Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 122 of 198
Found at i:39266102 original size:147 final size:148
Alignment explanation
Indices: 39265823--39266137 Score: 368
Period size: 147 Copynumber: 2.1 Consensus size: 148
39265813 CAGTCCTATC
* *
39265823 TCCCTGAAGTTGCAGTGTAGAGGGTCAAAATGATGGATCTTATCTCTCTGAAGTTGCAGTAAAAC
1 TCCCTGAAGTTGCAGTGGAGAGGGTCAAAATGATGGATCTTATCTCTCTGAAGTTGCAATAAAAC
* * * * * *
39265888 TGATCACATCAAACTTTATTAAAAATTACAAGTCTTATCCCCTGAAGTTGCAGTGGGGCAAGTTG
66 AGATCACATCAAACTTTATTAAAAACTACAAGTCTTATCCCCTAAAGTTACAGTGGAGCAAGCTG
* **
39265953 AAGATA-CGAGTCTTATT
131 AAGATAGCAAACCTTATT
* * * * *
39265970 TCCTTGAAGTTGCAGTGGA-ATGGGTCAAAATGATGGATCTTATCTTTTTGAAGTTGTAATAGAA
1 TCCCTGAAGTTGCAGTGGAGA-GGGTCAAAATGATGGATCTTATCTCTCTGAAGTTGCAATAAAA
* * * * *
39266034 CAGGTCGCATCAGACTTTATT-GAAGCTACAAGTCTTATCTCCCTAAAGTTACAGTGGAGC-AGA
65 CAGATCACATCAAACTTTATTAAAAACTACAAGTCTTATC-CCCTAAAGTTACAGTGGAGCAAG-
39266097 CTGAAGATAGCAAACCTTATT
128 CTGAAGATAGCAAACCTTATT
**
39266118 TCCCTGAAGTTATAGTGGAG
1 TCCCTGAAGTTGCAGTGGAG
39266138 CAAATTGAAG
Statistics
Matches: 139, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
146 18 0.13
147 97 0.70
148 24 0.17
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (148 bp):
TCCCTGAAGTTGCAGTGGAGAGGGTCAAAATGATGGATCTTATCTCTCTGAAGTTGCAATAAAAC
AGATCACATCAAACTTTATTAAAAACTACAAGTCTTATCCCCTAAAGTTACAGTGGAGCAAGCTG
AAGATAGCAAACCTTATT
Found at i:39268024 original size:13 final size:13
Alignment explanation
Indices: 39268006--39268045 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
39267996 TGTGTATATA
39268006 ATTATTTTATTAT
1 ATTATTTTATTAT
39268019 ATTATTTTATTACGT
1 ATTATTTTATTA--T
39268034 ATTA-TTTATTAT
1 ATTATTTTATTAT
39268046 GTCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 12 0.48
14 7 0.28
15 5 0.20
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (13 bp):
ATTATTTTATTAT
Found at i:39268198 original size:3 final size:3
Alignment explanation
Indices: 39268190--39268235 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
39268180 GATTATTTGC
39268190 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
39268236 TACTTATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39268335 original size:24 final size:21
Alignment explanation
Indices: 39268288--39268349 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
39268278 ATACACATGC
*
39268288 ATATTTTTATAATATATGTAT
1 ATATTTTTATAATATATATAT
39268309 ATTATTTTTATAATATATATACGT
1 A-TATTTTTATAATATATATA--T
*
39268333 AT-TTTTTATATTATATA
1 ATATTTTTATAATATATA
39268350 ATTTATACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 32 0.89
23 1 0.03
24 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (21 bp):
ATATTTTTATAATATATATAT
Found at i:39268462 original size:19 final size:20
Alignment explanation
Indices: 39268411--39268532 Score: 77
Period size: 22 Copynumber: 6.0 Consensus size: 20
39268401 ATATACATGT
*
39268411 TTATATTTTTTAT-TATATC
1 TTATATTTTATATATATATC
* * *
39268430 TTGTAATATATATATATA-C
1 TTATATTTTATATATATATC
*
39268449 TTATATTTTATATATATATT
1 TTATATTTTATATATATATC
* * *
39268469 TCTATAATTTAAATACATATCC
1 T-TATATTTTATATATATAT-C
* * *
39268491 ATATATATATATATATATATA
1 TTATAT-TTTATATATATATC
*
39268512 TATATATATATATATATATAT
1 T-TATAT-TTTATATATATAT
39268533 ATATCTATAT
Statistics
Matches: 78, Mismatches: 19, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
19 25 0.32
20 5 0.06
21 19 0.24
22 29 0.37
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (20 bp):
TTATATTTTATATATATATC
Found at i:39268657 original size:2 final size:2
Alignment explanation
Indices: 39268435--39268639 Score: 116
Period size: 2 Copynumber: 104.0 Consensus size: 2
39268425 ATATCTTGTA
* * *
39268435 AT AT AT AT AT AT ACT -T AT AT -T TT AT AT AT AT AT TT CT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * **
39268475 AT TT AA AT AC AT AT CC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
39268517 AT AT AT AT AT AT AT AT AT AT CT AT AT CCT -T AT AT TT AT AC AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
* * * * * * * * *
39268559 AC AT AT AA AT AT AC AT AC AT GCT TT TT AT CT -T AC A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
** *
39268600 GG AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39268640 CTTTTACTTA
Statistics
Matches: 154, Mismatches: 40, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
1 6 0.04
2 145 0.94
3 3 0.02
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39274417 original size:2 final size:2
Alignment explanation
Indices: 39274410--39274470 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
39274400 AAGAAAGGTG
*
39274410 TA TA TA TA TA CA 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
39274452 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
39274471 CAATACACCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39274599 original size:12 final size:12
Alignment explanation
Indices: 39274578--39274609 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39274568 TTATATAATC
*
39274578 TTATTCATTTCT
1 TTATTTATTTCT
39274590 TTATTTATTTCT
1 TTATTTATTTCT
39274602 TTATTTAT
1 TTATTTAT
39274610 ATTTTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTATTTCT
Found at i:39277246 original size:12 final size:12
Alignment explanation
Indices: 39277216--39277248 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39277206 ATGCAACAGG
39277216 AAACCAGCA-GC
1 AAACCAGCATGC
39277227 AAACCAGCATGC
1 AAACCAGCATGC
*
39277239 AGACCAGCAT
1 AAACCAGCAT
39277249 CCAAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:39278306 original size:21 final size:21
Alignment explanation
Indices: 39278282--39278334 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
39278272 CATTGTTTCT
*
39278282 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
39278303 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
39278324 AATCTCACCGC
1 AATCTCACCGC
39278335 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:39279524 original size:27 final size:24
Alignment explanation
Indices: 39279486--39279553 Score: 102
Period size: 23 Copynumber: 2.8 Consensus size: 24
39279476 AAAAATAAAA
39279486 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATA-TATAA--TTTTTT
39279513 ATTTACCAAAATATAT-ATTTTTT
1 ATTTACCAAAATATATAATTTTTT
39279536 ATTTACCAAAATATATAA
1 ATTTACCAAAATATATAA
39279554 AAAAATCAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
23 22 0.55
24 1 0.03
25 1 0.03
26 3 0.08
27 13 0.32
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTACCAAAATATATAATTTTTT
Found at i:39279681 original size:27 final size:27
Alignment explanation
Indices: 39279597--39279688 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
39279587 CGCCAATGGG
*
39279597 ATTGGCGGCACCAAAT-GTGCCAAAACC
1 ATTGGCGGCACC-AATGGTGCCAATACC
* *
39279624 ATTGGCGGCTCCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
39279651 ATTGGCGGCACCAATGGTGCC-ATACTA
1 ATTGGCGGCACCAATGGTGCCAATAC-C
39279678 ATTGGCGGCAC
1 ATTGGCGGCAC
39279689 TACTCGTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.11
27 51 0.89
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:39279787 original size:11 final size:11
Alignment explanation
Indices: 39279771--39279810 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
39279761 GTTGCTGCGG
39279771 AAAAGAAGAGA
1 AAAAGAAGAGA
39279782 AAAAG-AGAGA
1 AAAAGAAGAGA
* *
39279792 AAAAGAGGAAA
1 AAAAGAAGAGA
39279803 AAAAGAAG
1 AAAAGAAG
39279811 GTATTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:39279805 original size:10 final size:10
Alignment explanation
Indices: 39279771--39279804 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
39279761 GTTGCTGCGG
39279771 AAAAGAAGAGA
1 AAAAG-AGAGA
39279782 AAAAGAGAGA
1 AAAAGAGAGA
39279792 AAAAGAG-GA
1 AAAAGAGAGA
39279801 AAAA
1 AAAA
39279805 AAGAAGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.26
10 12 0.52
11 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAAGAGAGA
Found at i:39279934 original size:3 final size:3
Alignment explanation
Indices: 39279918--39279955 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
39279908 AAAATAATAG
*
39279918 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
39279956 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:39279960 original size:3 final size:3
Alignment explanation
Indices: 39279954--39279997 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
39279944 ATTATTATTA
39279954 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
39279998 AGTATTAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:39280212 original size:26 final size:26
Alignment explanation
Indices: 39280183--39280235 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
39280173 TTTTAGTGTG
*
39280183 TATTATTTTGAGTATAAAATTATTAA
1 TATTATTTTGAGTATAAAATTAATAA
39280209 TATTATTTTGAGTATAAAATTAATAA
1 TATTATTTTGAGTATAAAATTAATAA
39280235 T
1 T
39280236 TTTAGTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TATTATTTTGAGTATAAAATTAATAA
Found at i:39280258 original size:12 final size:12
Alignment explanation
Indices: 39280241--39280271 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39280231 ATAATTTTAG
39280241 TGTGTATTATTT
1 TGTGTATTATTT
39280253 TGTGTATTATTT
1 TGTGTATTATTT
*
39280265 TGAGTAT
1 TGTGTAT
39280272 AAAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:39280279 original size:26 final size:25
Alignment explanation
Indices: 39280181--39280280 Score: 73
Period size: 26 Copynumber: 4.0 Consensus size: 25
39280171 AATTTTAGTG
39280181 TGTATTATTTTGAGTATAAAATTATT
1 TGTATTATTTTGAGTATAAAATT-TT
**
39280207 AATATTATTTTGAGTATAAAA---T
1 TGTATTATTTTGAGTATAAAATTTT
* * * * **
39280229 T-AATAATTTTAGTGTGTATTATTTT
1 TGTATTATTTT-GAGTATAAAATTTT
39280254 GTGTATTATTTTGAGTATAAAATTTT
1 -TGTATTATTTTGAGTATAAAATTTT
39280280 T
1 T
39280281 TTTAAGTAAT
Statistics
Matches: 53, Mismatches: 15, Indels: 13
0.65 0.19 0.16
Matches are distributed among these distances:
21 7 0.13
22 7 0.13
25 2 0.04
26 30 0.57
27 7 0.13
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (25 bp):
TGTATTATTTTGAGTATAAAATTTT
Found at i:39280864 original size:18 final size:18
Alignment explanation
Indices: 39280821--39280865 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
39280811 TTGACATGGT
*
39280821 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
**
39280839 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
39280857 TGGTGGCGA
1 TGGTGGCGA
39280866 TCATTGGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.49, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:39283117 original size:27 final size:26
Alignment explanation
Indices: 39283058--39283119 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
39283048 AAATTACCTT
*
39283058 TTTTCTTTTTTCTTCCTTCCTTCTTC
1 TTTTCTTTTTTCTTCCTTCCTTCTCC
39283084 TTCTTCTTTTTT-TTCTCTTCTCATT-TCC
1 TT-TTCTTTTTTCTTC-CTTC-C-TTCTCC
39283112 TTTTCTTT
1 TTTTCTTT
39283120 CCTTCTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 5 0.16
27 19 0.61
28 5 0.16
29 2 0.06
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTCTTTTTTCTTCCTTCCTTCTCC
Found at i:39283120 original size:22 final size:21
Alignment explanation
Indices: 39283089--39283164 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 21
39283079 TCTTCTTCTT
*
39283089 CTTTTTTTTCTCTTCTCATTTC
1 CTTTTCTTTCTCTTCTC-TTTC
39283111 CTTTTCTTTC-C-T-TCTTT-
1 CTTTTCTTTCTCTTCTCTTTC
*
39283128 C-TTTCTTTTTCTTCTCTTTTC
1 CTTTTCTTTCTCTTCTC-TTTC
39283149 CTTTTC-TTCTTCTTCT
1 CTTTTCTTTC-TCTTCT
39283165 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
16 7 0.16
17 2 0.05
18 4 0.09
19 4 0.09
20 4 0.09
21 4 0.09
22 19 0.43
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (21 bp):
CTTTTCTTTCTCTTCTCTTTC
Found at i:39283125 original size:38 final size:35
Alignment explanation
Indices: 39283078--39283164 Score: 120
Period size: 38 Copynumber: 2.4 Consensus size: 35
39283068 TCTTCCTTCC
*
39283078 TTCTTCTTCTTCTTTTTTTTCTCTTCTCATTTCCTT
1 TTCTTCTTCTTCTTTCTTTT-TCTTCTCATTTCCTT
*
39283114 TTCTTTCCTTCTTTCTTTCTTTTTCTTCTCTTTTCCTT
1 TTC-TT-CTTC-TTCTTTCTTTTTCTTCTCATTTCCTT
39283152 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
39283165 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
35 4 0.09
36 7 0.15
37 4 0.09
38 21 0.46
39 10 0.22
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (35 bp):
TTCTTCTTCTTCTTTCTTTTTCTTCTCATTTCCTT
Found at i:39283141 original size:17 final size:16
Alignment explanation
Indices: 39283055--39283159 Score: 54
Period size: 17 Copynumber: 6.2 Consensus size: 16
39283045 ATAAAATTAC
39283055 CTTTTTTCTTTTTTCTT
1 CTTTTTTC-TTTTTCTT
** *
39283072 CCTTCCTTCTTCTTCTT
1 -CTTTTTTCTTTTTCTT
39283089 CTTTTTT-TTCTCTTC-T
1 CTTTTTTCTT-T-TTCTT
*
39283105 CATTTCCTTT-TCTTTCCTT
1 C-TTT--TTTCT-TTTTCTT
39283124 CTTTCTTTCTTTTTCTT
1 CTTT-TTTCTTTTTCTT
* *
39283141 CTCTTTTCCTTTTCTT
1 CTTTTTTCTTTTTCTT
39283157 CTT
1 CTT
39283160 CTTCTNNNNN
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
15 2 0.03
16 20 0.29
17 26 0.38
18 12 0.18
19 7 0.10
20 1 0.01
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (16 bp):
CTTTTTTCTTTTTCTT
Found at i:39283162 original size:17 final size:17
Alignment explanation
Indices: 39283057--39283162 Score: 71
Period size: 16 Copynumber: 6.1 Consensus size: 17
39283047 AAAATTACCT
*
39283057 TTTTTCTTTT-TTCTTC
1 TTTTCCTTTTCTTCTTC
*
39283073 -CTTCCTTCTTCTTCTTC
1 TTTTCCTT-TTCTTCTTC
39283090 TTTT--TTTTC-TCTTC
1 TTTTCCTTTTCTTCTTC
39283104 TCATTTCCTTTTCTTTCCTTC
1 T--TTTCCTTTTC-TT-CTTC
*
39283125 TTTCTTTCTTTTTCTTC-TC
1 --T-TTTCCTTTTCTTCTTC
39283144 TTTTCCTTTTCTTCTTC
1 TTTTCCTTTTCTTCTTC
39283161 TT
1 TT
39283163 CTNNNNNNNN
Statistics
Matches: 71, Mismatches: 6, Indels: 25
0.70 0.06 0.25
Matches are distributed among these distances:
14 6 0.08
15 8 0.11
16 19 0.27
17 11 0.15
18 7 0.10
19 2 0.03
20 2 0.03
21 6 0.08
22 9 0.13
23 1 0.01
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCCTTTTCTTCTTC
Found at i:39283452 original size:25 final size:25
Alignment explanation
Indices: 39283421--39283488 Score: 102
Period size: 25 Copynumber: 2.6 Consensus size: 25
39283411 GGTTTTTTTG
39283421 ATATATTTTGGTAAATAAAAAATA-T
1 ATATATTTTGGTAAATAAAAAA-AGT
39283446 ATATATTTTGGTAAATAAAAAAAGTT
1 ATATATTTTGGTAAATAAAAAAAG-T
39283472 ATAATATTTTGGTAAAT
1 AT-ATATTTTGGTAAAT
39283489 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 1 0.03
25 22 0.55
26 3 0.08
27 14 0.35
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (25 bp):
ATATATTTTGGTAAATAAAAAAAGT
Found at i:39284503 original size:2 final size:2
Alignment explanation
Indices: 39284496--39284535 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39284486 TATGCATGTT
39284496 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
39284536 AAGATTATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39284764 original size:32 final size:34
Alignment explanation
Indices: 39284728--39284804 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
39284718 ACTCTAATTC
39284728 TATTTTTAA-G-ATTAT-TAAGATAGTAATATATT
1 TATTTTTAATGTATT-TGTAAGATAGTAATATATT
39284760 TA--TTTAATGTATTTGTAAGATAGTAATATATT
1 TATTTTTAATGTATTTGTAAGATAGTAATATATT
39284792 TA--TTTAATGTATT
1 TATTTTTAATGTATT
39284805 ACAAATAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
30 5 0.12
31 2 0.05
32 35 0.83
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (34 bp):
TATTTTTAATGTATTTGTAAGATAGTAATATATT
Found at i:39292610 original size:2 final size:2
Alignment explanation
Indices: 39292603--39292632 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39292593 GCCTCAAAGG
*
39292603 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39292633 CAATAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39292761 original size:53 final size:55
Alignment explanation
Indices: 39292647--39292792 Score: 199
Period size: 53 Copynumber: 2.7 Consensus size: 55
39292637 AATAGTTACG
* * *
39292647 TAGGAATCAAATTGTTAAAATATAATTTCCCATAATAATATCCTATAATATCCCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAAT-ATATCCTATAATATCCCAT
* * *
39292703 TAGGAATCAAATTGCTAAGAA-ATAATATCCCATAATAT-T-TTGTAATATCTCAT
1 TAGGAATCAAATTGCTAA-AAGATAATATCCCATAATATATCCTATAATATCCCAT
39292756 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATA
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATA
39292793 ATATATTAAC
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
52 2 0.02
53 45 0.54
54 1 0.01
55 2 0.02
56 31 0.37
57 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (55 bp):
TAGGAATCAAATTGCTAAAAGATAATATCCCATAATATATCCTATAATATCCCAT
Found at i:39294631 original size:23 final size:23
Alignment explanation
Indices: 39294578--39294633 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
39294568 AAAAATTTCA
* * **
39294578 CCACAAATGTATCACAGAATATT
1 CCACAAAGGCATCACAGAATACG
* *
39294601 CCATAAAGGCATCATAGAATACG
1 CCACAAAGGCATCACAGAATACG
39294624 CCACAAAGGC
1 CCACAAAGGC
39294634 TTTGTAGAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (23 bp):
CCACAAAGGCATCACAGAATACG
Found at i:39305615 original size:25 final size:25
Alignment explanation
Indices: 39305587--39305635 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
39305577 TACAGTCTAT
* *
39305587 CTATAGTAGTCTCAGTATATACTAC
1 CTATAATAGTCTCAGGATATACTAC
* *
39305612 CTATAATAGTTTTAGGATATACTA
1 CTATAATAGTCTCAGGATATACTA
39305636 TCAAAAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (25 bp):
CTATAATAGTCTCAGGATATACTAC
Found at i:39315235 original size:35 final size:35
Alignment explanation
Indices: 39315189--39315315 Score: 175
Period size: 35 Copynumber: 3.6 Consensus size: 35
39315179 ACTCTCTGTT
* *
39315189 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
* * *
39315224 TTGGTGTGTTTCGAAAGGATTAGCTCTTATAAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
39315259 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
*
39315294 TCTGGTGTGGTTT-GGTTGGATT
1 T-TGGTGT-GTTTCGGATGGATT
39315316 GTCGATGTAC
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 63 0.78
36 14 0.17
37 4 0.05
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.41
Consensus pattern (35 bp):
TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
Found at i:39317137 original size:21 final size:22
Alignment explanation
Indices: 39317107--39317148 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
39317097 CACTTCACAA
*
39317107 TCATAAGTCATACATCATCATC
1 TCATAAGTCAAACATCATCATC
*
39317129 TCAT-AGTCAAATATCATCAT
1 TCATAAGTCAAACATCATCAT
39317149 AAAGTCCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (22 bp):
TCATAAGTCAAACATCATCATC
Found at i:39319274 original size:42 final size:40
Alignment explanation
Indices: 39319222--39319340 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 40
39319212 GTGTTATCAA
*
39319222 ATAT-CGATGCCACTGTCCTAGACAGGGTCTTACACGAAATC
1 ATATACGATGCCA-TGTCC-AGACATGGTCTTACACGAAATC
* *
39319263 ATATACGATGCCGATGTCCCAGACATGATCTTACACGTAATC
1 ATATACGATGCC-ATGT-CCAGACATGGTCTTACACGAAATC
39319305 -TATAATCGATGCCAATGTCCAGACATGGTCTTACAC
1 ATAT-A-CGATGCC-ATGTCCAGACATGGTCTTACAC
39319341 TATATCACAT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
41 7 0.10
42 47 0.69
43 14 0.21
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (40 bp):
ATATACGATGCCATGTCCAGACATGGTCTTACACGAAATC
Found at i:39323029 original size:50 final size:50
Alignment explanation
Indices: 39322914--39323015 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
39322904 ACATAGAATC
*
39322914 ATAAGAGAAGCACAACTAGTGATATTTCAACATCTGAAGCTACACAAAAT
1 ATAAGAAAAGCACAACTAGTGATATTTCAACATCTGAAGCTACACAAAAT
*
39322964 ATAAGAGAAGCACAACTAGTGATATTTCAACATCTGAAGCTACACAAAAT
1 ATAAGAAAAGCACAACTAGTGATATTTCAACATCTGAAGCTACACAAAAT
39323014 AT
1 AT
39323016 CAAAAAATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.23
Consensus pattern (50 bp):
ATAAGAAAAGCACAACTAGTGATATTTCAACATCTGAAGCTACACAAAAT
Found at i:39329276 original size:40 final size:40
Alignment explanation
Indices: 39329216--39329418 Score: 284
Period size: 40 Copynumber: 5.1 Consensus size: 40
39329206 AGATCAATTG
* *
39329216 AACACACCAGAC--AAGCTCATAAGAGCTAATCCAACCGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
* *
39329254 AACACACCAAACAGAAGCTCATAAGAGTTGATCCAATCGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
* *
39329294 AACACGCCAAACAGAAGCTCATAAGAGCTGATCCAACTGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
* *
39329334 AACACACCAGACAGAAGCTCATAAGAGTTGATCCAACCGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
* * * *
39329374 AACACGCCAAATAGAACCTCATAAGAGCTGATCCAACTGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
39329414 AACAC
1 AACAC
39329419 GCTAAATAGA
Statistics
Matches: 145, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
38 11 0.08
40 134 0.92
ACGTcount: A:0.44, C:0.28, G:0.15, T:0.13
Consensus pattern (40 bp):
AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
Found at i:39329361 original size:80 final size:80
Alignment explanation
Indices: 39329228--39329418 Score: 328
Period size: 80 Copynumber: 2.4 Consensus size: 80
39329218 CACACCAGAC
* * *
39329228 AAGCTCATAAGAGCTAATCCAACCGAAACACACCAAACAGAAGCTCATAAGAGTTGATCCAATCG
1 AAGCTCATAAGAGCTGATCCAACTGAAACACACCAAACAGAAGCTCATAAGAGTTGATCCAACCG
39329293 AAACACGCCAAACAG
66 AAACACGCCAAACAG
*
39329308 AAGCTCATAAGAGCTGATCCAACTGAAACACACCAGACAGAAGCTCATAAGAGTTGATCCAACCG
1 AAGCTCATAAGAGCTGATCCAACTGAAACACACCAAACAGAAGCTCATAAGAGTTGATCCAACCG
*
39329373 AAACACGCCAAATAG
66 AAACACGCCAAACAG
*
39329388 AACCTCATAAGAGCTGATCCAACTGAAACAC
1 AAGCTCATAAGAGCTGATCCAACTGAAACAC
39329419 GCTAAATAGA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 105 1.00
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (80 bp):
AAGCTCATAAGAGCTGATCCAACTGAAACACACCAAACAGAAGCTCATAAGAGTTGATCCAACCG
AAACACGCCAAACAG
Found at i:39345310 original size:6 final size:6
Alignment explanation
Indices: 39345301--39345327 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39345291 TAATTAGTTG
39345301 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
39345328 GAAAATAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:39346767 original size:9 final size:9
Alignment explanation
Indices: 39346753--39346783 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39346743 GTTAAACGAA
39346753 TCGAGTTAT
1 TCGAGTTAT
*
39346762 TCGAGTTAA
1 TCGAGTTAT
39346771 TCGAGTTAT
1 TCGAGTTAT
39346780 TCGA
1 TCGA
39346784 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:39346865 original size:9 final size:9
Alignment explanation
Indices: 39346838--39346874 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
39346828 TGAGTTTTCG
39346838 AATTCGAAT
1 AATTCGAAT
* *
39346847 AACTCAAAT
1 AATTCGAAT
39346856 AATTCGAAT
1 AATTCGAAT
39346865 AATTCGAAT
1 AATTCGAAT
39346874 A
1 A
39346875 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:39349715 original size:6 final size:6
Alignment explanation
Indices: 39349704--39349839 Score: 263
Period size: 6 Copynumber: 22.7 Consensus size: 6
39349694 TAATAGTTAA
*
39349704 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTCTAT
1 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT
39349752 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT
1 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT
39349800 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGT
1 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGT
39349840 CAAGATGAGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 128 1.00
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.50
Consensus pattern (6 bp):
GTGTAT
Found at i:39357835 original size:33 final size:32
Alignment explanation
Indices: 39357793--39357893 Score: 105
Period size: 33 Copynumber: 3.4 Consensus size: 32
39357783 ACAATATCCT
39357793 ATAATATCCCATTAGGAATCAAATTGCTAAGAA
1 ATAATATCCCATTAGGAATCAAATTGCTAA-AA
39357826 ATAATATCCCA-T---AAT-AATATT-CT----
1 ATAATATCCCATTAGGAATCAA-ATTGCTAAAA
39357849 ATAATATCCCATTAGGAATCAAATTGCTAAAA
1 ATAATATCCCATTAGGAATCAAATTGCTAAAA
39357881 GATAATATCCCAT
1 -ATAATATCCCAT
39357894 AATAATATCC
Statistics
Matches: 56, Mismatches: 0, Indels: 24
0.70 0.00 0.30
Matches are distributed among these distances:
23 11 0.20
24 1 0.02
27 6 0.11
28 8 0.14
29 6 0.11
32 1 0.02
33 23 0.41
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.31
Consensus pattern (32 bp):
ATAATATCCCATTAGGAATCAAATTGCTAAAA
Found at i:39357835 original size:56 final size:56
Alignment explanation
Indices: 39357749--39357904 Score: 269
Period size: 56 Copynumber: 2.8 Consensus size: 56
39357739 AGTAGTTATG
* *
39357749 TAGGAATCAAATTGCTAAAAGATAATATCCCATGACAATATCCTATAATATCCCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAATATCCCAT
*
39357805 TAGGAATCAAATTGCTAAGAA-ATAATATCCCATAATAATATTCTATAATATCCCAT
1 TAGGAATCAAATTGCTAA-AAGATAATATCCCATAATAATATCCTATAATATCCCAT
39357861 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCT
39357905 TACAAAAGAA
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
55 2 0.02
56 90 0.96
57 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.30
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAATATCCCAT
Found at i:39359614 original size:2 final size:2
Alignment explanation
Indices: 39359602--39359638 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
39359592 TAAATCAAGG
39359602 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39359639 GGTAGTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39362294 original size:43 final size:43
Alignment explanation
Indices: 39362228--39362356 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 43
39362218 ATAGGATTTC
* *
39362228 CGATATGTG-TTATCGTGAAAGACCACGTTTGGGACGTTGGCAT
1 CGATATGTGTTTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * ***
39362271 CGGTTTGTGTTTACGTGTAAGACC-CTGTCTGGGATAATGGCAT
1 CGATATGTGTTTACGTGTAAGACCAC-GTCTGGGACGTTGGCAT
* *
39362314 CGATATATGTTTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
39362357 TGTACGAGCT
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
42 1 0.01
43 64 0.93
44 4 0.06
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (43 bp):
CGATATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:39379409 original size:63 final size:64
Alignment explanation
Indices: 39379303--39379423 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 64
39379293 CCTTGGCCCA
* * *
39379303 TGTGACCTTAAATCCAAAACAGTGAGTTACACGACCTAAACACACGCCTGTGT-CCTTAGCCTG
1 TGTGACCTTAAATCCAAAACAATAAGTTACACGACCTAAACACACGCCCGTGTGCCTTAGCCTG
* * ** *
39379366 TGTGATCC-TAAATCCAAAACAATAAGTTACACGGCTTGGACACATGCCCGTGTGCCTT
1 TGTGA-CCTTAAATCCAAAACAATAAGTTACACGACCTAAACACACGCCCGTGTGCCTT
39379424 TAATTTGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 42 0.88
64 6 0.12
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (64 bp):
TGTGACCTTAAATCCAAAACAATAAGTTACACGACCTAAACACACGCCCGTGTGCCTTAGCCTG
Found at i:39388897 original size:29 final size:27
Alignment explanation
Indices: 39388836--39389114 Score: 218
Period size: 28 Copynumber: 9.8 Consensus size: 27
39388826 AATTCTGGGT
* *
39388836 TAAAACTATAAAATTTATAAAATAGGGG
1 TAAAACTATAAAATCTAAAAAATA-GGG
*
39388864 AAAAACTATAAAATCTAAAAAAATATGGG
1 TAAAACTATAAAATCT-AAAAAATA-GGG
* * *
39388893 TAAAACTTTAAAATCTGAAAAATAAGAG
1 TAAAACTATAAAATCTAAAAAAT-AGGG
* * *
39388921 CAAAATTATAAAATCTTAAAAATAGAGG
1 TAAAACTATAAAATCTAAAAAATAG-GG
*
39388949 CAAAACTATAAAATCTAAAAAATAAGGG
1 TAAAACTATAAAATCTAAAAAAT-AGGG
39388977 -ACAAACCTATAAAATCTAAAAAAATAAGGG
1 TA-AAA-CTATAAAATCT-AAAAAAT-AGGG
* *
39389007 GAAAACTACAAAATCTAAAAAATAGGG
1 TAAAACTATAAAATCTAAAAAATAGGG
* ** * *
39389034 GAAATTTTGTAAAATCTAGAAAATAGGGG
1 TAAA-ACTATAAAATCTAAAAAATA-GGG
* *
39389063 TAACAAATTTTAAAAATCTAAAAAATAGGAG
1 T-A-AAACTAT-AAAATCTAAAAAATAGG-G
* *
39389094 TAAAATTGTAAAATCTAAAAA
1 TAAAACTATAAAATCTAAAAA
39389115 CATGGATTCA
Statistics
Matches: 211, Mismatches: 26, Indels: 28
0.80 0.10 0.11
Matches are distributed among these distances:
27 11 0.05
28 102 0.48
29 57 0.27
30 22 0.10
31 19 0.09
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.23
Consensus pattern (27 bp):
TAAAACTATAAAATCTAAAAAATAGGG
Found at i:39388905 original size:57 final size:57
Alignment explanation
Indices: 39388831--39389114 Score: 259
Period size: 57 Copynumber: 4.9 Consensus size: 57
39388821 AATATAATTC
* * *
39388831 TGGGTTAAAACTATAAAATTTATAAAATAGGGGAAAAACTATAAAATCTAAAAAAATA
1 TGGG-TAAAACTATAAAATCTAAAAAATAGGGGAAAAATTATAAAATCTAAAAAAATA
* * * * * *
39388889 TGGGTAAAACTTTAAAATCTGAAAAATAAGAGCAAAATTATAAAATCT-TAAAAATA
1 TGGGTAAAACTATAAAATCTAAAAAATAGGGGAAAAATTATAAAATCTAAAAAAATA
* * **
39388945 -GAGGCAAAACTATAAAATCTAAAAAATAAGGGACAAACCTATAAAATCTAAAAAAATA
1 TG-GGTAAAACTATAAAATCTAAAAAATAGGGGA-AAAATTATAAAATCTAAAAAAATA
* * * ** * *
39389003 AGGGGAAAACTACAAAATCTAAAAAATAGGGGAAATTTTGTAAAATCT-AGAAAATA
1 TGGGTAAAACTATAAAATCTAAAAAATAGGGGAAAAATTATAAAATCTAAAAAAATA
* * * * * *
39389059 GGGGTAACAAATTTTAAAAATCTAAAAAATAGGAGTAAAATTGTAAAATCTAAAAA
1 TGGGT-A-AAACTAT-AAAATCTAAAAAATAGGGGAAAAATTATAAAATCTAAAAA
39389115 CATGGATTCA
Statistics
Matches: 183, Mismatches: 35, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
55 1 0.01
56 43 0.23
57 61 0.33
58 43 0.23
59 32 0.17
60 3 0.02
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.23
Consensus pattern (57 bp):
TGGGTAAAACTATAAAATCTAAAAAATAGGGGAAAAATTATAAAATCTAAAAAAATA
Found at i:39391657 original size:25 final size:23
Alignment explanation
Indices: 39391586--39391653 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 23
39391576 TTATTTTTCC
39391586 ATCTTAATTTTTTTAATCTCTACGA
1 ATCTTAA-TTTTTTAATCTCTAC-A
* *
39391611 ATC-T-ACTTTTT-AT-TCTTCA
1 ATCTTAATTTTTTAATCTCTACA
39391630 ATCTTAATTTTTTAATCTCTACA
1 ATCTTAATTTTTTAATCTCTACA
39391653 A
1 A
39391654 AATCGACATA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
19 4 0.11
20 5 0.14
21 8 0.23
22 7 0.20
23 7 0.20
24 1 0.03
25 3 0.09
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (23 bp):
ATCTTAATTTTTTAATCTCTACA
Found at i:39392192 original size:17 final size:19
Alignment explanation
Indices: 39392156--39392206 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 19
39392146 TTCTGTATGC
39392156 AATTGAAAACTTAAAATTA
1 AATTGAAAACTTAAAATTA
*
39392175 AATT-AAAAC-TAAATTTA
1 AATTGAAAACTTAAAATTA
*
39392192 AATTGAAAGCTTAAA
1 AATTGAAAACTTAAA
39392207 TTGAAGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.39
18 9 0.32
19 8 0.29
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (19 bp):
AATTGAAAACTTAAAATTA
Found at i:39396837 original size:79 final size:79
Alignment explanation
Indices: 39396706--39396860 Score: 220
Period size: 79 Copynumber: 2.0 Consensus size: 79
39396696 TGATGGTACG
* * * * * * * * *
39396706 CCTCTGCGATACTCTGTTGATGAAGAATATGCGATATTTGAATATTTTAGATTTATTGTTACTGA
1 CCTCTACGATACTCTATTGATAAAGAATATACGATATCTAAATATGTTAGATTGATTATTACTGA
39396771 TTTTGATTTATCAC
66 TTTTGATTTATCAC
*
39396785 CCTCTACGTTACTCTATTGATAAAGAATATACGATATCTAAATATGTTAGATTGATTATTACTGA
1 CCTCTACGATACTCTATTGATAAAGAATATACGATATCTAAATATGTTAGATTGATTATTACTGA
39396850 TTTTGATTTAT
66 TTTTGATTTAT
39396861 AACTGTGCAC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (79 bp):
CCTCTACGATACTCTATTGATAAAGAATATACGATATCTAAATATGTTAGATTGATTATTACTGA
TTTTGATTTATCAC
Found at i:39401792 original size:8 final size:8
Alignment explanation
Indices: 39401781--39401816 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
39401771 GATAGGTTGA
39401781 TATTTTGG
1 TATTTTGG
39401789 TATTTTGG
1 TATTTTGG
39401797 TATTTTGG
1 TATTTTGG
39401805 TATTTTGG
1 TATTTTGG
39401813 TATT
1 TATT
39401817 GGTTACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.22, T:0.64
Consensus pattern (8 bp):
TATTTTGG
Found at i:39412796 original size:67 final size:67
Alignment explanation
Indices: 39412688--39412988 Score: 489
Period size: 67 Copynumber: 4.5 Consensus size: 67
39412678 CAAGTTCATC
*
39412688 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAGAAACATAATGCAAATATA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAAAAACATAATGCAAATATA
39412753 TG
66 TG
* * * *
39412755 TAAATAATTGAAGCTGATATAAGAATGGAAATTCAATAGAAAAACAAAAACATAATGAAAATATA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAAAAACATAATGCAAATATA
39412820 TG
66 TG
* * *
39412822 TAAATAATTTAAGTTGATACAAGAATGAAAATTCAATAGAAAAATAGAAACATAATGCAAATATA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAAAAACATAATGCAAATATA
39412887 --
66 TG
* * *
39412887 TATATAATTTAAGTTGATACAAGAATGAAAGTTCAATAGAAAAACAAAAACATAATGCAAATATA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAAAAACATAATGCAAATATA
39412952 TG
66 TG
39412954 TAAATAATTGAAGTTGATACAAGAATGAAAATTCA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCA
39412989 CTACATAAAT
Statistics
Matches: 213, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
65 61 0.29
67 152 0.71
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.26
Consensus pattern (67 bp):
TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAAAAACATAATGCAAATATA
TG
Found at i:39412968 original size:132 final size:133
Alignment explanation
Indices: 39412688--39412988 Score: 507
Period size: 132 Copynumber: 2.3 Consensus size: 133
39412678 CAAGTTCATC
39412688 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAGAAACATAATGCAAATATA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAGAAACATAATGCAAATATA
*
39412753 TGTAAATAATTGAAGCTGATATAAGAATGGAAATTCAATAGAAAAACAAAAACATAATGAAAATA
66 -GTAAATAATTGAAGCTGATACAAGAATGGAAATTCAATAGAAAAACAAAAACATAATGAAAATA
39412818 TATG
130 TATG
* *
39412822 TAAATAATTTAAGTTGATACAAGAATGAAAATTCAATAGAAAAATAGAAACATAATGCAAATATA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAGAAACATAATGCAAATATA
* * * *
39412887 -TATATAATTTAAGTTGATACAAGAAT-GAAAGTTCAATAGAAAAACAAAAACATAATGCAAATA
66 GTAAATAATTGAAGCTGATACAAGAATGGAAA-TTCAATAGAAAAACAAAAACATAATGAAAATA
39412950 TATG
130 TATG
39412954 TAAATAATTGAAGTTGATACAAGAATGAAAATTCA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCA
39412989 CTACATAAAT
Statistics
Matches: 158, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
131 4 0.03
132 91 0.58
134 63 0.40
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.26
Consensus pattern (133 bp):
TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATAGAAAAACAGAAACATAATGCAAATATA
GTAAATAATTGAAGCTGATACAAGAATGGAAATTCAATAGAAAAACAAAAACATAATGAAAATAT
ATG
Found at i:39417864 original size:29 final size:29
Alignment explanation
Indices: 39417804--39417865 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
39417794 ATACTATTAT
* * *
39417804 TATAATTATTATCATTATAACTATTATTA
1 TATAACTATTATCATTATAACTATAATCA
*
39417833 TATAACTATTATCATTATTA-TATAATACA
1 TATAACTATTATCATTATAACTATAAT-CA
39417862 TATA
1 TATA
39417866 TATATTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (29 bp):
TATAACTATTATCATTATAACTATAATCA
Found at i:39421967 original size:16 final size:16
Alignment explanation
Indices: 39421948--39421991 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
39421938 TGTATTGGAT
39421948 TAGAGGTGTAATGAAA
1 TAGAGGTGTAATGAAA
*
39421964 TAGAGGTGTAATGGAA
1 TAGAGGTGTAATGAAA
39421980 TAGAGGTGTAAT
1 TAGAGGTGTAAT
39421992 AGCAAATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.27
Consensus pattern (16 bp):
TAGAGGTGTAATGAAA
Found at i:39422075 original size:39 final size:43
Alignment explanation
Indices: 39421970--39422079 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
39421960 GAAATAGAGG
39421970 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
39422015 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
39422055 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
39422080 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:39422233 original size:25 final size:25
Alignment explanation
Indices: 39422201--39422255 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
39422191 TAATTTAATC
*
39422201 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
39422225 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
39422250 ATATAT
1 ATATAT
39422256 AAATTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:39422241 original size:24 final size:25
Alignment explanation
Indices: 39422190--39422263 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 25
39422180 TCAATAATAA
* *
39422190 ATAATTTAATCATATTTAAACATAATT
1 ATAATTAAAT-ATA-TTAAATATAATT
*
39422217 ATTATTAAATATATTAAATAT-ATT
1 ATAATTAAATATATTAAATATAATT
39422241 ATAATTAAA-ATATATAAAT-TAAT
1 ATAATTAAATATAT-TAAATATAAT
39422264 AAAATTCTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 5 0.12
24 18 0.44
25 7 0.17
26 3 0.07
27 8 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAATTAAATATATTAAATATAATT
Found at i:39422269 original size:23 final size:25
Alignment explanation
Indices: 39422223--39422269 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
39422213 AATTATTATT
* *
39422223 AAATATATTAAATATATTATAATTA
1 AAATATATTAAATATAATAAAATTA
39422248 AAATATA-TAAAT-TAATAAAATT
1 AAATATATTAAATATAATAAAATT
39422270 CTTAATAANN
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
25 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATATATTAAATATAATAAAATTA
Found at i:39424834 original size:16 final size:16
Alignment explanation
Indices: 39424813--39424845 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39424803 GATACAATAT
*
39424813 AACAAAGGATAAGCAA
1 AACAAAGGATAACCAA
39424829 AACAAAGGATAACCAA
1 AACAAAGGATAACCAA
39424845 A
1 A
39424846 GTAACATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.15, G:0.15, T:0.06
Consensus pattern (16 bp):
AACAAAGGATAACCAA
Found at i:39428946 original size:4 final size:4
Alignment explanation
Indices: 39428937--39428962 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
39428927 GGCCGTTAGT
39428937 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
39428963 ACCTTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:39434994 original size:3 final size:3
Alignment explanation
Indices: 39434980--39435013 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
39434970 CATGACTCTG
* *
39434980 CAT CAC CAT CAT CAT CAT CAT CAC CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
39435014 GTGACTGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.26
Consensus pattern (3 bp):
CAT
Found at i:39449018 original size:17 final size:18
Alignment explanation
Indices: 39448984--39449018 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39448974 AGTTGTCATA
39448984 TTAAAATAATTATAATTT
1 TTAAAATAATTATAATTT
*
39449002 TTAAAGTAATT-TAATTT
1 TTAAAATAATTATAATTT
39449019 ATAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTAAAATAATTATAATTT
Found at i:39451773 original size:33 final size:27
Alignment explanation
Indices: 39451703--39451762 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
39451693 TTGCCTTTGC
39451703 TGTCCAATTAAGGTGAAATAGAGCTCA
1 TGTCCAATTAAGGTGAAATAGAGCTCA
39451730 TGTCCAATTAAGGTGAAATAGAGCTCA
1 TGTCCAATTAAGGTGAAATAGAGCTCA
39451757 TGTCCA
1 TGTCCA
39451763 TGTATAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (27 bp):
TGTCCAATTAAGGTGAAATAGAGCTCA
Found at i:39452227 original size:92 final size:91
Alignment explanation
Indices: 39452066--39452261 Score: 232
Period size: 92 Copynumber: 2.1 Consensus size: 91
39452056 CAAACTAATT
* * * ** *
39452066 TTTTAATATTTCATTTTAATATTATAGTTTTTATTTATTTTACTTCCATGTTTCTAAATTATTTT
1 TTTTATTATTTCATTTTAATATTATAGTTTTTATTTATTTAACTTACAAATTCCTAAATTATTTT
*
39452131 TAATAGTAGTATGAAGTAATACAATA
66 TAATAGTAGAATGAAGTAATACAATA
* * * *
39452157 TTTTGTTATTTCA-TTTAATATTATAGTTTTTTTTTTAATTTAAGTTACAAATTCCTATATTATT
1 TTTTATTATTTCATTTTAATATTATAG-TTTTTATTT-ATTTAACTTACAAATTCCTAAATTATT
* * * *
39452221 TTTAATAGTAGAATGTATTAATTCAATG
64 TTTAATAGTAGAATGAAGTAATACAATA
39452249 TTTTATTATTTCA
1 TTTTATTATTTCA
39452262 GTTACAATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
90 13 0.15
91 19 0.22
92 55 0.63
ACGTcount: A:0.32, C:0.06, G:0.07, T:0.56
Consensus pattern (91 bp):
TTTTATTATTTCATTTTAATATTATAGTTTTTATTTATTTAACTTACAAATTCCTAAATTATTTT
TAATAGTAGAATGAAGTAATACAATA
Found at i:39452280 original size:19 final size:20
Alignment explanation
Indices: 39452256--39452294 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
39452246 ATGTTTTATT
39452256 ATTTCAGTTAC-AATTTTTA
1 ATTTCAGTTACAAATTTTTA
*
39452275 ATTTCAGTTTCAAATTTTTA
1 ATTTCAGTTACAAATTTTTA
39452295 TACTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTCAGTTACAAATTTTTA
Found at i:39452306 original size:21 final size:21
Alignment explanation
Indices: 39452282--39452325 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
39452272 TTAATTTCAG
*
39452282 TTTCAAATTTTTATACTATAT
1 TTTCAAATTTCTATACTATAT
39452303 TTTCAAATTTCTATACTATAT
1 TTTCAAATTTCTATACTATAT
39452324 TT
1 TT
39452326 AAATGTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTCAAATTTCTATACTATAT
Found at i:39454205 original size:16 final size:16
Alignment explanation
Indices: 39454184--39454214 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39454174 AAATATGATC
39454184 TTAATTTTTATTTTTA
1 TTAATTTTTATTTTTA
39454200 TTAATTTTTATTTTT
1 TTAATTTTTATTTTT
39454215 CTCTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTAATTTTTATTTTTA
Found at i:39461901 original size:17 final size:17
Alignment explanation
Indices: 39461867--39461901 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39461857 ATAAAAAGAC
*
39461867 AAAAAATATAAAATATT
1 AAAAAATATAAAACATT
*
39461884 AAAAAATATATAACATT
1 AAAAAATATAAAACATT
39461901 A
1 A
39461902 TATAAAGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATATAAAACATT
Found at i:39469812 original size:83 final size:83
Alignment explanation
Indices: 39469711--39470255 Score: 421
Period size: 84 Copynumber: 6.6 Consensus size: 83
39469701 ATTAAATCAA
* * *
39469711 AAATAAAAT-TTGTTAAACGACGGGAATAAATCTCGAAACAGAATTATTTGATTACGTCTTTGTT
1 AAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAGAATTATTTAATTACTTCTTTGTT
39469775 TGGAAACAAAACAATATC
66 TGGAAACAAAACAATATC
* * * **
39469793 GAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACA-AATTTTATTTAATTCAATTC-GA
1 AAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAGAA--TTATTTAATT-ACTTCTTT
* * * * * *
39469856 ATTTGAAAATAAAATAAAATA
63 GTTTGGAAACAAAACAATATC
* * * *
39469877 AAATAAAATCTTGTTAAACAACGGGAATAAATCCCGAAAAAGATTTTATTTAATTTAATTTCTCA
1 AAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAGA-ATTATTTAA-TT-ACTTCT--
**
39469942 TT-TTTGGCTACAAAATCAA-ATC
61 TTGTTTGGAAACAAAA-CAATATC
* * *
39469964 AAAT-AAATCTTAG-TAAACGGCGAGAATAAATCCCGAAACAGAATTATTTGATTA-TATCTTTG
1 AAATAAAATCTT-GTTAAACGACGGGAATAAATCCCGAAACAGAATTATTTAATTACT-TCTTTG
*
39470026 TTTGAAAACAAAACAATATC
64 TTTGGAAACAAAACAATATC
* * * *
39470046 AAATAAAATCTTGTTAAACGGA-AGGAATAAATCCCGAAATAGATTTTATTTAATTTAATTC-TT
1 AAATAAAATCTTGTTAAAC-GACGGGAATAAATCCCGAAACAGA-ATTATTTAA-TTACTTCTTT
* *
39470109 ATTTGG-AA-ATAA-AATA--
63 GTTTGGAAACAAAACAATATC
* * *
39470125 AAATAAAATCTTGTTAAACGACGGGAATAAATTCTGAAACA-AATTTTATTTAATTTGATTTCTC
1 AAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAGAA--TTATTTAA-TT-ACTTCT-
39470189 ATT-TTT-GACAACAAAATCAA-ATC
61 -TTGTTTGGA-AACAAAA-CAATATC
* * *
39470212 AAAT-AAATCTTATTAAACGGCGAGAATAAATCCCGAAACA-AATT
1 AAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAGAATT
39470256 TTATTTTATT
Statistics
Matches: 369, Mismatches: 59, Indels: 68
0.74 0.12 0.14
Matches are distributed among these distances:
78 3 0.01
79 45 0.12
80 4 0.01
81 10 0.03
82 35 0.09
83 69 0.19
84 90 0.24
85 23 0.06
86 68 0.18
87 20 0.05
88 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (83 bp):
AAATAAAATCTTGTTAAACGACGGGAATAAATCCCGAAACAGAATTATTTAATTACTTCTTTGTT
TGGAAACAAAACAATATC
Found at i:39469869 original size:5 final size:5
Alignment explanation
Indices: 39469861--39469885 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39469851 TTCGAATTTG
39469861 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
39469886 CTTGTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:39469999 original size:86 final size:87
Alignment explanation
Indices: 39469779--39470347 Score: 524
Period size: 86 Copynumber: 6.7 Consensus size: 87
39469769 TTTGTTTGGA
* *
39469779 AACAAAA-CAATATCGAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAAATTTTATT
1 AACAAAATCAA-ATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAAATTTTATT
* * * *
39469843 TAATTCAA-TTC-GA-ATTTGAA
65 TAATTTAATTTCTCATTTTTGAC
* * * ** *
39469863 AATAAAATAAAATAAAATAAAATCTTGTTAAACAACGGGAATAAATCCCGAAA-AAGATTTTATT
1 AACAAAATCAAATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAA-ATTTTATT
*
39469927 TAATTTAATTTCTCATTTTTGGC
65 TAATTTAATTTCTCATTTTTGAC
*
39469950 TACAAAATCAAATCAAAT-AAATCTTAG-TAAACGGCGAGAATAAATCCCGAAACAGAA--TTAT
1 AACAAAATCAAATCAAATAAAATCTT-GTTAAACGGCGAGAATAAATCCCGAAACA-AATTTTAT
* * *
39470011 TTGA-TT-ATATCT--TTGTTTGAA
64 TTAATTTAATTTCTCATT-TTTGAC
* * *
39470032 AACAAAA-CAATATCAAATAAAATCTTGTTAAACGG-AAGGAATAAATCCCGAAATAGATTTTAT
1 AACAAAATCAA-ATCAAATAAAATCTTGTTAAACGGCGA-GAATAAATCCCGAAACAAATTTTAT
* *
39470095 TTAATTTAA-TTCTTA-TTTGGA-
64 TTAATTTAATTTCTCATTTTTGAC
* * * * *
39470116 AATAAAAT---A--AAATAAAATCTTGTTAAACGACGGGAATAAATTCTGAAACAAATTTTATTT
1 AACAAAATCAAATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAAATTTTATTT
*
39470176 AATTTGATTTCTCATTTTTGAC
66 AATTTAATTTCTCATTTTTGAC
*
39470198 AACAAAATCAAATCAAAT-AAATCTTATTAAACGGCGAGAATAAATCCCGAAACAAATTTTATTT
1 AACAAAATCAAATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAAATTTTATTT
* * *
39470262 TATTTAATTTCTCGTTTTTGGC
66 AATTTAATTTCTCATTTTTGAC
* * * * * * **
39470284 AACAAAATCAAAATGAAAT-AAATC-CGTTGAACGGCGGGAATCAATCCCAAAACGGATTTTATT
1 AACAAAATC-AAATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAAATTTTATT
39470347 T
65 T
39470348 TACTCGTTTT
Statistics
Matches: 396, Mismatches: 59, Indels: 58
0.77 0.12 0.11
Matches are distributed among these distances:
79 49 0.12
80 5 0.01
81 11 0.03
82 27 0.07
83 37 0.09
84 74 0.19
85 22 0.06
86 132 0.33
87 38 0.10
88 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (87 bp):
AACAAAATCAAATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAAATTTTATTT
AATTTAATTTCTCATTTTTGAC
Found at i:39470220 original size:248 final size:249
Alignment explanation
Indices: 39469724--39470255 Score: 800
Period size: 248 Copynumber: 2.1 Consensus size: 249
39469714 TAAAATTTGT
* * * * *
39469724 TAAACGACGGGAATAAATCTCGAAACAGAATTATTTGATTACGTCTTTGTTTGGAAACAAAACAA
1 TAAACGGCGAGAATAAATCCCGAAACAGAATTATTTGATTACATCTTTGTTTGAAAACAAAACAA
* **
39469789 TATCGAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAAATTTTATTTAATTCAATTC
66 TATCAAATAAAATCTTGTTAAACGGAAGGAATAAATCCCGAAACAAATTTTATTTAATTCAATTC
39469854 GAATTTGAAAATAAAATAAAATAAAATAAAATCTTGTTAAACAACGGGAATAAATCCCGAAAAAG
131 GAATTTG---A-AAAATAAAATAAAATAAAATCTTGTTAAACAACGGGAATAAATCCCGAAAAAG
* *
39469919 ATTTTATTTAATTTAATTTCTCATTTTTGGCTACAAAATCAAATCAAATAAATCTTAG
192 ATTTTATTTAATTTAATTTCTCATTTTTGACAACAAAATCAAATCAAATAAATCTTAG
*
39469977 TAAACGGCGAGAATAAATCCCGAAACAGAATTATTTGATTATATCTTTGTTTGAAAACAAAACAA
1 TAAACGGCGAGAATAAATCCCGAAACAGAATTATTTGATTACATCTTTGTTTGAAAACAAAACAA
* * *
39470042 TATCAAATAAAATCTTGTTAAACGGAAGGAATAAATCCCGAAATAGATTTTATTTAATTTAATTC
66 TATCAAATAAAATCTTGTTAAACGGAAGGAATAAATCCCGAAACAAATTTTATTTAATTCAATTC
** * * * *
39470107 TTATTTG-GAAATAAAATAAAATAAAATCTTGTTAAACGACGGGAATAAATTCTGAAACAA-ATT
131 GAATTTGAAAAATAAAATAAAATAAAATCTTGTTAAACAACGGGAATAAATCCCGAAA-AAGATT
* *
39470170 TTATTTAATTTGATTTCTCATTTTTGACAACAAAATCAAATCAAATAAATCTTAT
195 TTATTTAATTTAATTTCTCATTTTTGACAACAAAATCAAATCAAATAAATCTTAG
39470225 TAAACGGCGAGAATAAATCCCGAAACA-AATT
1 TAAACGGCGAGAATAAATCCCGAAACAGAATT
39470256 TTATTTTATT
Statistics
Matches: 256, Mismatches: 22, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
247 4 0.02
248 127 0.50
249 2 0.01
253 123 0.48
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (249 bp):
TAAACGGCGAGAATAAATCCCGAAACAGAATTATTTGATTACATCTTTGTTTGAAAACAAAACAA
TATCAAATAAAATCTTGTTAAACGGAAGGAATAAATCCCGAAACAAATTTTATTTAATTCAATTC
GAATTTGAAAAATAAAATAAAATAAAATCTTGTTAAACAACGGGAATAAATCCCGAAAAAGATTT
TATTTAATTTAATTTCTCATTTTTGACAACAAAATCAAATCAAATAAATCTTAG
Found at i:39470399 original size:79 final size:79
Alignment explanation
Indices: 39470309--39470505 Score: 261
Period size: 79 Copynumber: 2.5 Consensus size: 79
39470299 AAATAAATCC
* *
39470309 GTTGAACGGCGGGAATCAATCCCAAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAACAAAA
1 GTTGAATGGCGGGAATCAATCCCGAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAACAAAA
39470374 ATTGGAATAAAATA
66 ATTGGAATAAAATA
** * * *
39470388 GTTGAATGGCGGGAATCAATCTTGAAACAGA-TTTAGTTTTACTCGTTTTTTGAAATAAAATAAA
1 GTTGAATGGCGGGAATCAATCCCGAAACGGATTTTA-TTTTACTCGTTTTTGGAAATAAAACAAA
* *
39470452 ATTTGGAATAAAATC
65 AATTGGAATAAAATA
* * * *
39470467 GTTAAATGGCGGGAACCAATCCCGAAATGAATTTTATTT
1 GTTGAATGGCGGGAATCAATCCCGAAACGGATTTTATTT
39470506 ACCTTTAATT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
78 4 0.04
79 92 0.92
80 4 0.04
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (79 bp):
GTTGAATGGCGGGAATCAATCCCGAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAACAAAA
ATTGGAATAAAATA
Found at i:39475083 original size:108 final size:109
Alignment explanation
Indices: 39474844--39475231 Score: 563
Period size: 109 Copynumber: 3.6 Consensus size: 109
39474834 TTAATTATTC
* * * * *
39474844 TAAATTGTTTGTATTTAGTTTAGTG-TT-TTGAGATCTTTTATGAATGTAATTTTTTTGTTTTTT
1 TAAATTGTTTGTGTTTAATTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTTTT-ATTTTT
*
39474907 TAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTA
65 TAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTA
*
39474952 TAAATTGTTTGTGTTTAATTTAGTG-TT-TTGTGATTTTTTTATGAATGTAAAATTTTTTATTTT
1 TAAATTGTTTGTGTTTAATTTAGTGTTTATTGTGA-TTTTTTATGAATGT-AATTTTTTTATTTT
* *
39475015 TTAAAATTATTTTAAAGTCATTTT-TTAGTAATTTATGGTTAGG-TA
64 TT-AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTA
* *
39475060 TAAATTGTTTGTGTTTAATTTAGTGTTTATTGTGATTTTTTATGAATGTATTTTTTTTGTTTTTT
1 TAAATTGTTTGTGTTTAATTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTTTTATTTTTT
* *
39475125 TAATTATTTTAAAGTTATTTTGTTAGTAATTTATTATTAGGTTA
66 AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTA
* *
39475169 TAAATTGTTTGTGTTTAGTTTAATGTTTATTGTGATTTTTTATGAATGTAATTTTTTTATTTT
1 TAAATTGTTTGTGTTTAATTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTTTTATTTT
39475232 AAAGTTATTT
Statistics
Matches: 253, Mismatches: 20, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
107 19 0.08
108 87 0.34
109 114 0.45
110 33 0.13
ACGTcount: A:0.25, C:0.01, G:0.14, T:0.60
Consensus pattern (109 bp):
TAAATTGTTTGTGTTTAATTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTTTTATTTTTT
AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTA
Found at i:39475233 original size:97 final size:95
Alignment explanation
Indices: 39475122--39475326 Score: 286
Period size: 97 Copynumber: 2.1 Consensus size: 95
39475112 TTTTTTGTTT
* * * *
39475122 TTTTAATTATTTTAAAGTTATTTTGTTAGTAATTTATTATTAGGTTATAAATTGTTTGTGTTTAG
1 TTTTATTTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATT-ATT-TGTTTAG
* * * * *
39475187 TTTAATGTTTATTGTGATTTTTTATGAATGTAA
64 TTTAATGTGTAATATGACTTGTTAT-AATGTAA
39475220 TTTT-TTTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTATTTGTTTAGTT
1 TTTTATTTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTATTTGTTTAGTT
39475284 TAATGTGTAATATGACTTGTTATAATGTAA
66 TAATGTGTAATATGACTTGTTATAATGTAA
*
39475314 TTTTATTTGTTTT
1 TTTTATTTATTTT
39475327 TTTATTTATT
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
94 11 0.11
95 34 0.35
96 2 0.02
97 45 0.47
98 4 0.04
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (95 bp):
TTTTATTTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTATTTGTTTAGTT
TAATGTGTAATATGACTTGTTATAATGTAA
Found at i:39475591 original size:22 final size:22
Alignment explanation
Indices: 39475551--39475613 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
39475541 ATTTATGAGA
* * *
39475551 TATTTTTTATTATAATTATAC-
1 TATTATTTACTATATTTATACG
39475572 TATTATTGTACTATATTTAT-CG
1 TATTATT-TACTATATTTATACG
* *
39475594 TATTATTTACTGTATGTATA
1 TATTATTTACTATATTTATA
39475614 ATATAAATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (22 bp):
TATTATTTACTATATTTATACG
Found at i:39476637 original size:33 final size:33
Alignment explanation
Indices: 39476595--39476681 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
39476585 ACCACCGAAG
39476595 TACTCGACTCCTCCCGGCTCACATCCACCACAA
1 TACTCGACTCCTCCCGGCTCACATCCACCACAA
* * * ** *
39476628 TACTAGACTCCTCCCGACCCGTATCCACCACAG
1 TACTCGACTCCTCCCGGCTCACATCCACCACAA
*
39476661 TACTCCACTCCTCCCGGCTCA
1 TACTCGACTCCTCCCGGCTCA
39476682 AGTTCATCAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.22, C:0.48, G:0.10, T:0.20
Consensus pattern (33 bp):
TACTCGACTCCTCCCGGCTCACATCCACCACAA
Found at i:39480781 original size:25 final size:26
Alignment explanation
Indices: 39480753--39480801 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
39480743 ATAAATATTA
*
39480753 AACTAA-ACAAATAA-TTTATAATAGT
1 AACTAACA-AAATAACTTTAAAATAGT
39480778 AACTAACAAAATAACTTTAAAATA
1 AACTAACAAAATAACTTTAAAATA
39480802 AATTAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (26 bp):
AACTAACAAAATAACTTTAAAATAGT
Found at i:39480790 original size:105 final size:106
Alignment explanation
Indices: 39480543--39480809 Score: 324
Period size: 115 Copynumber: 2.4 Consensus size: 106
39480533 AACTAATAAT
* * * *
39480543 TAATTTATAATAGTTACTAACAAAATAAATTTCAAATAAATTAAAAAATATTAAAAAGATTACAT
1 TAATTTATAATAGTAACTAACAAAATAACTTTAAAATAAATT-AAAAATAGTAAAAAGATTACAT
39480608 TCATAACCTAACAAATCACAATAAACCATAAACCCTAAACAAA
65 TCATAACCTAACAAATCACAATAAACCATAAA-CCTAAACAAA
* * **
39480651 CAATTAACCTAATCACAAAACTTACTGACAAAATAACTTTAAAATAAATTAAAAATCAGTAAAAA
1 TAATTTA--TAAT-A-GTAAC-TA---ACAAAATAACTTTAAAATAAATTAAAAAT-AGTAAAAA
*
39480716 -ATTACATTCATAACCTAACAAATCACAATAAA-TATTAAA-CTAAACAAA
57 GATTACATTCATAACCTAACAAATCACAATAAACCA-TAAACCTAAACAAA
39480764 TAATTTATAATAGTAACTAACAAAATAACTTTAAAATAAATTAAAA
1 TAATTTATAATAGTAACTAACAAAATAACTTTAAAATAAATTAAAA
39480810 TCAACATAAA
Statistics
Matches: 136, Mismatches: 13, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
105 27 0.20
108 7 0.05
109 3 0.02
110 5 0.04
111 5 0.04
112 2 0.01
113 16 0.12
114 1 0.01
115 42 0.31
116 28 0.21
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (106 bp):
TAATTTATAATAGTAACTAACAAAATAACTTTAAAATAAATTAAAAATAGTAAAAAGATTACATT
CATAACCTAACAAATCACAATAAACCATAAACCTAAACAAA
Found at i:39480809 original size:10 final size:11
Alignment explanation
Indices: 39480785--39480830 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
39480775 AGTAACTAAC
*
39480785 AAAATAACTTT
1 AAAATAACATT
39480796 AAAATAA-ATT
1 AAAATAACATT
39480806 AAAATCAACA-T
1 AAAAT-AACATT
*
39480817 AAAATAACAAT
1 AAAATAACATT
39480828 AAA
1 AAA
39480831 CAAACTACAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 11 0.35
11 19 0.61
12 1 0.03
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATAACATT
Found at i:39481107 original size:27 final size:27
Alignment explanation
Indices: 39481029--39481107 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
39481019 CAAAATTGCT
* * * *
39481029 TCACTGGTGCTGCCTATTAGATAGAGG
1 TCACCGGTCCTGCCTATCAGATAGGGG
*
39481056 TCACCAGTGCC-GCCTATCAGATAGGGG
1 TCACCGGT-CCTGCCTATCAGATAGGGG
*
39481083 TCACCGGTCCTGCCTATCAAATAGG
1 TCACCGGTCCTGCCTATCAGATAGG
39481108 CACCACCCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.24
Consensus pattern (27 bp):
TCACCGGTCCTGCCTATCAGATAGGGG
Found at i:39481333 original size:29 final size:29
Alignment explanation
Indices: 39481289--39481344 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
39481279 GGCACCATCG
39481289 CTACTGACATAACATTTTCGTATTTAACC
1 CTACTGACATAACATTTTCGTATTTAACC
*
39481318 CTACTGACATACCATTTTCGTATTTAA
1 CTACTGACATAACATTTTCGTATTTAA
39481345 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (29 bp):
CTACTGACATAACATTTTCGTATTTAACC
Found at i:39484529 original size:44 final size:45
Alignment explanation
Indices: 39484450--39484534 Score: 111
Period size: 46 Copynumber: 1.9 Consensus size: 45
39484440 CACGTTGGAT
*
39484450 TCAACACACAACAACCACCCTTTGTAATCAATGATATCCGGTGGGA
1 TCAACACACAACAACCACCCTTTATAATCAATGATA-CCGGTGGGA
* * *
39484496 TCAACACATAGCAACCA-CC-TTATAATTAATGATACCGGT
1 TCAACACACAACAACCACCCTTTATAATCAATGATACCGGT
39484535 TCACATAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 5 0.14
44 13 0.37
45 2 0.06
46 15 0.43
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (45 bp):
TCAACACACAACAACCACCCTTTATAATCAATGATACCGGTGGGA
Found at i:39484598 original size:51 final size:51
Alignment explanation
Indices: 39484540--39484730 Score: 228
Period size: 51 Copynumber: 3.8 Consensus size: 51
39484530 CCGGTTCACA
* * *
39484540 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTACCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATACACG
* * *
39484591 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGATACACG
* * * *
39484642 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGATACACG
*
39484692 TAGTAGCTTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
39484731 TTCACTTTCA
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
49 4 0.03
50 40 0.34
51 71 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATACACG
Found at i:39484721 original size:101 final size:102
Alignment explanation
Indices: 39484538--39484722 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
39484528 TACCGGTTCA
* *
39484538 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTACCCGATACATGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTACCCGATACACGTAGTAGCCTGCA
39484603 CATAGTACTACACACGTGATCGAAGCTATCCGATACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGATACG
* * * *
39484640 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCTTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTACCCGATACACGTAGTAGCCTGC
39484703 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
39484723 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 37 0.49
102 35 0.46
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTACCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGATACG
Found at i:39495024 original size:3 final size:3
Alignment explanation
Indices: 39495018--39495052 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
39495008 ATAATAATAA
*
39495018 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39495053 ATAATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:39495053 original size:6 final size:6
Alignment explanation
Indices: 39495003--39495055 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
39494993 ATGATGATAA
* * * * * *
39495003 TAATAA TAATAA TAATAT TATTAT TATTAT TATTAT TATTAT TAATAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
39495051 TAATA
1 TAATA
39495056 ATATTAACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TAATAT
Found at i:39495057 original size:9 final size:9
Alignment explanation
Indices: 39494999--39495062 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
39494989 ATTAATGATG
*
39494999 ATAATAATA
1 ATAATATTA
*
39495008 ATAATAATA
1 ATAATATTA
*
39495017 ATATTATTA
1 ATAATATTA
* *
39495026 TTATTATTA
1 ATAATATTA
* *
39495035 TTATTATTA
1 ATAATATTA
*
39495044 TTAATATTA
1 ATAATATTA
39495053 ATAATATTA
1 ATAATATTA
39495062 A
1 A
39495063 CATCAAACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATAATATTA
Found at i:39495879 original size:21 final size:20
Alignment explanation
Indices: 39495849--39495887 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39495839 TTTTTTTTAA
39495849 AAAAAGAGAA-AAAGACAATT
1 AAAAAGAGAAGAAA-ACAATT
39495869 AAAAAGAAGAAGAAAACAA
1 AAAAAG-AGAAGAAAACAA
39495888 AACGCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 8 0.47
22 3 0.18
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAGAGAAGAAAACAATT
Found at i:39499362 original size:34 final size:34
Alignment explanation
Indices: 39499307--39499435 Score: 168
Period size: 34 Copynumber: 3.8 Consensus size: 34
39499297 CATGGATTTT
* * * * *
39499307 CTACCGTACTGATTTGTTATAAGCATGTCTATTA
1 CTACCATATTGATCTGTTATAAGCATGTTTATTG
*
39499341 CTATCATATTGATCTGTTATAAGCATGTTTATTG
1 CTACCATATTGATCTGTTATAAGCATGTTTATTG
* *
39499375 CTACCGTATTGATTTGTTATAAGCATGTTTATTG
1 CTACCATATTGATCTGTTATAAGCATGTTTATTG
* *
39499409 CTACCATATTGAACTATTATAAGCATG
1 CTACCATATTGATCTGTTATAAGCATG
39499436 CCATATGGCA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 82 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (34 bp):
CTACCATATTGATCTGTTATAAGCATGTTTATTG
Found at i:39499382 original size:68 final size:68
Alignment explanation
Indices: 39499307--39499435 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 68
39499297 CATGGATTTT
* * *
39499307 CTACCGTACTGATTTGTTATAAGCATGTCTATTACTATCATATTGATCTGTTATAAGCATGTTTA
1 CTACCGTACTGATTTGTTATAAGCATGTCTATTACTACCATATTGAACTATTATAAGCATGTTTA
39499372 TTG
66 TTG
* * *
39499375 CTACCGTATTGATTTGTTATAAGCATGTTTATTGCTACCATATTGAACTATTATAAGCATG
1 CTACCGTACTGATTTGTTATAAGCATGTCTATTACTACCATATTGAACTATTATAAGCATG
39499436 CCATATGGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (68 bp):
CTACCGTACTGATTTGTTATAAGCATGTCTATTACTACCATATTGAACTATTATAAGCATGTTTA
TTG
Found at i:39501016 original size:45 final size:43
Alignment explanation
Indices: 39500967--39501069 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 43
39500957 ACACTGATGG
* *
39500967 GTGGTTAATCCACCTTGTATTAGTAGCTTTTATCTAAACCAATGA
1 GTGGTTTATCCACC--GTATTAGTAGCTTTTATCTAAACCAATAA
* * **
39501012 GTGGTTTATCAACACCGTATTAGTAGCTTTTTTTTGCACCAATAA
1 GTGGTTTATC--CACCGTATTAGTAGCTTTTATCTAAACCAATAA
39501057 GTGGTTTATCCAC
1 GTGGTTTATCCAC
39501070 ACCATACTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
43 3 0.06
45 43 0.86
47 4 0.08
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (43 bp):
GTGGTTTATCCACCGTATTAGTAGCTTTTATCTAAACCAATAA
Found at i:39501072 original size:45 final size:45
Alignment explanation
Indices: 39500983--39501072 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
39500973 AATCCACCTT
*
39500983 GTATTAGTAGCTTTTATCTAAACCAATGAGTGGTTTATCAACACC
1 GTATTAGTAGCTTTTATCTAAACCAATAAGTGGTTTATCAACACC
* * ** *
39501028 GTATTAGTAGCTTTTTTTTGCACCAATAAGTGGTTTATCCACACC
1 GTATTAGTAGCTTTTATCTAAACCAATAAGTGGTTTATCAACACC
39501073 ATACTAGTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (45 bp):
GTATTAGTAGCTTTTATCTAAACCAATAAGTGGTTTATCAACACC
Found at i:39508096 original size:19 final size:19
Alignment explanation
Indices: 39508074--39508120 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
39508064 AATATATTTC
*
39508074 TTTTGAATTTTTATAAA-TA
1 TTTTGAATTTTGA-AAATTA
39508093 TTTTGAATTTTGAAAATTA
1 TTTTGAATTTTGAAAATTA
39508112 TTTTGAATT
1 TTTTGAATT
39508121 ATTTTGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TTTTGAATTTTGAAAATTA
Found at i:39509221 original size:19 final size:19
Alignment explanation
Indices: 39509197--39509233 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39509187 TTTTCTGTTC
*
39509197 TTTTATGATTGCTCTTTTT
1 TTTTATGATAGCTCTTTTT
39509216 TTTTATGATAGCTCTTTT
1 TTTTATGATAGCTCTTTT
39509234 CTCTTAACAA
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:0.14, C:0.11, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTATGATAGCTCTTTTT
Found at i:39516780 original size:24 final size:24
Alignment explanation
Indices: 39516738--39516789 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39516728 AATCAAAGTC
** *
39516738 AAATATATTATGCTAATAAATGCT
1 AAATATATTATAATAATAAATACT
*
39516762 AAATATATTATAATCATAAATACT
1 AAATATATTATAATAATAAATACT
39516786 AAAT
1 AAAT
39516790 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATAATAATAAATACT
Found at i:39520741 original size:43 final size:41
Alignment explanation
Indices: 39520671--39520796 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 41
39520661 AGGACTCCAA
*
39520671 TATGTGTTTTCATGTAAGACTACGTCTGGGACGTCGGCATCGAC
1 TATGTGTTTTCATGTAAGAC-CCGTCTGGGACGT-GGCATCG-C
* *
39520715 T-TGTGTTTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGG
1 TATGTGTTTTCATGTAAGACCC-GTCTGGGAC-GTGGCATCGC
* *
39520757 TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TATGTGTTTTCATGTAAGACC-CGTCTGGGACG-TGGCAT
39520797 TGTACGAGTT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
42 3 0.04
43 64 0.90
44 4 0.06
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (41 bp):
TATGTGTTTTCATGTAAGACCCGTCTGGGACGTGGCATCGC
Found at i:39521688 original size:47 final size:47
Alignment explanation
Indices: 39521634--39521900 Score: 471
Period size: 47 Copynumber: 5.7 Consensus size: 47
39521624 ATGAGTTGAA
* *
39521634 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAGTGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
39521681 CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
*
39521728 CCAATTTGTTACATATATGCTGTTCAATTTTGATGTTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
*
39521775 CCAATTTGTTACATATATGCTGTTCAATTTTGATGTTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
*
39521822 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
* *
39521869 CCAACTTGTTACATATATGCTGTCCAGTTTTG
1 CCAATTTGTTACATATATGCTGTCCAATTTTG
39521901 GCGTAAAAAT
Statistics
Matches: 213, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 213 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (47 bp):
CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
Found at i:39521911 original size:47 final size:47
Alignment explanation
Indices: 39521634--39521942 Score: 429
Period size: 47 Copynumber: 6.6 Consensus size: 47
39521624 ATGAGTTGAA
* * *
39521634 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAGTGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGACGTTTAAATGCTGC
*
39521681 CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGACGTTTAAATGCTGC
* *
39521728 CCAATTTGTTACATATATGCTGTTCAATTTTGATGTTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGACGTTTAAATGCTGC
* *
39521775 CCAATTTGTTACATATATGCTGTTCAATTTTGATGTTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGACGTTTAAATGCTGC
* *
39521822 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGACGTTTAAATGCTGC
* * * **
39521869 CCAACTTGTTACATATATGCTGTCCAGTTTTGGCGTAAAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGACGTTTAAATGCTGC
* ** ** *
39521916 TCAAACTGTTGTATATATGCTGCCCAA
1 CCAATTTGTTACATATATGCTGTCCAA
39521943 ATTGTTGTAT
Statistics
Matches: 243, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 243 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (47 bp):
CCAATTTGTTACATATATGCTGTCCAATTTTGACGTTTAAATGCTGC
Found at i:39521937 original size:23 final size:23
Alignment explanation
Indices: 39521909--39521959 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
39521899 TGGCGTAAAA
*
39521909 ATGCTGCTCAAACTGTTGTATAT
1 ATGCTGCCCAAACTGTTGTATAT
* *
39521932 ATGCTGCCCAAATTGTTGTATTT
1 ATGCTGCCCAAACTGTTGTATAT
39521955 ATGCT
1 ATGCT
39521960 ATCCAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (23 bp):
ATGCTGCCCAAACTGTTGTATAT
Found at i:39521965 original size:23 final size:23
Alignment explanation
Indices: 39521917--39521968 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
39521907 AAATGCTGCT
* *
39521917 CAAACTGTTGTATATATGCTGCC
1 CAAATTGTTGTATATATGCTACC
* *
39521940 CAAATTGTTGTATTTATGCTATC
1 CAAATTGTTGTATATATGCTACC
39521963 CAAATT
1 CAAATT
39521969 TTGGTGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (23 bp):
CAAATTGTTGTATATATGCTACC
Found at i:39522678 original size:9 final size:9
Alignment explanation
Indices: 39522611--39522677 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
39522601 GTAGTGATTC
*
39522611 AATTTGGTT
1 AATTCGGTT
39522620 AATTCGGTT
1 AATTCGGTT
*
39522629 AATTCGGGT
1 AATTCGGTT
*
39522638 AATTCGGGT
1 AATTCGGTT
39522647 AATTCGGTT
1 AATTCGGTT
*
39522656 AATTCGATT
1 AATTCGGTT
*
39522665 AATTTGGTT
1 AATTCGGTT
39522674 AATT
1 AATT
39522678 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39522858 original size:12 final size:12
Alignment explanation
Indices: 39522841--39522865 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39522831 TGTTATTTCG
39522841 GGTCGGTTAACC
1 GGTCGGTTAACC
39522853 GGTCGGTTAACC
1 GGTCGGTTAACC
39522865 G
1 G
39522866 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:39522990 original size:2 final size:2
Alignment explanation
Indices: 39522983--39523015 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39522973 AAGAAAATGT
39522983 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
39523016 TCGAATGTGT
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:39525142 original size:24 final size:24
Alignment explanation
Indices: 39525127--39525178 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39525117 AATCAAAGTC
39525127 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
39525151 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
39525175 AAAT
1 AAAT
39525179 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:39528833 original size:40 final size:40
Alignment explanation
Indices: 39528788--39528863 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
39528778 ATATCAGGGG
*
39528788 ACGTGG-CAGGAAAACGCGTCCCT-GAGGAAGCGTTTTGCCT
1 ACGTGGACA-GAAAACGC-TCCCTCAAGGAAGCGTTTTGCCT
* *
39528828 ACGTGGACAGAAATCGCTCCCTCAAGGACGCGTTTT
1 ACGTGGACAGAAAACGCTCCCTCAAGGAAGCGTTTT
39528864 CCTGCTACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
39 5 0.16
40 24 0.77
41 2 0.06
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (40 bp):
ACGTGGACAGAAAACGCTCCCTCAAGGAAGCGTTTTGCCT
Found at i:39529036 original size:22 final size:21
Alignment explanation
Indices: 39529008--39529073 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
39528998 ACTAAATCCT
39529008 TTCTCTCAATTTCTCTTTAATA
1 TTCTCTCAATTTCTCTTTAA-A
* *
39529030 TTCTCTCAAATTC-CTCTCAAA
1 TTCTCTCAATTTCTCT-TTAAA
*
39529051 TTCCTCTCAAATTTCTATTTAAA
1 TT-CTCTC-AATTTCTCTTTAAA
39529074 AGAGCTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 5 0.14
22 20 0.57
23 9 0.26
24 1 0.03
ACGTcount: A:0.27, C:0.26, G:0.00, T:0.47
Consensus pattern (21 bp):
TTCTCTCAATTTCTCTTTAAA
Found at i:39529048 original size:11 final size:11
Alignment explanation
Indices: 39529032--39529063 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
39529022 CTTTAATATT
39529032 CTCTCAAATTC
1 CTCTCAAATTC
39529043 CTCTCAAATTC
1 CTCTCAAATTC
39529054 CTCTCAAATT
1 CTCTCAAATT
39529064 TCTATTTAAA
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:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:39530814 original size:30 final size:30
Alignment explanation
Indices: 39530747--39530814 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
39530737 GACGACGACG
* *
39530747 CAAGCCCATCAACAAGACCCAGACATTCAC
1 CAAGCCCATCAACAACACCCAGACAATCAC
** * * *
39530777 CCGGCCCATCATCATCACCCATACAATCAC
1 CAAGCCCATCAACAACACCCAGACAATCAC
39530807 CAAGCCCA
1 CAAGCCCA
39530815 GCAATAGCAC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.44, G:0.09, T:0.12
Consensus pattern (30 bp):
CAAGCCCATCAACAACACCCAGACAATCAC
Found at i:39533804 original size:25 final size:25
Alignment explanation
Indices: 39533763--39533819 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
39533753 ACAATCCATG
** * *
39533763 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAATCATATAACATT
39533788 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
39533813 TATATCA
1 TAAATCA
39533820 ATTCTTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:39533916 original size:20 final size:19
Alignment explanation
Indices: 39533868--39533917 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
39533858 TAACAGAAAT
*
39533868 TTATCCGTATCAACCGTAA
1 TTATCCATATCAACCGTAA
* *
39533887 CTTATACATATCAACGGTAA
1 -TTATCCATATCAACCGTAA
39533907 TTCATCCATAT
1 TT-ATCCATAT
39533918 AATTACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (19 bp):
TTATCCATATCAACCGTAA
Found at i:39534125 original size:23 final size:23
Alignment explanation
Indices: 39534066--39534157 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 23
39534056 GAGCCATGAT
*
39534066 CGGTAAGCTCATTCCGAGCTGATAAA
1 CGGTAAGCTCA-TACGAGCTG--AAA
* *
39534092 TGGTAAACTC-TATCGAGCTGAAA
1 CGGTAAGCTCATA-CGAGCTGAAA
39534115 CGGTAAGCTCTATA-GAGCTGAAA
1 CGGTAAGCTC-ATACGAGCTGAAA
39534138 CGGTAAGCTCATACGAGCTG
1 CGGTAAGCTCATACGAGCTG
39534158 TGGTGAGTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.05
23 36 0.63
24 1 0.02
25 9 0.16
26 8 0.14
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (23 bp):
CGGTAAGCTCATACGAGCTGAAA
Found at i:39537299 original size:126 final size:126
Alignment explanation
Indices: 39537074--39537364 Score: 501
Period size: 126 Copynumber: 2.3 Consensus size: 126
39537064 CCAAACATGT
* *
39537074 GCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCAT
*
39537139 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTAGTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* *
39537200 GCTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTTTTTCAGTACTTCTGCTGACAAAGCATCAT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCAT
39537265 GCTTAAAGCGTTTTTGACACTAGTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTAGTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* * * *
39537326 GCTACTATAGCAAAAGTGCGTCCACGTGAGAGATTCTTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
39537365 AAATTAACAA
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 154 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (126 bp):
GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCAT
GCTTAAAGCGTTTTTGACACTAGTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
Found at i:39537550 original size:96 final size:95
Alignment explanation
Indices: 39537397--39537677 Score: 322
Period size: 97 Copynumber: 2.9 Consensus size: 95
39537387 AGTAACCCTA
* *
39537397 AACCCCAAACCCTAATTTATTTAAGGTTTTTACTT-AAAACCCTAAACACTAAACCCTAATCTAA
1 AACCCTAAACCCTAATTTATTT--GATTTTT-CTTAAAAACCCTAAACACTAAACCCTAATCTAA
39537461 TTTTATAAAAATTTATAATTAATTTACTCAAGT
63 TTTTATAAAAATTTATAATTAATTTACTCAAGT
* * * *
39537494 AACCGTGAACCCTAATTTATTTGATTTTTCGTTAAAAACCCTTAACTCTAAACCCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTGATTTTTC-TTAAAAACCCTAAACACTAAACCCTAATCTAA-T
* *
39537559 TTTTTAAAAA--T-TAATTAAATTACTCAAGT
64 TTTATAAAAATTTATAATTAATTTACTCAAGT
* ** * *
39537588 AACCCTAAACCCTAATTTAATTGATTTTTTTCTTAAAAAAACAATAAACACGAAA-CCTAATCCA
1 AACCCTAAACCCTAATTTATTTGA--TTTTTCTT--AAAAACCCTAAACACTAAACCCTAATCTA
39537652 ATTTTA-AAAAATTTATAATTAATTTA
62 ATTTTATAAAAATTTATAATTAATTTA
39537678 ATTGACAAAC
Statistics
Matches: 155, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
94 44 0.28
95 15 0.10
96 43 0.28
97 53 0.34
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.37
Consensus pattern (95 bp):
AACCCTAAACCCTAATTTATTTGATTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTT
TATAAAAATTTATAATTAATTTACTCAAGT
Found at i:39539007 original size:18 final size:17
Alignment explanation
Indices: 39538993--39539027 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
39538983 TAGAAAAGTT
39538993 AAAA-AAAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
39539009 AAAAGAAAAAAG-AAAG
1 AAAAGAAAAAAGAAAAG
39539025 AAA
1 AAA
39539028 GGGTTTACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:39539017 original size:16 final size:16
Alignment explanation
Indices: 39538993--39539027 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
39538983 TAGAAAAGTT
39538993 AAAAAAAAAAGAAAAGA
1 AAAAAAAAAAG-AAAGA
*
39539010 AAAGAAAAAAGAAAGA
1 AAAAAAAAAAGAAAGA
39539026 AA
1 AA
39539028 GGGTTTACTG
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAAGA
Found at i:39540563 original size:25 final size:24
Alignment explanation
Indices: 39540535--39540588 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
39540525 TTATTACTTG
*
39540535 AAAATTAAAAATA-TATATAATCTAA
1 AAAATTAAAAAAATTATAT-AT-TAA
39540560 AAAATTAAAAAAATTATATATTAA
1 AAAATTAAAAAAATTATATATTAA
39540584 AAAAT
1 AAAAT
39540589 CGAAGTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.30
25 14 0.52
26 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAATTAAAAAAATTATATATTAA
Done.