26 final size:26
Alignment explanation
Indices: 544870--544923 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
544860 AACCCAGGAA
544870 TGTCACTGCATGAACATGTCCAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
544896 TGTCACTGCATGAACATGTCCAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
544922 TG
1 TG
544924 CGCCCAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (26 bp):
TGTCACTGCATGAACATGTCCAGAAT
Found at i:549324 original size:16 final size:17
Alignment explanation
Indices: 549292--549324 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
549282 TACAAATAAG
549292 AATGAAAATGAAACTAT
1 AATGAAAATGAAACTAT
*
549309 AATGCAAATG-AACTAT
1 AATGAAAATGAAACTAT
549325 CAAGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
AATGAAAATGAAACTAT
Found at i:553364 original size:16 final size:16
Alignment explanation
Indices: 553339--553401 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 16
553329 CAAAATTTTC
553339 AGGCTGTGTGCCTAGT
1 AGGCTGTGTGCCTAGT
* *
553355 AGGCTTTGTGCCGGTGTGTTT
1 AGGCTGTGTGCC--T-AG--T
553376 AGGCTGTGTGCCTAGT
1 AGGCTGTGTGCCTAGT
*
553392 AGGCTTTGTG
1 AGGCTGTGTG
553402 TTAGTGTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
16 21 0.57
18 2 0.05
19 2 0.05
21 12 0.32
ACGTcount: A:0.10, C:0.16, G:0.38, T:0.37
Consensus pattern (16 bp):
AGGCTGTGTGCCTAGT
Found at i:553389 original size:37 final size:36
Alignment explanation
Indices: 553334--553595 Score: 292
Period size: 37 Copynumber: 7.0 Consensus size: 36
553324 GCTTACAAAA
*
553334 TTTTCAGGCTGTGTGCCTAGTAGGCTTTGTGCCGGTG
1 TTTT-AGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTG
**
553371 TGTTTAGGCTGTGTGCCTAGTAGGCTTTGTGTTAGTG
1 T-TTTAGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTG
*
553408 TTTTTAGGCTGTGTGCCTAGTAGTAGGCTTTGTGCCGGTG
1 -TTTTAGGCTGTGTGCC---TAGTAGGCTTTGTGTCGGTG
*
553448 TTTTCAGGCTGTGTGCTTAGTAGGCTTTGTGTCGGTG
1 TTTT-AGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTG
* *
553485 TTTTTAGG-TAGTGTGCCTAGTAGGCTATGTGTCAGTG
1 -TTTTAGGCT-GTGTGCCTAGTAGGCTTTGTGTCGGTG
* * * * *
553522 TTTTCAAGCTATGTGCCTAGTAGACTTCGTGCCGGTG
1 TTTT-AGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTG
* *
553559 TATTTAGGCTATGTGCCTAGTAGGCTTTATGTCGGTG
1 T-TTTAGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTG
553596 ACCCAAGAAC
Statistics
Matches: 191, Mismatches: 23, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
36 5 0.03
37 142 0.74
38 12 0.06
39 4 0.02
40 28 0.15
ACGTcount: A:0.12, C:0.15, G:0.33, T:0.40
Consensus pattern (36 bp):
TTTTAGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTG
Found at i:553537 original size:114 final size:111
Alignment explanation
Indices: 553334--553595 Score: 366
Period size: 114 Copynumber: 2.3 Consensus size: 111
553324 GCTTACAAAA
* *
553334 TTTTCAGGCTGTGTGCCTAGTAGGCTTTGTGCCGGTGTGTTTAGGCTGTGTGCCTAGTAGGCTTT
1 TTTTCAGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTGTGTTTAGGCTGTGTGCCTAGTAGGCTAT
* * * * *
553399 GTGTTAGTGTTTTTAGGCTGTGTGCCTAGTAGTAGGCTTTGTGCCGGTG
66 GTGTCAGTGTTTTCAAGCTATGTGCCTAGTAG-A--CTTCGTGCCGGTG
* *
553448 TTTTCAGGCTGTGTGCTTAGTAGGCTTTGTGTCGGTGTTTTTAGG-TAGTGTGCCTAGTAGGCTA
1 TTTTCAGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTGTGTTTAGGCT-GTGTGCCTAGTAGGCTA
553512 TGTGTCAGTGTTTTCAAGCTATGTGCCTAGTAGACTTCGTGCCGGTG
65 TGTGTCAGTGTTTTCAAGCTATGTGCCTAGTAGACTTCGTGCCGGTG
* *
553559 TATTT-AGGCTATGTGCCTAGTAGGCTTTATGTCGGTG
1 T-TTTCAGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTG
553596 ACCCAAGAAC
Statistics
Matches: 134, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
111 42 0.31
112 3 0.02
113 2 0.01
114 87 0.65
ACGTcount: A:0.12, C:0.15, G:0.33, T:0.40
Consensus pattern (111 bp):
TTTTCAGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTGTGTTTAGGCTGTGTGCCTAGTAGGCTAT
GTGTCAGTGTTTTCAAGCTATGTGCCTAGTAGACTTCGTGCCGGTG
Found at i:554331 original size:2 final size:2
Alignment explanation
Indices: 554324--554349 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
554314 GGTGGAACTA
554324 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
554350 CGGTAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:566963 original size:27 final size:27
Alignment explanation
Indices: 566768--566952 Score: 203
Period size: 27 Copynumber: 6.9 Consensus size: 27
566758 CATGGTCAAA
** *
566768 ATTTTGTATCTGGCTTAAATAAGCGAT
1 ATTTTGTATCTGGCTCGAATGAGCGAT
* *
566795 ATTTTGTATTTGGCTCGAATGAACGAT
1 ATTTTGTATCTGGCTCGAATGAGCGAT
* *
566822 ATTTTGTATCTGACTCGAATGAGCGGT
1 ATTTTGTATCTGGCTCGAATGAGCGAT
* * *
566849 ATTTTGTATATGGCTCGAATGCGTGAT
1 ATTTTGTATCTGGCTCGAATGAGCGAT
* *
566876 ATTTTGTATCTAGCTCAAATGCA-CGAT
1 ATTTTGTATCTGGCTCGAATG-AGCGAT
* *
566903 ATTCTGTATCCGGCTCGAATGCA-CGAT
1 ATTTTGTATCTGGCTCGAATG-AGCGAT
*
566930 ATTATGTATCTGGCTCGAATGAG
1 ATTTTGTATCTGGCTCGAATGAG
566953 TGCTATTATG
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
26 1 0.01
27 130 0.99
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (27 bp):
ATTTTGTATCTGGCTCGAATGAGCGAT
Found at i:569567 original size:337 final size:337
Alignment explanation
Indices: 568952--569625 Score: 1267
Period size: 337 Copynumber: 2.0 Consensus size: 337
568942 ACTAGCTGCA
*
568952 GTGTGACTATAGTAGGTCTCGCTTTTCCAATTCCTAGCTTCCTAAAGACAAACATAGGCATTAAA
1 GTGTGACTATAGTAGGTCTCGCTTTTCCAATTCCTAGCTTCCTAAAGACAAACATAAGCATTAAA
*
569017 TTTATACTTTCTCCTAAATTGCATAATGCCTTACCAATGATTTCCAATTGAACAAGGGACAGTAA
66 TTTATACTTGCTCCTAAATTGCATAATGCCTTACCAATGATTTCCAATTGAACAAGGGACAGTAA
* * *
569082 AACTCTTTGGGTCCTTCAACTTTGGAGGCAATTTATTCATGAACTTCGTTGTGCACCCTTCAGTG
131 AACTCTTTGGGTCCTTCAACTTTGGAGGCAATTTATTCATCAACTTCGCTGTACACCCTTCAGTG
*
569147 GGAGCAATAGTTTCAAATTCCCCCAATCTTTGCTTCTTTGACAAAATATATTTCATGAATTTCAC
196 GGAGAAATAGTTTCAAATTCCCCCAATCTTTGCTTCTTTGACAAAATATATTTCATGAATTTCAC
569212 ATAATTGGGTATTTGCTCCAAAGCTTCTACTAACGGTATGTTAATATGGAGTTGCTTTAGGACAT
261 ATAATTGGGTATTTGCTCCAAAGCTTCTACTAACGGTATGTTAATATGGAGTTGCTTTAGGACAT
569277 CCAAAAATCTTT
326 CCAAAAATCTTT
*
569289 GTGTGACTATAGTAGGTCTCGCTTTTCCAATTTCTAGCTTCCTAAAGACAAACATAAGCATTAAA
1 GTGTGACTATAGTAGGTCTCGCTTTTCCAATTCCTAGCTTCCTAAAGACAAACATAAGCATTAAA
*
569354 TTTATACTTGCTCCTAAATTGTATAATGCCTTACCAATGATTTCCAATTGAACAAGGGACAGTAA
66 TTTATACTTGCTCCTAAATTGCATAATGCCTTACCAATGATTTCCAATTGAACAAGGGACAGTAA
*
569419 AACTCTTTGGGTCCTTTAACTTTGGAGGCAATTTATTCATCAACTTCGCTGTACACCCTTCAGTG
131 AACTCTTTGGGTCCTTCAACTTTGGAGGCAATTTATTCATCAACTTCGCTGTACACCCTTCAGTG
569484 GGAGAAATAGTTTCAAATTCCCCCAATCTTTGCTTCTTTGACAAAATATATTTCATGAATTTCAC
196 GGAGAAATAGTTTCAAATTCCCCCAATCTTTGCTTCTTTGACAAAATATATTTCATGAATTTCAC
569549 ATAATTGGGTATTTGCTCCAAAGCTTCTACTAACGGTATGTTAATATGGAGTTGCTTTAGGACAT
261 ATAATTGGGTATTTGCTCCAAAGCTTCTACTAACGGTATGTTAATATGGAGTTGCTTTAGGACAT
569614 CCAAAAATCTTT
326 CCAAAAATCTTT
569626 TGAACTTAAA
Statistics
Matches: 328, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
337 328 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (337 bp):
GTGTGACTATAGTAGGTCTCGCTTTTCCAATTCCTAGCTTCCTAAAGACAAACATAAGCATTAAA
TTTATACTTGCTCCTAAATTGCATAATGCCTTACCAATGATTTCCAATTGAACAAGGGACAGTAA
AACTCTTTGGGTCCTTCAACTTTGGAGGCAATTTATTCATCAACTTCGCTGTACACCCTTCAGTG
GGAGAAATAGTTTCAAATTCCCCCAATCTTTGCTTCTTTGACAAAATATATTTCATGAATTTCAC
ATAATTGGGTATTTGCTCCAAAGCTTCTACTAACGGTATGTTAATATGGAGTTGCTTTAGGACAT
CCAAAAATCTTT
Found at i:580294 original size:31 final size:31
Alignment explanation
Indices: 580256--580317 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
580246 TTTTTCTAAG
580256 AAAGATGCAAAACCTAGGATGATTAGGTGGA
1 AAAGATGCAAAACCTAGGATGATTAGGTGGA
580287 AAAGATGCAAAACCTAGGATGATTAGGTGGA
1 AAAGATGCAAAACCTAGGATGATTAGGTGGA
580318 TCCTTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.29, T:0.19
Consensus pattern (31 bp):
AAAGATGCAAAACCTAGGATGATTAGGTGGA
Found at i:583609 original size:15 final size:15
Alignment explanation
Indices: 583583--583621 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
583573 GTATTGAGGC
*
583583 AGAAGTAGAAGAAAGA
1 AGAAGAAGAAGAAA-A
583599 A-AAGAAGAAGAAAA
1 AGAAGAAGAAGAAAA
583613 AGAAGAAGA
1 AGAAGAAGA
583622 CGTTGCCCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (15 bp):
AGAAGAAGAAGAAAA
Found at i:583620 original size:12 final size:13
Alignment explanation
Indices: 583589--583621 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
583579 AGGCAGAAGT
583589 AGAAGAA-AGAAA
1 AGAAGAAGAGAAA
583601 AGAAGAAGA-AAA
1 AGAAGAAGAGAAA
583613 AGAAGAAGA
1 AGAAGAAGA
583622 CGTTGCCCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAGAAA
Found at i:584051 original size:17 final size:17
Alignment explanation
Indices: 584029--584084 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
584019 ATTATCATTA
584029 CATTTTTATTGTCTCTG
1 CATTTTTATTGTCTCTG
584046 CA-TTTTACTTGT-TCTCG
1 CATTTTTA-TTGTCTCT-G
*
584063 CATTTTCATTGTCGT-TG
1 CATTTTTATTGTC-TCTG
584080 CATTT
1 CATTT
584085 CCATTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 8 0.24
17 19 0.58
18 5 0.15
19 1 0.03
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.55
Consensus pattern (17 bp):
CATTTTTATTGTCTCTG
Found at i:589142 original size:2 final size:2
Alignment explanation
Indices: 589135--589183 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
589125 CCATATACAT
589135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
589177 TA CA TA T
1 TA TA TA T
589184 TAGTTAAAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:589492 original size:27 final size:28
Alignment explanation
Indices: 589434--589665 Score: 170
Period size: 28 Copynumber: 8.2 Consensus size: 28
589424 TTTCATTTAT
* *
589434 TATCCTTTCGAATATATCCTTTTCAAATA
1 TATCCTTTCGGATATAACCTTTTC-AATA
* *
589463 TATCCATCCGGATATAACCTTTTCAA-A
1 TATCCTTTCGGATATAACCTTTTCAATA
* *
589490 TATACTTTCGGATATAATCTTTTCAATGA
1 TATCCTTTCGGATATAACCTTTTCAAT-A
*
589519 TATCCTTTCGGATAT-CCCTTTTC-ATA
1 TATCCTTTCGGATATAACCTTTTCAATA
* * * *
589545 GTATTCTTACGGATATAACATTTTCATTGA
1 -TATCCTTTCGGATATAACCTTTTCAAT-A
* * *
589575 TATCCTTGCAGATAT-CCCTTTTCAATAA
1 TATCCTTTCGGATATAACCTTTTCAAT-A
* * * *
589603 TATCCTTGCGCATAT-TCCTTTTCATTGA
1 TATCCTTTCGGATATAACCTTTTCAAT-A
* * *
589631 TATCCTTGCAGATAT-CCCTTTTCAATAA
1 TATCCTTTCGGATATAACCTTTTCAAT-A
589659 TATCCTT
1 TATCCTT
589666 ATGGGTATTC
Statistics
Matches: 164, Mismatches: 33, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 38 0.23
28 76 0.46
29 48 0.29
30 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (28 bp):
TATCCTTTCGGATATAACCTTTTCAATA
Found at i:589570 original size:112 final size:112
Alignment explanation
Indices: 589453--589654 Score: 241
Period size: 112 Copynumber: 1.8 Consensus size: 112
589443 GAATATATCC
* * *
589453 TTTTCAAAT-ATATCCATCCGGATATAACCTTTTC-A-AATATACTTTCGGATATAAT-CTTTTC
1 TTTTC-AATGATATCCATCCAGATAT-ACCTTTTCAATAATATACTTGCGCATAT--TCCTTTTC
* *
589514 AATGATATCCTTTCGGATATCCCTTTTCATAGTATTCTTACGGATATAACA
62 AATGATATCCTTGCAGATATCCCTTTTCATAGTATTCTTACGGATATAACA
* * * * * *
589565 TTTTCATTGATATCCTTGCAGATATCCCTTTTCAATAATATCCTTGCGCATATTCCTTTTCATTG
1 TTTTCAATGATATCCATCCAGATATACCTTTTCAATAATATACTTGCGCATATTCCTTTTCAATG
589630 ATATCCTTGCAGATATCCCTTTTCA
66 ATATCCTTGCAGATATCCCTTTTCA
589655 ATAATATCCT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
111 10 0.13
112 51 0.68
113 14 0.19
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.43
Consensus pattern (112 bp):
TTTTCAATGATATCCATCCAGATATACCTTTTCAATAATATACTTGCGCATATTCCTTTTCAATG
ATATCCTTGCAGATATCCCTTTTCATAGTATTCTTACGGATATAACA
Found at i:589596 original size:28 final size:28
Alignment explanation
Indices: 589508--589702 Score: 194
Period size: 28 Copynumber: 7.0 Consensus size: 28
589498 CGGATATAAT
* *
589508 CTTTTCAATGATATCCTTTCGGATATCC
1 CTTTTCATTGATATCCTTGCGGATATCC
* * * *
589536 CTTTTCATAG-TATTCTTACGGATATAAC
1 CTTTTCATTGATATCCTTGCGGATAT-CC
* *
589564 ATTTTCATTGATATCCTTGCAGATATCC
1 CTTTTCATTGATATCCTTGCGGATATCC
* * * *
589592 CTTTTCAATAATATCCTTGCGCATATTC
1 CTTTTCATTGATATCCTTGCGGATATCC
*
589620 CTTTTCATTGATATCCTTGCAGATATCC
1 CTTTTCATTGATATCCTTGCGGATATCC
* * ** * *
589648 CTTTTCAATAATATCCTTATGGGTATTC
1 CTTTTCATTGATATCCTTGCGGATATCC
*
589676 CTTTTCATTGATACCCTTGCGGATATC
1 CTTTTCATTGATATCCTTGCGGATATC
589703 TCTTCTCAAT
Statistics
Matches: 129, Mismatches: 36, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
27 13 0.10
28 104 0.81
29 12 0.09
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.43
Consensus pattern (28 bp):
CTTTTCATTGATATCCTTGCGGATATCC
Found at i:589662 original size:56 final size:56
Alignment explanation
Indices: 589508--589728 Score: 282
Period size: 56 Copynumber: 3.9 Consensus size: 56
589498 CGGATATAAT
* * * * * *
589508 CTTTTCAATGATATCCTTTCGGATATCCCTTTTC-ATAGTATTCTTACGGATATAAC
1 CTTTTCATTGATATCCTTGCAGATATCCCTTTTCAATAATATCCTTACGGATAT-TC
* * *
589564 ATTTTCATTGATATCCTTGCAGATATCCCTTTTCAATAATATCCTTGCGCATATTC
1 CTTTTCATTGATATCCTTGCAGATATCCCTTTTCAATAATATCCTTACGGATATTC
* *
589620 CTTTTCATTGATATCCTTGCAGATATCCCTTTTCAATAATATCCTTATGGGTATTC
1 CTTTTCATTGATATCCTTGCAGATATCCCTTTTCAATAATATCCTTACGGATATTC
* * * * *
589676 CTTTTCATTGATACCCTTGCGGATATCTCTTCTCAATAATATCTTTACGGATA
1 CTTTTCATTGATATCCTTGCAGATATCCCTTTTCAATAATATCCTTACGGATA
589729 AAGAAATCAA
Statistics
Matches: 143, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
56 128 0.90
57 15 0.10
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (56 bp):
CTTTTCATTGATATCCTTGCAGATATCCCTTTTCAATAATATCCTTACGGATATTC
Found at i:590238 original size:21 final size:20
Alignment explanation
Indices: 590200--590238 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
590190 TTTCATAACT
* *
590200 TCAAAATCTAACACTTTCTA
1 TCAAAATCAAACAATTTCTA
590220 TCAAAATTCAAACAATTTC
1 TCAAAA-TCAAACAATTTC
590239 ACTCTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
TCAAAATCAAACAATTTCTA
Found at i:593064 original size:15 final size:14
Alignment explanation
Indices: 593041--593140 Score: 71
Period size: 14 Copynumber: 7.1 Consensus size: 14
593031 TTTCAATTAT
*
593041 TATCCTTTCGGATA
1 TATCCTTTCAGATA
*
593055 TATCCTTTTCATATA
1 TATCC-TTTCAGATA
* *
593070 TATCCATCCAGATA
1 TATCCTTTCAGATA
*
593084 TAACCTTTTCA-A-A
1 TATCC-TTTCAGATA
*
593097 TATCCTTTCAAATA
1 TATCCTTTCAGATA
*
593111 TAACCTTTTCA-ATGA
1 TATCC-TTTCAGAT-A
*
593126 TATCCTTTCGGATA
1 TATCCTTTCAGATA
593140 T
1 T
593141 CCCTTTTCAT
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
12 5 0.07
13 6 0.09
14 29 0.43
15 27 0.40
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (14 bp):
TATCCTTTCAGATA
Found at i:593134 original size:14 final size:14
Alignment explanation
Indices: 593031--593134 Score: 61
Period size: 15 Copynumber: 7.3 Consensus size: 14
593021 TTTTCGACCT
*
593031 TTTCAATTATTATCC
1 TTTCAAATA-TATCC
**
593046 TTTCGGATATATCC
1 TTTCAAATATATCC
*
593060 TTTTCATATATATCC
1 -TTTCAAATATATCC
* * * *
593075 ATCCAGATATAACC
1 TTTCAAATATATCC
593089 TTTTC-AA-ATATCC
1 -TTTCAAATATATCC
*
593102 TTTCAAATATAACC
1 TTTCAAATATATCC
593116 TTTTC-AATGATATCC
1 -TTTCAAAT-ATATCC
593131 TTTC
1 TTTC
593135 GGATATCCCT
Statistics
Matches: 68, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
12 4 0.06
13 7 0.10
14 28 0.41
15 29 0.43
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (14 bp):
TTTCAAATATATCC
Found at i:593140 original size:29 final size:28
Alignment explanation
Indices: 593027--593188 Score: 150
Period size: 29 Copynumber: 5.7 Consensus size: 28
593017 TACCTTTTCG
593027 ACCTTTTCAATTATTATCCTTTCGGATATA
1 ACCTTTTCAA-TA-TATCCTTTCGGATATA
* * * *
593057 TCCTTTTCATATATATCCATCCAGATATA
1 ACCTTTTCA-ATATATCCTTTCGGATATA
**
593086 ACCTTTTCAA-ATATCCTTTCAAATATA
1 ACCTTTTCAATATATCCTTTCGGATATA
593113 ACCTTTTCAATGATATCCTTTCGGATAT-
1 ACCTTTTCAAT-ATATCCTTTCGGATATA
* * *
593141 CCCTTTTC-ATAGTTTCCTTACGGATATA
1 ACCTTTTCAATA-TATCCTTTCGGATATA
* *
593169 ACATTTTCATTGATATCCTT
1 ACCTTTTCAAT-ATATCCTT
593189 GCAGGTATCC
Statistics
Matches: 108, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
26 1 0.01
27 39 0.36
28 14 0.13
29 42 0.39
30 11 0.10
31 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (28 bp):
ACCTTTTCAATATATCCTTTCGGATATA
Found at i:593140 original size:56 final size:55
Alignment explanation
Indices: 593027--593241 Score: 164
Period size: 56 Copynumber: 3.8 Consensus size: 55
593017 TACCTTTTCG
* *
593027 ACCTTTTCAATTATTATCCTTTCGGATATATCCTTTTCATAT-ATATCCATCCAGATAT
1 ACCTTTTCAA--A-TATCCTTTCGGATATAACCTTTTCA-ATGATATCCTTCCAGATAT
** * *
593085 AACCTTTTCAAATATCCTTTCAAATATAACCTTTTCAATGATATCCTTTCGGATAT
1 -ACCTTTTCAAATATCCTTTCGGATATAACCTTTTCAATGATATCCTTCCAGATAT
* * * * * * * *
593141 CCCTTTTCATAGTTTCCTTACGGATATAACATTTTCATTGATATCCTTGCAGGTAT
1 ACCTTTTCA-AATATCCTTTCGGATATAACCTTTTCAATGATATCCTTCCAGATAT
* * * * * *
593197 CCCTCTTCAATAATATCCTTACGCATAT-TCCTTTTCATTGATATC
1 ACCTTTTC-A-AATATCCTTTCGGATATAACCTTTTCAATGATATC
593242 ATTGTGGATT
Statistics
Matches: 130, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
55 10 0.08
56 93 0.72
57 17 0.13
59 10 0.08
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (55 bp):
ACCTTTTCAAATATCCTTTCGGATATAACCTTTTCAATGATATCCTTCCAGATAT
Found at i:593205 original size:28 final size:28
Alignment explanation
Indices: 593114--593307 Score: 88
Period size: 28 Copynumber: 7.1 Consensus size: 28
593104 TCAAATATAA
* *
593114 CCTTTTCAATGATATCCTTTC-GGATATC
1 CCTTTTCATTGATATCCTTGCAGG-TATC
* * * *
593142 CCTTTTCATAG-TTTCCTTAC-GGATATAA
1 CCTTTTCATTGATATCCTTGCAGG-TAT-C
*
593170 CATTTTCATTGATATCCTTGCAGGTATC
1 CCTTTTCATTGATATCCTTGCAGGTATC
* * * *
593198 CCTCTTCAATAATATCCTTACGCA--TATT
1 CCTTTTCATTGATATCCTT--GCAGGTATC
* *
593226 CCTTTTCATTGATATCATTG-TGG-A--
1 CCTTTTCATTGATATCCTTGCAGGTATC
* * *
593250 --TTTTCATTGATATCATTG-TGGATATT
1 CCTTTTCATTGATATCCTTGCAGG-TATC
* *
593276 CATTTTCATTGATATCCTTGCAGATATC
1 CCTTTTCATTGATATCCTTGCAGGTATC
593304 CCTT
1 CCTT
593308 CTCAATAATA
Statistics
Matches: 127, Mismatches: 25, Indels: 28
0.71 0.14 0.16
Matches are distributed among these distances:
22 21 0.17
24 1 0.01
26 2 0.02
27 13 0.10
28 74 0.58
29 11 0.09
30 5 0.04
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.44
Consensus pattern (28 bp):
CCTTTTCATTGATATCCTTGCAGGTATC
Found at i:593256 original size:22 final size:22
Alignment explanation
Indices: 593228--593279 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
593218 CGCATATTCC
593228 TTTTCATTGATATCATTGTGGA
1 TTTTCATTGATATCATTGTGGA
593250 TTTTCATTGATATCATTGTGGA
1 TTTTCATTGATATCATTGTGGA
*
593272 TATTCATT
1 TTTTCATT
593280 TTCATTGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (22 bp):
TTTTCATTGATATCATTGTGGA
Found at i:593500 original size:21 final size:20
Alignment explanation
Indices: 593472--593510 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
593462 GTTTCTCTCG
593472 TTTCTTT-ATCTAAATAATAA
1 TTTCTTTAAT-TAAATAATAA
593492 TTTCATTTAATTAAATAAT
1 TTTC-TTTAATTAAATAAT
593511 TCAAATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTCTTTAATTAAATAATAA
Found at i:594881 original size:13 final size:13
Alignment explanation
Indices: 594863--594887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
594853 TTTATTTTCT
594863 TTTTGCTGTTATA
1 TTTTGCTGTTATA
594876 TTTTGCTGTTAT
1 TTTTGCTGTTAT
594888 CTTCCCTAAT
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:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (13 bp):
TTTTGCTGTTATA
Found at i:595863 original size:20 final size:21
Alignment explanation
Indices: 595840--595880 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
595830 AAAAAACTTT
595840 TAAATTACAA-AAAA-TATAAA
1 TAAATTA-AATAAAATTATAAA
595860 TAAATTAAATAAAATTATAAA
1 TAAATTAAATAAAATTATAAA
595881 CACATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 11 0.58
21 6 0.32
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATTAAATAAAATTATAAA
Found at i:595997 original size:29 final size:29
Alignment explanation
Indices: 595955--596030 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
595945 ATAAAAAAAC
* * *
595955 TAAAAAATATTAGAAATTCTAAAATATTG
1 TAAAAATTATTAGAAATTCAAAAAGATTG
595984 TAAAAATTATTAG-AATTCAAAAAGATTG
1 TAAAAATTATTAGAAATTCAAAAAGATTG
*
596012 TATAAAATTATTAAAAATT
1 TA-AAAATTATTAGAAATT
596031 GTTAAGAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 15 0.37
29 22 0.54
30 4 0.10
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAAAATTATTAGAAATTCAAAAAGATTG
Found at i:596877 original size:8 final size:9
Alignment explanation
Indices: 596856--596885 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
596846 AAAAAGTAAT
596856 TTTTTTATA
1 TTTTTTATA
596865 TTTTTTATA
1 TTTTTTATA
596874 TTTTTTA-A
1 TTTTTTATA
596882 TTTT
1 TTTT
596886 GTAACTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTATA
Found at i:596884 original size:17 final size:17
Alignment explanation
Indices: 596856--596965 Score: 59
Period size: 17 Copynumber: 6.5 Consensus size: 17
596846 AAAAAGTAAT
596856 TTTTTTATATTTTTTATA
1 TTTTTTA-ATTTTTTATA
*
596874 TTTTTTAATTTTGTA-A
1 TTTTTTAATTTTTTATA
* * *
596890 -CTTATAATTTTTTGGGTA
1 TTTTTTAATTTTTT--ATA
* *
596908 -TTTTAAATAATTTTATAA
1 TTTTTTAAT-TTTTTAT-A
*
596926 TTTTATAA-TTTTTATA
1 TTTTTTAATTTTTTATA
* *
596942 -ATTTTAATTTTTTTTA
1 TTTTTTAATTTTTTATA
596958 TTTTTTAA
1 TTTTTTAA
596966 AGATTAATTT
Statistics
Matches: 67, Mismatches: 17, Indels: 17
0.66 0.17 0.17
Matches are distributed among these distances:
15 15 0.22
16 9 0.13
17 20 0.30
18 14 0.21
19 9 0.13
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTTTTAATTTTTTATA
Found at i:596940 original size:9 final size:8
Alignment explanation
Indices: 596914--596947 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
596904 GGTATTTTAA
596914 ATAATTTT
1 ATAATTTT
596922 ATAATTTT
1 ATAATTTT
596930 ATAATTTTT
1 ATAA-TTTT
596939 ATAATTTT
1 ATAATTTT
596947 A
1 A
596948 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATAATTTT
Found at i:596961 original size:15 final size:15
Alignment explanation
Indices: 596918--596953 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
596908 TTTTAAATAA
596918 TTTTATAATTTTATAAT
1 TTTTATAA-TTT-TAAT
596935 TTTTATAATTTTAAT
1 TTTTATAATTTTAAT
596950 TTTT
1 TTTT
596954 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATAATTTTAAT
Found at i:603111 original size:29 final size:29
Alignment explanation
Indices: 603076--603131 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
603066 AAAATATAAT
*
603076 TTTTAAA-AGATTAAATTAAAATTTTATCA
1 TTTTAAAGAG-TTAAAATAAAATTTTATCA
*
603105 TTTTAAAGAGTTAAAATATAATTTTAT
1 TTTTAAAGAGTTAAAATAAAATTTTAT
603132 TTTTATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTTAAAGAGTTAAAATAAAATTTTATCA
Found at i:603878 original size:21 final size:21
Alignment explanation
Indices: 603844--603883 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
603834 ATTAGTTGAA
** *
603844 AATATATAGTTATATATTATC
1 AATATATAAATATAAATTATC
603865 AATATATAAATATAAATTA
1 AATATATAAATATAAATTA
603884 ATTCTAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
AATATATAAATATAAATTATC
Found at i:604274 original size:23 final size:24
Alignment explanation
Indices: 604230--604290 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 24
604220 ATTTACATTT
604230 TTAAATAAAATATAAATATAATTTTC
1 TTAAATAAAA-A-AAATATAATTTTC
*
604256 TTAAATAAAAAAAA-GTAATTTTC
1 TTAAATAAAAAAAATATAATTTTC
*
604279 --AAATATAAAAAA
1 TTAAATAAAAAAAA
604291 CATAGGAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 11 0.33
23 8 0.24
24 3 0.09
25 1 0.03
26 10 0.30
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (24 bp):
TTAAATAAAAAAAATATAATTTTC
Found at i:604693 original size:31 final size:31
Alignment explanation
Indices: 604615--604694 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 31
604605 CATTTATAAA
*
604615 TAATATTA-TATTTAAATCATTTGATATTTATT
1 TAATATTATTA-TTAAA-AATTTGATATTTATT
**
604647 TATATAAAATT-TTAAAAATTT-ATAATTTATT
1 TA-ATATTATTATTAAAAATTTGAT-ATTTATT
604678 TAATATTATTATTAAAA
1 TAATATTATTATTAAAA
604695 GTGAGTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
30 8 0.21
31 19 0.49
32 7 0.18
33 4 0.10
34 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
TAATATTATTATTAAAAATTTGATATTTATT
Found at i:606626 original size:52 final size:50
Alignment explanation
Indices: 606460--606628 Score: 223
Period size: 50 Copynumber: 3.3 Consensus size: 50
606450 TTAATAAAAT
* * *
606460 CATGCATTATGTAACTCTCATGTTTGTTAAGTATGCATCAT-AAGTAATGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTAA-GA
* * *
606510 CATGCATTATGTAATTCTCATGTTAGTTAATTTTGCATCATAAATTATGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTAAGA
* *
606560 CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCATTAAATTAAGT
1 CATGCATTATGTAACTCTCATGTTAGTT-AAGTTTGCATCA-TAAATTAAGA
*
606612 CATGCATTAAGTAACTC
1 CATGCATTATGTAACTC
606629 ATTTTTTCAT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
50 66 0.63
51 14 0.13
52 24 0.23
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (50 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTAAGA
Found at i:606802 original size:55 final size:54
Alignment explanation
Indices: 606743--606865 Score: 185
Period size: 55 Copynumber: 2.2 Consensus size: 54
606733 TTTTTAATGC
*
606743 ATAAGTT-ATAATGTGTTTATTTTCATAAATAAATATGTGTATCTCTAGTTAATTG
1 ATAAGTTAATAA--TGTTTATTTTCATAAATAAAAATGTGTATCTCTAGTTAATTG
*
606798 ATAAGTTGAATAATGTTTATTTTCATAAATAAAAATGTGTGTCTCTAGTTAATTG
1 ATAAGTT-AATAATGTTTATTTTCATAAATAAAAATGTGTATCTCTAGTTAATTG
606853 ATAAGTTGAATAA
1 ATAAGTT-AATAA
606866 GAATGTGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
55 60 0.94
57 4 0.06
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (54 bp):
ATAAGTTAATAATGTTTATTTTCATAAATAAAAATGTGTATCTCTAGTTAATTG
Found at i:610645 original size:50 final size:50
Alignment explanation
Indices: 610591--610817 Score: 267
Period size: 50 Copynumber: 4.5 Consensus size: 50
610581 TTCTTCATTT
* * *
610591 AATAAAGTCATGTATTGTGTAACTCTCATATTAGTTAAGTATACATCATA
1 AATAAAGACATGCATTATGTAACTCTCATATTAGTTAAGTATACATCATA
* * *
610641 AATAATGACATGCATTATGTAACTCTCATATTAGTTAAGTATAAATTATA
1 AATAAAGACATGCATTATGTAACTCTCATATTAGTTAAGTATACATCATA
* * *
610691 AATAAAGACATGCATTATGTAACTCTCATGTTAGTTAAGTTTTCATCATA
1 AATAAAGACATGCATTATGTAACTCTCATATTAGTTAAGTATACATCATA
* * * * *
610741 AATTATGACATGCATTATGTAACTC-CAATGTTAGTTAAAGTTTGCATCATTA
1 AATAAAGACATGCATTATGTAACTCTC-ATATTAGTT-AAGTATACATCA-TA
* * *
610793 AATTAAGTCATGCATTAAGTAACTC
1 AATAAAGACATGCATTATGTAACTC
610818 ATTCGTTCAT
Statistics
Matches: 156, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 120 0.77
51 11 0.07
52 24 0.15
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (50 bp):
AATAAAGACATGCATTATGTAACTCTCATATTAGTTAAGTATACATCATA
Found at i:613182 original size:34 final size:35
Alignment explanation
Indices: 613095--613173 Score: 108
Period size: 35 Copynumber: 2.2 Consensus size: 35
613085 AATGAATAAT
613095 AAATAAAATAAATAATT-AAAATCATGCTAATTAAAC
1 AAAT-AAA-AAATAATTAAAAATCATGCTAATTAAAC
613131 AAATAAAAAATAATTAAAAATCATG-TCAATTAAAC
1 AAATAAAAAATAATTAAAAATCATGCT-AATTAAAC
*
613166 AAACAAAA
1 AAATAAAA
613174 TTGGTTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
34 9 0.22
35 27 0.68
36 4 0.10
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.24
Consensus pattern (35 bp):
AAATAAAAAATAATTAAAAATCATGCTAATTAAAC
Found at i:614865 original size:49 final size:49
Alignment explanation
Indices: 614787--615300 Score: 243
Period size: 49 Copynumber: 10.4 Consensus size: 49
614777 TTCGTCGTAG
* * * *
614787 TGGCTTTATTCTACTCCCTCTTCGATTTTAGGGTGTTAGATCTTCCGTTA
1 TGGCTTCAATCTA-TCCCTCTTCGGTTTTAGGGTGTTAGATCGTCCGTTA
* * *
614837 TGGCTTCAATCTATCCCTCTTTGGTTTTAGGGTGTTAGGTCTTCCGTTA
1 TGGCTTCAATCTATCCCTCTTCGGTTTTAGGGTGTTAGATCGTCCGTTA
* * * * * *
614886 CGGCTTCAATCTATCCCTCTTTGGTTTTAAGGTGTAAGATCGACCGTTG
1 TGGCTTCAATCTATCCCTCTTCGGTTTTAGGGTGTTAGATCGTCCGTTA
* * * * * * * ** **
614935 CGGCTTTAATCTTTTCTTCTTTGGTTTTAGGGTCTTAGATCCACTATTA
1 TGGCTTCAATCTATCCCTCTTCGGTTTTAGGGTGTTAGATCGTCCGTTA
* * * * * *
614984 TGACTTCAATCTATCTCTCTTCGATTTTAAGGTGTTAGGTCCAT-CGTTA
1 TGGCTTCAATCTATCCCTCTTCGGTTTTAGGGTGTTAGAT-CGTCCGTTA
** * * * * *
615033 CAGCTTCAACCTATCCCTCTTAGGTTTTAAGGT-TAAGATTCGT-CATTA
1 TGGCTTCAATCTATCCCTCTTCGGTTTTAGGGTGTTAGA-TCGTCCGTTA
* * * * **
615081 TGACTTTAATCCT-TCCCTCTTCAGTTTTAGGGTGTTAGGTCCG-CTATTA
1 TGGCTTCAAT-CTATCCCTCTTCGGTTTTAGGGTGTTAGAT-CGTCCGTTA
* * * * ** * * * *
615130 CGGCTTCAACCAATCCCTGTTCAATTTTGAAGGTGTAAGATTCGT-CATTG
1 TGGCTTCAATCTATCCCTCTTCGGTTTT-AGGGTGTTAGA-TCGTCCGTTA
** * * * * * *
615180 CAGTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGATCCGT-CATTG
1 TGGCTTCAATCTATCCCTCTTCGGTTTTAGGGTGTTAGAT-CGTCCGTTA
* * * * * * * * * *
615229 CGACTTTAATCTATCCCTATTTGGTTTTAAGGTGTTAGGTCCGTTCTTTG
1 TGGCTTCAATCTATCCCTCTTCGGTTTTAGGGTGTTAGAT-CGTCCGTTA
615279 TGGCTTCAA-CATATCCCTCTTC
1 TGGCTTCAATC-TATCCCTCTTC
615301 AACTCTAAGA
Statistics
Matches: 355, Mismatches: 96, Indels: 26
0.74 0.20 0.05
Matches are distributed among these distances:
48 34 0.10
49 255 0.72
50 65 0.18
51 1 0.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (49 bp):
TGGCTTCAATCTATCCCTCTTCGGTTTTAGGGTGTTAGATCGTCCGTTA
Found at i:615059 original size:98 final size:96
Alignment explanation
Indices: 614796--615266 Score: 290
Period size: 98 Copynumber: 4.8 Consensus size: 96
614786 GTGGCTTTAT
* * *
614796 TCTACTCCCTCTTCGATTTTAGGGTGTTAGAT-CTTCCGTTATGGCTTCAATCTATCCCTCTTTG
1 TCTA-TCCCTCTTCGATTTTAAGGTGTTAGATCCAT-CGTTACGGCTTCAATCTATCCCTCTTTG
* * * *
614860 GTTTTAGGGTGTTAGGTCTTCC-GTTACGGCTTCAA
64 GTTTTAGGGT-TTAGATC--CCTATTATGACTTCAA
* * * * * * * * * *
614895 TCTATCCCTCTTTGGTTTTAAGGTGTAAGATCGACCGTTGCGGCTTTAATCTTTTCTTCTTTGGT
1 TCTATCCCTCTTCGATTTTAAGGTGTTAGATCCATCGTTACGGCTTCAATCTATCCCTCTTTGGT
614960 TTTAGGGTCTTAGATCCACTATTATGACTTCAA
66 TTTAGGGT-TTAGATCC-CTATTATGACTTCAA
* * * * *
614993 TCTATCTCTCTTCGATTTTAAGGTGTTAGGTCCATCGTTACAGCTTCAACCTATCCCTCTTAGGT
1 TCTATCCCTCTTCGATTTTAAGGTGTTAGATCCATCGTTACGGCTTCAATCTATCCCTCTTTGGT
* * * * *
615058 TTTAAGGTTAAGATTCGTCATTATGACTTTAA
66 TTTAGGGTTTAGATCCCT-ATTATGACTTCAA
* * * * * * * *
615090 TCCT-TCCCTCTTC-AGTTTTAGGGTGTTAGGTCC-GCTATTACGGCTTCAACCAATCCCTGTTC
1 T-CTATCCCTCTTCGA-TTTTAAGGTGTTAGATCCATC-GTTACGGCTTCAATCTATCCCTCTTT
** * * * * *
615152 AATTTTGAAGGTGTAAGATTCGTCA-T-TGCAGTTTCAA
63 GGTTTT-AGGGT-TTAGATCCCT-ATTATG-A-CTTCAA
* * * * * * *
615189 TCTTTCCCTCTTCGATTTTAAGGTGTTAGATCCGTCATTGCGACTTTAATCTATCCCTATTTGGT
1 TCTATCCCTCTTCGATTTTAAGGTGTTAGATCCATCGTTACGGCTTCAATCTATCCCTCTTTGGT
*
615254 TTTAAGGTGTTAG
66 TTTAGGGT-TTAG
615267 GTCCGTTCTT
Statistics
Matches: 295, Mismatches: 63, Indels: 29
0.76 0.16 0.07
Matches are distributed among these distances:
96 4 0.01
97 72 0.24
98 148 0.50
99 69 0.23
100 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (96 bp):
TCTATCCCTCTTCGATTTTAAGGTGTTAGATCCATCGTTACGGCTTCAATCTATCCCTCTTTGGT
TTTAGGGTTTAGATCCCTATTATGACTTCAA
Found at i:615163 original size:147 final size:146
Alignment explanation
Indices: 614861--615271 Score: 405
Period size: 147 Copynumber: 2.8 Consensus size: 146
614851 CCCTCTTTGG
* * * *
614861 TTTTAGGGTGTTAGGTCTTCCGTTACGGCTTCAATCTATCCCTCTTTGGTTTTAAGGTGTAAGA-
1 TTTTAAGGTGTTAGGTCAT-CGTTACAGCTTCAATCTATCCCTCTTAGGTTTTAAGGTGTAAGAT
* * * * * * * * * *
614925 TCGACCGTTGCGGCTTTAATCTTTTCTTCTTTGGTTTTAGGGTCTTAGATCCACTATTATGACTT
65 TCG-TCATTGCGACTTTAATCCTTCCCTCTTTGGTTTTAGGGTGTTAGGTCCGCTATTACGACTT
* * * *
614990 CAATCTATCTCTCTTCGA
129 CAACCAATCCCTCTTCAA
*
615008 TTTTAAGGTGTTAGGTCCATCGTTACAGCTTCAACCTATCCCTCTTAGGTTTTAAGGT-TAAGAT
1 TTTTAAGGTGTTAGGT-CATCGTTACAGCTTCAATCTATCCCTCTTAGGTTTTAAGGTGTAAGAT
** ** *
615072 TCGTCATTATGACTTTAATCCTTCCCTCTTCAGTTTTAGGGTGTTAGGTCCGCTATTACGGCTTC
65 TCGTCATTGCGACTTTAATCCTTCCCTCTTTGGTTTTAGGGTGTTAGGTCCGCTATTACGACTTC
*
615137 AACCAATCCCTGTTCAA
130 AACCAATCCCTCTTCAA
* * * * * * * * * *
615154 TTTTGAAGGTGTAAGATTCGTCATTGCAGTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGA
1 TTTT-AAGGTGTTAG-GTCATCGTTACAGCTTCAATCTATCCCTCTTAGGTTTTAAGGTGTAAGA
* * *
615219 TCCGTCATTGCGACTTTAAT-CTATCCCTATTTGGTTTTAAGGTGTTAGGTCCG
64 TTCGTCATTGCGACTTTAATCCT-TCCCTCTTTGGTTTTAGGGTGTTAGGTCCG
615272 TTCTTTGTGG
Statistics
Matches: 215, Mismatches: 43, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
146 68 0.32
147 97 0.45
148 50 0.23
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (146 bp):
TTTTAAGGTGTTAGGTCATCGTTACAGCTTCAATCTATCCCTCTTAGGTTTTAAGGTGTAAGATT
CGTCATTGCGACTTTAATCCTTCCCTCTTTGGTTTTAGGGTGTTAGGTCCGCTATTACGACTTCA
ACCAATCCCTCTTCAA
Found at i:615208 original size:99 final size:99
Alignment explanation
Indices: 614980--615227 Score: 280
Period size: 97 Copynumber: 2.5 Consensus size: 99
614970 TAGATCCACT
* * *
614980 ATTATGAC-TTCAATCTATCTCTCTTCGATTTTAAGGTGTTAGGTCC-ATCGTTACAGCTTCAAC
1 ATTATGACTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGATCATTACAGCTTCAAC
* *
615043 CTATCCCTCTTAGGTTTTAAGGTTAAGATTCGTC
66 CAATCCCTCTTAGATTTTAAGGTTAAGATTCGTC
* * * *
615077 ATTATGACTTT-AATCCTTCCCTCTTC-AGTTTTAGGGTGTTAGGTCCGCT-ATTACGGCTTCAA
1 ATTATGACTTTCAATCTTTCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGATCATTACAGCTTCAA
*
615139 CCAATCCCTGTTCA-ATTTTGAAGGTGTAAGATTCGTC
65 CCAATCCCTCTT-AGATTTT-AAGGT-TAAGATTCGTC
* *
615176 A-T-TGCAGTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGATCCG-TCATT
1 ATTATG-ACTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGATCATT
615228 GCGACTTTAA
Statistics
Matches: 127, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
96 1 0.01
97 64 0.50
98 15 0.12
99 46 0.36
100 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (99 bp):
ATTATGACTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGATCATTACAGCTTCAAC
CAATCCCTCTTAGATTTTAAGGTTAAGATTCGTC
Found at i:615245 original size:99 final size:98
Alignment explanation
Indices: 614980--615261 Score: 283
Period size: 99 Copynumber: 2.9 Consensus size: 98
614970 TAGATCCACT
* * * *
614980 ATTATGAC-TTCAATCTATCTCTCTTCGATTTTAAGGTGTTAGGTCCATCGTTAC-AGCTTCAAC
1 ATTATGACTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCATTACGA-CTTCAAC
*
615043 CTATCCCTCTTAGGTTTTAAGGTTAAGATTCGTC
65 CTATCCCTCTTAGATTTTAAGGTTAAGATTCGTC
* * *
615077 ATTATGACTTT-AATCCTTCCCTCTTC-AGTTTTAGGGTGTTAGGTCCG-CTATTACGGCTTCAA
1 ATTATGACTTTCAATCTTTCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGTC-ATTACGACTTCAA
* *
615139 CCAATCCCTGTTCA-ATTTTGAAGGTGTAAGATTCGTC
64 CCTATCCCTCTT-AGATTTT-AAGGT-TAAGATTCGTC
* * * * *
615176 A-T-TGCAGTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGATCCGTCATTGCGACTTTAAT
1 ATTATG-ACTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCATTACGACTTCAAC
* * *
615239 CTATCCCTATTTGGTTTTAAGGT
65 CTATCCCTCTTAGATTTTAAGGT
615262 GTTAGGTCCG
Statistics
Matches: 151, Mismatches: 22, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
96 2 0.01
97 63 0.42
98 18 0.12
99 66 0.44
100 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (98 bp):
ATTATGACTTTCAATCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCATTACGACTTCAACC
TATCCCTCTTAGATTTTAAGGTTAAGATTCGTC
Found at i:616825 original size:36 final size:36
Alignment explanation
Indices: 616780--616859 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
616770 AGTATTCTTA
*
616780 AATTCACATGCCAATTCATTATCAAACATATTTGCTT
1 AATT-ACATGCCAATTCATTACCAAACATATTTGCTT
616817 AATTACATGCCAATTCATTACCAAACATATTTGCTT
1 AATTACATGCCAATTCATTACCAAACATATTTGCTT
616853 AATTACA
1 AATTACA
616860 ACATTAAGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 38 0.90
37 4 0.10
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (36 bp):
AATTACATGCCAATTCATTACCAAACATATTTGCTT
Found at i:617578 original size:192 final size:195
Alignment explanation
Indices: 617306--617672 Score: 456
Period size: 200 Copynumber: 1.9 Consensus size: 195
617296 CTATAAAGTA
* * *
617306 TTCCCTAACGATGCTGCTCACACGAGCTGTTAAGAGTATGCAATAAGCATAGTCCCAACCATCGT
1 TTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCAATAAGCATAATCCCAACCATCGT
* *
617371 AGGGCCTGTAATCCATTTAGGATTCATA-TC-TCT-TTCCT-GAGTCACGATACTGCTCAGACGA
66 AGGGCCTGTAATCCATTTAGGATCCATATTCTTCTATTCCTCGAGTCACGATACTGCTCACACGA
* * *
617432 GCTGTCGAGGACTCGCAACATATGCAGTACCTCAGCCATCGATACGATATATGTGCATATAACTG
131 GCTGTCGACGACTCGCAACATATGCAGTACCCCAACCATCGATACGATATATGTGCATATAACTG
* * * * * * *
617497 TTCCCTAAC-ATGCTGCTTACACGAGTTGTCGAGAATATGCACTTATGCATAAATCTCAGCCATC
1 TTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCA-ATAAGCAT-AATCCCAACCATC
* * * * *
617561 GTAGGGCTTGTAATCCATTTAGGATCCATATTTCTTTTCTCATTTCTCGATTCATGATGCTGCTC
64 GTAGGGCCTGTAATCCATTTAGGATCCATA-TTC--TTCT-ATTCCTCGAGTCACGATACTGCTC
*
617626 ACACGAGCTGTCGACGACTCGCAACATATGCGGTACCCCAACCATCG
125 ACACGAGCTGTCGACGACTCGCAACATATGCAGTACCCCAACCATCG
617673 CGTCGGTTTC
Statistics
Matches: 145, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
190 27 0.19
191 15 0.10
192 38 0.26
194 2 0.01
197 3 0.02
199 4 0.03
200 56 0.39
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (195 bp):
TTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCAATAAGCATAATCCCAACCATCGT
AGGGCCTGTAATCCATTTAGGATCCATATTCTTCTATTCCTCGAGTCACGATACTGCTCACACGA
GCTGTCGACGACTCGCAACATATGCAGTACCCCAACCATCGATACGATATATGTGCATATAACTG
Found at i:620141 original size:49 final size:50
Alignment explanation
Indices: 620086--620196 Score: 179
Period size: 49 Copynumber: 2.2 Consensus size: 50
620076 TCTTCTTCTT
* * *
620086 TTTTTTTAAGCCGCCGTTTCAGGTTTTCAATTCAAATTTTTGGATTTTGA
1 TTTTTTTAAGCAGCCGTTTCAGGTTTTCAACTCAAACTTTTGGATTTTGA
*
620136 -TTTTTTGAGCAGCCGTTTCAGGTTTTCAACTCAAACTTTTGGATTTTGA
1 TTTTTTTAAGCAGCCGTTTCAGGTTTTCAACTCAAACTTTTGGATTTTGA
620185 TTTTTTTAAGCA
1 TTTTTTTAAGCA
620197 AAATATTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 45 0.82
50 10 0.18
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (50 bp):
TTTTTTTAAGCAGCCGTTTCAGGTTTTCAACTCAAACTTTTGGATTTTGA
Found at i:635614 original size:4 final size:4
Alignment explanation
Indices: 635605--635629 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
635595 ACATTCAATC
635605 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
635630 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:636163 original size:6 final size:6
Alignment explanation
Indices: 636152--636179 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
636142 TCACATGTAT
636152 ATCTCA ATCTCA ATCTCA ATCTCA ATCT
1 ATCTCA ATCTCA ATCTCA ATCTCA ATCT
636180 TATGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (6 bp):
ATCTCA
Found at i:655206 original size:20 final size:20
Alignment explanation
Indices: 655170--655207 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
655160 CTAAGAATCT
*
655170 GAAACAACATAATGAAAAGC
1 GAAACAACATAAAGAAAAGC
655190 GAAACAA-ATAAAAGAAAA
1 GAAACAACAT-AAAGAAAA
655208 TAAATGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.68, C:0.11, G:0.13, T:0.08
Consensus pattern (20 bp):
GAAACAACATAAAGAAAAGC
Found at i:665279 original size:20 final size:20
Alignment explanation
Indices: 665194--665290 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
665184 ACAACAATTC
665194 TAACTTGTTTGAAAATCATTT
1 TAACTTGTTT-AAAATCATTT
* *
665215 TGA--TGTGTTAAAATGATTT
1 TAACTTGT-TTAAAATCATTT
* * * *
665234 TGATTTGGTTGAAATCATTT
1 TAACTTGTTTAAAATCATTT
*
665254 TTACTTGTTTAAAATCATTT
1 TAACTTGTTTAAAATCATTT
665274 TAACTTGATTTTAAAAT
1 TAACTTG--TTTAAAAT
665291 TGTTTCAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
19 15 0.25
20 34 0.56
21 4 0.07
22 8 0.13
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.49
Consensus pattern (20 bp):
TAACTTGTTTAAAATCATTT
Found at i:665400 original size:22 final size:23
Alignment explanation
Indices: 665374--665422 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
665364 TTTTGTCAAT
*
665374 TTTAATTTAT-ATTTAAAAATAC
1 TTTAATTTATAATATAAAAATAC
* *
665396 TTTAATTTGTAATATCAAAATAC
1 TTTAATTTATAATATAAAAATAC
665419 TTTA
1 TTTA
665423 TCAAATAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAATTTATAATATAAAAATAC
Found at i:669138 original size:114 final size:115
Alignment explanation
Indices: 668965--669180 Score: 319
Period size: 114 Copynumber: 1.9 Consensus size: 115
668955 TGGCCACTGA
*
668965 ATGGCCGACACCCCTTTTTTGTCAGAAAAAAATTTCAAAATTTATTGGTGTTGGCCATGCAATGG
1 ATGGCCGACACCCCCTTTTTG-CAGAAAAAAATTTCAAAATTTATTGGTGTTGGCCATGCAATGG
* *
669030 CCGTCACCCCCTTTTTGAGAAAAAAATTACATTTTTTGATGTTGTCCATTGC
65 CAGACACCCCCTTTTTGAGAAAAAAATTAC-TTTTTTGATGTTGTCCATTGC
* * * *
669082 ATGGCCGACACCCCCTTTTTG-AGAAAAAAA-TTCAAAATTTTTTTGTGTTGGTCATGCAATGGT
1 ATGGCCGACACCCCCTTTTTGCAGAAAAAAATTTCAAAATTTATTGGTGTTGGCCATGCAATGGC
* *
669145 AGACACTCCCTTTTTGAGAAAAAAATTGCTTTTTTG
66 AGACACCCCCTTTTTGAGAAAAAAATTACTTTTTTG
669181 GGAGTCGGCC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
113 7 0.08
114 54 0.60
115 9 0.10
117 20 0.22
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (115 bp):
ATGGCCGACACCCCCTTTTTGCAGAAAAAAATTTCAAAATTTATTGGTGTTGGCCATGCAATGGC
AGACACCCCCTTTTTGAGAAAAAAATTACTTTTTTGATGTTGTCCATTGC
Found at i:669150 original size:58 final size:58
Alignment explanation
Indices: 668951--669171 Score: 247
Period size: 56 Copynumber: 3.8 Consensus size: 58
668941 AAAATTTTGG
* * * *
668951 GTGTTGGCCACTG-AATGGCCGACACCCCTTTTTTGTCAGAAAAAAATTTCAAAATTTATTG
1 GTGTTGGTCA-TGCAATGGCCGACACCCCCTTTTTG--AGAAAAAAA-TTCAAAATTTTTTT
* * *
669012 GTGTTGGCCATGCAATGGCCGTCACCCCCTTTTTGAGAAAAAAATT--ACA-TTTTTT
1 GTGTTGGTCATGCAATGGCCGACACCCCCTTTTTGAGAAAAAAATTCAAAATTTTTTT
669067 GATGTT-GTCCATTGC-ATGGCCGACACCCCCTTTTTGAGAAAAAAATTCAAAATTTTTTT
1 G-TGTTGGT-CA-TGCAATGGCCGACACCCCCTTTTTGAGAAAAAAATTCAAAATTTTTTT
** *
669126 GTGTTGGTCATGCAATGGTAGACACTCCCTTTTTGAGAAAAAAATT
1 GTGTTGGTCATGCAATGGCCGACACCCCCTTTTTGAGAAAAAAATT
669172 GCTTTTTTGG
Statistics
Matches: 140, Mismatches: 11, Indels: 21
0.81 0.06 0.12
Matches are distributed among these distances:
55 6 0.04
56 39 0.28
57 6 0.04
58 39 0.28
59 18 0.13
60 2 0.01
61 30 0.21
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (58 bp):
GTGTTGGTCATGCAATGGCCGACACCCCCTTTTTGAGAAAAAAATTCAAAATTTTTTT
Found at i:669353 original size:60 final size:59
Alignment explanation
Indices: 669286--669454 Score: 197
Period size: 60 Copynumber: 2.9 Consensus size: 59
669276 CATTACATTA
*
669286 CCGACACCCCCTTTTTGAGGAAAAAAATTTTCAAAATTTTTTTTGTTGGCCATGCAATGG
1 CCGACACCCCCTTTTTGAGGAAAAAAATTTTCAAAATTTTTTGTGTTGGCCATGC-ATGG
* * * *
669346 CCGACACCCCCTTTTTGA-GAAAAAACTTGT----ATTTTTGGGTGTTGGCTATTGCATGG
1 CCGACACCCCCTTTTTGAGGAAAAAAATTTTCAAAATTTTT-TGTGTTGGCCA-TGCATGG
* *
669402 CCGACACCCCC-TTTTGAGAAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT
1 CCGACACCCCCTTTTTGAGGAAAAAAATTTTCAAAATTTTTT-GTGTTGGCCAT
669455 TTTGAGAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 17
0.76 0.09 0.14
Matches are distributed among these distances:
55 12 0.13
56 31 0.34
57 3 0.03
59 11 0.12
60 33 0.37
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (59 bp):
CCGACACCCCCTTTTTGAGGAAAAAAATTTTCAAAATTTTTTGTGTTGGCCATGCATGG
Found at i:669413 original size:116 final size:117
Alignment explanation
Indices: 669225--669454 Score: 340
Period size: 116 Copynumber: 2.0 Consensus size: 117
669215 AAAATTTTGC
* *
669225 ATGGCCGACACTCCCTTTTTGAGAAAAAAAATTGCATTTTTGGGTGTTGGTCATTACATTACCGA
1 ATGGCCGACACCCCCTTTTTGAGAAAAAAAATTGCATTTTTGGGTGTTGGTCATTACATGACCGA
* * *
669290 CACCCCCTTTTTGAGGAAAAAAATTTTCAAAATTTTTT-TTGTTGGCCATGCA
66 CACCCCC-TTTTGAGAAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCA
* * * *
669342 ATGGCCGACACCCCCTTTTTGAG-AAAAAACTTGTATTTTTGGGTGTTGG-CTATTGCATGGCCG
1 ATGGCCGACACCCCCTTTTTGAGAAAAAAAATTGCATTTTTGGGTGTTGGTC-ATTACATGACCG
669405 ACACCCCCTTTTGAGAAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT
65 ACACCCCCTTTTGAGAAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT
669455 TTTGAGAAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
115 29 0.28
116 51 0.50
117 22 0.22
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (117 bp):
ATGGCCGACACCCCCTTTTTGAGAAAAAAAATTGCATTTTTGGGTGTTGGTCATTACATGACCGA
CACCCCCTTTTGAGAAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCA
Found at i:669482 original size:41 final size:41
Alignment explanation
Indices: 669413--669491 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 41
669403 CGACACCCCC
*
669413 TTTTGAGAAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCA
1 TTTTGAGAAAAAAAAATATCAAAATTTTTTGGTGTTGGCCA
669454 TTTTGAGAAAAAAAAA-ATCAAAATTTTTTGGTGTTGGC
1 TTTTGAGAAAAAAAAATATCAAAATTTTTTGGTGTTGGC
669492 TATGCAATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 21 0.57
41 16 0.43
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (41 bp):
TTTTGAGAAAAAAAAATATCAAAATTTTTTGGTGTTGGCCA
Found at i:670596 original size:17 final size:17
Alignment explanation
Indices: 670576--670630 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
670566 AAAAAATAAT
670576 AATTAGAATATACAAGA
1 AATTAGAATATACAAGA
670593 AATTAGAA-A-A-AA-A
1 AATTAGAATATACAAGA
* *
670606 AATTAAAATATACAGGA
1 AATTAGAATATACAAGA
670623 AATTAGAA
1 AATTAGAA
670631 ATTAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.26
14 3 0.10
15 2 0.06
16 2 0.06
17 16 0.52
ACGTcount: A:0.64, C:0.04, G:0.11, T:0.22
Consensus pattern (17 bp):
AATTAGAATATACAAGA
Found at i:670616 original size:30 final size:30
Alignment explanation
Indices: 670567--670645 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
670557 TAAATTTTTA
*
670567 AAAAATAATAATTAGAATATACAAGAAATTAG
1 AAAAA-AA-AATTAAAATATACAAGAAATTAG
*
670599 AAAAAAAAATTAAAATATACAGGAAATTAG
1 AAAAAAAAATTAAAATATACAAGAAATTAG
** *
670629 AAATTAAATTTAAAATA
1 AAAAAAAAATTAAAATA
670646 AAAACGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 35 0.83
31 2 0.05
32 5 0.12
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.25
Consensus pattern (30 bp):
AAAAAAAAATTAAAATATACAAGAAATTAG
Found at i:670655 original size:30 final size:30
Alignment explanation
Indices: 670591--670673 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
670581 GAATATACAA
** * * * *
670591 GAAATTAGAAAAAAAAATTAAAATATACAG
1 GAAATTAGAAATTAAATTTAAAATAAAAAC
670621 GAAATTAGAAATTAAATTTAAAATAAAAAC
1 GAAATTAGAAATTAAATTTAAAATAAAAAC
*
670651 GAAATTACAAATTAAATTTAAAA
1 GAAATTAGAAATTAAATTTAAAA
670674 AGTAAACGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (30 bp):
GAAATTAGAAATTAAATTTAAAATAAAAAC
Found at i:671034 original size:161 final size:161
Alignment explanation
Indices: 670763--671090 Score: 640
Period size: 161 Copynumber: 2.0 Consensus size: 161
670753 GCTCGGCGAG
670763 GCCGAG-GCGTAGTACAGTTTGTTCAGGAGGCATTACATTGGTGTTCGTCGGCTCATCCTCGATG
1 GCCGAGCGCGTAGTACAGTTTGTTCAGGAGGCATTACATTGGTGTTCGTCGGCTCATCCTCGATG
670827 GTGTCAACATTGGGTGTCCCGATTGGTGTACATAGAAAGGTGGTAAAATCGTACGTATCATCAAC
66 GTGTCAACATTGGGTGTCCCGATTGGTGTACATAGAAAGGTGGTAAAATCGTACGTATCATCAAC
670892 GTAATCGAGAGTAGGTTGAGTGACCTGAGGT
131 GTAATCGAGAGTAGGTTGAGTGACCTGAGGT
670923 GCCGAGCGCGTAGTACAGTTTGTTCAGGAGGCATTACATTGGTGTTCGTCGGCTCATCCTCGATG
1 GCCGAGCGCGTAGTACAGTTTGTTCAGGAGGCATTACATTGGTGTTCGTCGGCTCATCCTCGATG
670988 GTGTCAACATTGGGTGTCCCGATTGGTGTACATAGAAAGGTGGTAAAATCGTACGTATCATCAAC
66 GTGTCAACATTGGGTGTCCCGATTGGTGTACATAGAAAGGTGGTAAAATCGTACGTATCATCAAC
*
671053 GTAATCTAGAGTAGGTTGAGTGACCTGAGGT
131 GTAATCGAGAGTAGGTTGAGTGACCTGAGGT
671084 GCCGAGC
1 GCCGAGC
671091 CAAAAATATC
Statistics
Matches: 166, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
160 6 0.04
161 160 0.96
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (161 bp):
GCCGAGCGCGTAGTACAGTTTGTTCAGGAGGCATTACATTGGTGTTCGTCGGCTCATCCTCGATG
GTGTCAACATTGGGTGTCCCGATTGGTGTACATAGAAAGGTGGTAAAATCGTACGTATCATCAAC
GTAATCGAGAGTAGGTTGAGTGACCTGAGGT
Found at i:671837 original size:86 final size:86
Alignment explanation
Indices: 671692--672118 Score: 640
Period size: 86 Copynumber: 5.0 Consensus size: 86
671682 GAAGGTTCAG
* * *
671692 AATAAATAATGTATTGTCAAATTAACACAATATTTGATATAAATTGTAATATAATAATAATAATT
1 AATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATT
671757 TTTATTTAAATATTTAAAATT
66 TTTATTTAAATATTTAAAATT
671778 AATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATT
1 AATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATT
671843 TTTATTTAAATATTTAAAATT
66 TTTATTTAAATATTTAAAATT
671864 AATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATT
1 AATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATT
671929 TTTATTTAAATATTTAAAATT
66 TTTATTTAAATATTTAAAATT
*
671950 AATAAATAATGTATTGTCAAATCAACATATTATTTGAT--AAA----AATAT-ATAATAATAATT
1 AATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATT
* *
672008 TGTATTTTAAATA-TGAAAATTT
66 TTTA-TTTAAATATTTAAAA-TT
* * * * * *
672030 GATAAATAATGTATTGTCAAATTAACACAATACTTGATATAAATTGTAATATAATAATAAT-TTT
1 AATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATT
672094 TTTATTTAAATAATGTT-AAATT
66 TTTATTTAAAT-AT-TTAAAATT
672116 AAT
1 AAT
672119 TTTAAATGTA
Statistics
Matches: 314, Mismatches: 15, Indels: 24
0.89 0.04 0.07
Matches are distributed among these distances:
79 20 0.06
80 48 0.15
82 3 0.01
84 3 0.01
85 7 0.02
86 221 0.70
87 11 0.04
88 1 0.00
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (86 bp):
AATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATT
TTTATTTAAATATTTAAAATT
Found at i:672241 original size:11 final size:12
Alignment explanation
Indices: 672219--672267 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
672209 AAACATGTTC
672219 ATTAATTTTCAA
1 ATTAATTTTCAA
*
672231 ATTAATTTCAACTTAA
1 ATTAATTT----TCAA
672247 ATTAATTTTCAA
1 ATTAATTTTCAA
672259 ATTAATTTT
1 ATTAATTTT
672268 TACACAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 20 0.65
16 11 0.35
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTAATTTTCAA
Found at i:672265 original size:16 final size:16
Alignment explanation
Indices: 672229--672263 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
672219 ATTAATTTTC
*
672229 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
672245 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
672262 AA
1 AA
672264 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:672276 original size:28 final size:28
Alignment explanation
Indices: 672219--672276 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
672209 AAACATGTTC
**
672219 ATTAATTTTCAAATTAATTTCAACTTAA
1 ATTAATTTTCAAATTAATTTCAACACAA
**
672247 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTTCAAATTAATTTCAACACAA
672275 AT
1 AT
672277 ATTCTTCGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAATTTTCAAATTAATTTCAACACAA
Found at i:676147 original size:62 final size:59
Alignment explanation
Indices: 676057--676174 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 59
676047 AAATAAAAAG
*
676057 GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGA-AAATTTTTTATCCGAGAACAA
1 GGGGTGTCGGCCATTGCATGACCAACACC-AAAAAA--T-ACAAATTTTTTATCCGAGAACAA
* *
676119 GGGGTGTCGGTCA-TGCAATGACCGACACCAAAAAATACAAATTTTTTATCCGAGAA
1 GGGGTGTCGGCCATTGC-ATGACCAACACCAAAAAATACAAATTTTTTATCCGAGAA
676175 AAGAATGTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
58 1 0.02
59 19 0.37
61 9 0.18
62 22 0.43
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (59 bp):
GGGGTGTCGGCCATTGCATGACCAACACCAAAAAATACAAATTTTTTATCCGAGAACAA
Found at i:676277 original size:87 final size:86
Alignment explanation
Indices: 676186--676346 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 86
676176 AGAATGTAAT
* * *
676186 TTTTTTTTCTCAAAAAGGGGGTGTTGACCATTACATGGCCAACACAAAAAAATTTTGAAAATTTT
1 TTTTTTTTCTCAAAAAGGGGGTGTCGACAATTACATGACCAACACAAAAAAATTTTG-AAATTTT
676251 TTTTCTCAAACCCAAAAATGCA
65 TTTTCTCAAACCCAAAAATGCA
* ** * * *
676273 TTTTTTTTCTCAAAAATGGGGTGTCGGTAATTGCATGACCAATACCAAAAAATTTTGAAATTTTT
1 TTTTTTTTCTCAAAAAGGGGGTGTCGACAATTACATGACCAACACAAAAAAATTTTGAAATTTTT
676338 TTTCTCAAA
66 TTTCTCAAA
676347 AAGGCATGGC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 17 0.26
87 48 0.74
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (86 bp):
TTTTTTTTCTCAAAAAGGGGGTGTCGACAATTACATGACCAACACAAAAAAATTTTGAAATTTTT
TTTCTCAAACCCAAAAATGCA
Found at i:678134 original size:9 final size:9
Alignment explanation
Indices: 678122--678159 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
678112 TAATTTTTTT
678122 AAATTATAA
1 AAATTATAA
678131 AAATTAT-A
1 AAATTATAA
678139 AAATTATTAA
1 AAATTA-TAA
678149 AAA-TATAA
1 AAATTATAA
678157 AAA
1 AAA
678160 AATTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 13 0.48
9 10 0.37
10 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:678144 original size:17 final size:17
Alignment explanation
Indices: 678122--678158 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
678112 TAATTTTTTT
678122 AAATTA-TAAAAATTATA
1 AAATTATTAAAAA-TATA
678139 AAATTATTAAAAATATA
1 AAATTATTAAAAATATA
678156 AAA
1 AAA
678159 AAATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTATTAAAAATATA
Found at i:679228 original size:13 final size:13
Alignment explanation
Indices: 679210--679272 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
679200 AATTCAGTAT
679210 TACTTTTGAAAAA
1 TACTTTTGAAAAA
679223 TACTTTT-AAAAA
1 TACTTTTGAAAAA
* **
679235 GT-GTGGTGAAAAA
1 -TACTTTTGAAAAA
*
679248 TA-TTTTTAAGAAA
1 TACTTTTGAA-AAA
679261 TACTTTTGAAAA
1 TACTTTTGAAAA
679273 TTTTAGTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
12 12 0.32
13 20 0.53
14 6 0.16
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (13 bp):
TACTTTTGAAAAA
Found at i:679497 original size:24 final size:25
Alignment explanation
Indices: 679465--679523 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
679455 TTAATATATG
*
679465 AAAT-ATTAATTA-TAAATATTTCT
1 AAATAATTAATTATTAAATATTTAT
*
679488 AAATAATTAA-TATTAATTATTTAT
1 AAATAATTAATTATTAAATATTTAT
*
679512 AAA-ATTTAATTA
1 AAATAATTAATTA
679524 GAATATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATAATTAATTATTAAATATTTAT
Done.