Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 56 of 103
Found at i:21383226 original size:110 final size:111
Alignment explanation
Indices: 21383028--21383298 Score: 375
Period size: 110 Copynumber: 2.4 Consensus size: 111
21383018 TACATAACCT
* * * * * *
21383028 TAAAACCTACTGAACAAAAGCCCCTAAACAACACGTGGATTGCACAAGTCACGTGCCACCACTCA
1 TAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTCA
* * * *
21383093 CGCTACAACAAGTAATGCCATATATAAAAACCAGTCACGCA-AGCC
66 CGCTACAACAAATAACGCAATATATAAAAACCAGTCACACACAGCC
21383138 TAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTCT
1 TAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTC-
* * *
21383203 A-GCTACAATAAATAACGCAATATATAAAAACCAGTCACACACTGTC
65 ACGCTACAACAAATAACGCAATATATAAAAACCAGTCACACACAGCC
* *
21383249 TAAAAAACTACTGAACAATAGCCTCAAAGCAACACATGAATTGCACAAGT
1 T-AAAAACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGT
21383299 TAGTCACGCA
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
110 93 0.65
111 4 0.03
112 46 0.32
ACGTcount: A:0.44, C:0.28, G:0.12, T:0.17
Consensus pattern (111 bp):
TAAAAACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTCA
CGCTACAACAAATAACGCAATATATAAAAACCAGTCACACACAGCC
Found at i:21384640 original size:48 final size:46
Alignment explanation
Indices: 21384582--21384739 Score: 157
Period size: 48 Copynumber: 3.5 Consensus size: 46
21384572 ACGGAACGTT
*
21384582 AACAAATATTCAGTCACGTAATGCCTACAAAGAACTCACGTAATGCTC
1 AACAAATATTCAGTCACGTAATG-CTA-AAAGAACTCACGCAATGCTC
** * *
21384630 AACAAATATTCAGTCACGT-AT--TAACTG---TCACGCAACGTTC
1 AACAAATATTCAGTCACGTAATGCTAAAAGAACTCACGCAATGCTC
* *
21384670 AACATATATTCAGTCACGTAATGCTTATATAGAACTCACGCAATGCTC
1 AACAAATATTCAGTCACGTAATGC-TA-AAAGAACTCACGCAATGCTC
* *
21384718 AACAAATATTCAGGCACTTAAT
1 AACAAATATTCAGTCACGTAAT
21384740 ACCAAATAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
40 28 0.31
41 2 0.02
43 2 0.02
44 4 0.04
45 2 0.02
47 2 0.02
48 49 0.55
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (46 bp):
AACAAATATTCAGTCACGTAATGCTAAAAGAACTCACGCAATGCTC
Found at i:21384647 original size:26 final size:25
Alignment explanation
Indices: 21384582--21384649 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 25
21384572 ACGGAACGTT
21384582 AACAAATATTCAGTCACGTAATGCC
1 AACAAATATTCAGTCACGTAATGCC
* * *
21384607 TACAAAGA---ACTCACGTAATGCTC
1 AACAAATATTCAGTCACGTAATGC-C
21384630 AACAAATATTCAGTCACGTA
1 AACAAATATTCAGTCACGTA
21384650 TTAACTGTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
22 12 0.36
23 7 0.21
25 6 0.18
26 8 0.24
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (25 bp):
AACAAATATTCAGTCACGTAATGCC
Found at i:21384709 original size:88 final size:87
Alignment explanation
Indices: 21384567--21384730 Score: 265
Period size: 88 Copynumber: 1.9 Consensus size: 87
21384557 CACGTAACGC
* *
21384567 CTGTCACGGAACGTTAACAAATATTCAGTCACGTAATGCCTACAAAGAACTCACGTAATGCTCAA
1 CTGTCACGCAACGTTAACAAATATTCAGTCACGTAATGCCTACAAAGAACTCACGCAATGCTCAA
21384632 CAAATATTCAGTCACGTATTAA
66 CAAATATTCAGTCACGTATTAA
* * * *
21384654 CTGTCACGCAACGTTCAACATATATTCAGTCACGTAATGCTTATATAGAACTCACGCAATGCTCA
1 CTGTCACGCAACGTT-AACAAATATTCAGTCACGTAATGCCTACAAAGAACTCACGCAATGCTCA
21384719 ACAAATATTCAG
65 ACAAATATTCAG
21384731 GCACTTAATA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 14 0.20
88 56 0.80
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (87 bp):
CTGTCACGCAACGTTAACAAATATTCAGTCACGTAATGCCTACAAAGAACTCACGCAATGCTCAA
CAAATATTCAGTCACGTATTAA
Found at i:21386755 original size:49 final size:45
Alignment explanation
Indices: 21386635--21386769 Score: 121
Period size: 45 Copynumber: 2.9 Consensus size: 45
21386625 ATCCATTAGT
* * * * *
21386635 ATCACGTGTGACAGTGATGGAACTTGTAATTTGATTTAAGAGTTA
1 ATCACGTGTAACAGTGACGAAACTTGTAATTTGATTTAAAAGTAA
* * *
21386680 ATTACGTGTAATAGTGAC-AGAGCTTGTAATTTGATTTCATTAAAGGTAA
1 ATCACGTGTAACAGTGACGA-AACTTGTAATTTGATTT-A--AAA-GTAA
* *
21386729 ATCATGTGTAACAGTGACGAAACTTGTAATTTG-GTTAAAAG
1 ATCACGTGTAACAGTGACGAAACTTGTAATTTGATTTAAAAG
21386770 GTTAATTATC
Statistics
Matches: 71, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
44 1 0.01
45 33 0.46
46 1 0.01
47 1 0.01
48 4 0.06
49 30 0.42
50 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (45 bp):
ATCACGTGTAACAGTGACGAAACTTGTAATTTGATTTAAAAGTAA
Found at i:21389014 original size:25 final size:26
Alignment explanation
Indices: 21388986--21389036 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
21388976 ATTTAAAATA
21388986 TTAAAATATTAAT-ATAA-AAATATTT
1 TTAAAATATTAATGATAATAAA-ATTT
* *
21389011 TTAATATTTTAATGATAATAAAATTT
1 TTAAAATATTAATGATAATAAAATTT
21389037 AAAGGAGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 11 0.50
26 8 0.36
27 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAAAATATTAATGATAATAAAATTT
Found at i:21392922 original size:16 final size:16
Alignment explanation
Indices: 21392898--21392928 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21392888 TTTTTCTCAA
*
21392898 TTTATTTCTTTGTTTC
1 TTTAGTTCTTTGTTTC
21392914 TTTAGTTCTTTGTTT
1 TTTAGTTCTTTGTTT
21392929 AAAGATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.10, T:0.74
Consensus pattern (16 bp):
TTTAGTTCTTTGTTTC
Found at i:21394264 original size:33 final size:30
Alignment explanation
Indices: 21394209--21394283 Score: 80
Period size: 33 Copynumber: 2.4 Consensus size: 30
21394199 TTAGTATTAC
21394209 AATATTAACATATTTAAAATATTATTAT-ATT
1 AATATTAA-ATATTTAAAATATT-TTATAATT
*
21394240 AATATTAAATATTCTTAAATATATTTTTTAATT
1 AATATTAAATA-T-TTAAA-ATATTTTATAATT
*
21394273 AAAATTAAATA
1 AATATTAAATA
21394284 AAGAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 3 0.08
31 9 0.24
32 8 0.21
33 18 0.47
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
AATATTAAATATTTAAAATATTTTATAATT
Found at i:21399462 original size:8 final size:8
Alignment explanation
Indices: 21399449--21399473 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21399439 TAATGTTTGA
21399449 AAAAATTT
1 AAAAATTT
21399457 AAAAATTT
1 AAAAATTT
21399465 AAAAATTT
1 AAAAATTT
21399473 A
1 A
21399474 TTTGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAAATTT
Found at i:21399872 original size:20 final size:22
Alignment explanation
Indices: 21399842--21399891 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
21399832 TAAAAAATAA
*
21399842 AAAAAAATTTAAA-ATTTTTTT
1 AAAATAATTTAAAGATTTTTTT
21399863 -AAATAATTTAAAGATTTTTTT
1 AAAATAATTTAAAGATTTTTTT
21399884 AAAATAAT
1 AAAATAAT
21399892 GTCATTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.42
21 8 0.31
22 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAATAATTTAAAGATTTTTTT
Found at i:21409220 original size:17 final size:17
Alignment explanation
Indices: 21409200--21409235 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
21409190 ATAACTATTA
21409200 AAAAAT-AATAATAAAAT
1 AAAAATAAATAA-AAAAT
21409217 AAAAATAAATAAAAAAT
1 AAAAATAAATAAAAAAT
21409234 AA
1 AA
21409236 GTATTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAATAAATAAAAAAT
Found at i:21411135 original size:39 final size:39
Alignment explanation
Indices: 21411092--21411202 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 39
21411082 TAGGAGACCA
* * * *
21411092 AAACAGAAAGTTTTTCGTTGCAGCGAAATTGTAACCCAG
1 AAACAGAAAGTTTCTCGCTGCAACAAAATTGTAACCCAG
*
21411131 AAACAGAATGTTTCTCGCTGCAACAAAATTGTAACCCAG
1 AAACAGAAAGTTTCTCGCTGCAACAAAATTGTAACCCAG
* * * *
21411170 AAACAAAAAGTTTCTCGCTACAGCAAAAATGTA
1 AAACAGAAAGTTTCTCGCTGCAACAAAATTGTA
21411203 TTTCGCTGCA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (39 bp):
AAACAGAAAGTTTCTCGCTGCAACAAAATTGTAACCCAG
Found at i:21411230 original size:22 final size:21
Alignment explanation
Indices: 21411182--21411234 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21411172 ACAAAAAGTT
* *
21411182 TCTCGCTACAGCAAAAATGTA
1 TCTCGCTGCAGCAAAAATGCA
* *
21411203 TTTCGCTGCAGCGAAAATGCA
1 TCTCGCTGCAGCAAAAATGCA
21411224 TCCTCGCTGCA
1 T-CTCGCTGCA
21411235 ACGAGTTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (21 bp):
TCTCGCTGCAGCAAAAATGCA
Found at i:21411672 original size:43 final size:43
Alignment explanation
Indices: 21411550--21411681 Score: 122
Period size: 43 Copynumber: 3.1 Consensus size: 43
21411540 CCCATCATCA
* * * * *
21411550 TCATCACCAGCTCATGCGCACTCCTTACTCGCACATGGCTGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
* * * * ** *
21411593 CCATCACCGGGTTATGCACACTCACTACTCATACATAACCGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
* *
21411636 TCATC-CTCGGCTTATGCGCATTCCCTACTCGCACATAGCCGAG
1 TCATCAC-CGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
21411679 TCA
1 TCA
21411682 ATATAATTAC
Statistics
Matches: 67, Mismatches: 21, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
42 1 0.01
43 66 0.99
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (43 bp):
TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
Found at i:21416124 original size:88 final size:89
Alignment explanation
Indices: 21415959--21416129 Score: 227
Period size: 88 Copynumber: 1.9 Consensus size: 89
21415949 AAGATTCTTG
* * ** * *
21415959 CTTTTTAACGAGATCAAGCGATAACCCTTACACAATCTTCAAAGGGATTCTTTCTTTTTAAAGGG
1 CTTTTTAACAAGATCAAGCAATAACCCTTACACAATCCACAAAAGGATTCTTGCTTTTTAAAGGG
*
21416024 ATCAAGCAATAACCCTTATATCGA
66 ATCAAACAATAACCCTTATATCGA
* * *
21416048 CTTTTT-ACAAGATCAAGCAATAACCTTTATACAATCCACAAAAGGATTCTTGCTTTTTAATGGG
1 CTTTTTAACAAGATCAAGCAATAACCCTTACACAATCCACAAAAGGATTCTTGCTTTTTAAAGGG
**
21416112 ATCAAATGATAACCCTTA
66 ATCAAACAATAACCCTTA
21416130 CACTAACTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
88 64 0.91
89 6 0.09
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (89 bp):
CTTTTTAACAAGATCAAGCAATAACCCTTACACAATCCACAAAAGGATTCTTGCTTTTTAAAGGG
ATCAAACAATAACCCTTATATCGA
Found at i:21417683 original size:20 final size:21
Alignment explanation
Indices: 21417653--21417699 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
21417643 TTAAATTCCA
*
21417653 GAGAGCTTCCACCAAA-GTATC
1 GAGA-CTTCCACAAAATGTATC
21417674 GAGACTTCCACAAAATGTATC
1 GAGACTTCCACAAAATGTATC
21417695 GAGAC
1 GAGAC
21417700 CTTATCTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
GAGACTTCCACAAAATGTATC
Found at i:21417765 original size:21 final size:21
Alignment explanation
Indices: 21417739--21417792 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
21417729 TCAAGTGTCC
21417739 AAGTATCAAGACCAACTTGCA
1 AAGTATCAAGACCAACTTGCA
21417760 AAGTATCAAGACCAACTTGCA
1 AAGTATCAAGACCAACTTGCA
*
21417781 AAGTATCGAGAC
1 AAGTATCAAGAC
21417793 ATCATTTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (21 bp):
AAGTATCAAGACCAACTTGCA
Found at i:21419011 original size:14 final size:14
Alignment explanation
Indices: 21418992--21419019 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21418982 CTTAGAGAAG
21418992 GTGATTATGATATT
1 GTGATTATGATATT
21419006 GTGATTATGATATT
1 GTGATTATGATATT
21419020 AGCTATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
GTGATTATGATATT
Found at i:21420625 original size:8 final size:9
Alignment explanation
Indices: 21420612--21420705 Score: 61
Period size: 10 Copynumber: 10.3 Consensus size: 9
21420602 TTATGTATCG
21420612 TATTTA-AT
1 TATTTATAT
21420620 TATTTATAT
1 TATTTATAT
*
21420629 TATATATAT
1 TATTTATAT
21420638 ATATATTATAT
1 -TAT-TTATAT
21420649 TA-TTATA-
1 TATTTATAT
*
21420656 TATATATA-
1 TATTTATAT
*
21420664 TATATATAT
1 TATTTATAT
*
21420673 ATATATATAT
1 -TATTTATAT
*
21420683 ATATATATAT
1 -TATTTATAT
*
21420693 ATATATATAT
1 -TATTTATAT
21420703 TAT
1 TAT
21420706 ATGTANAAGT
Statistics
Matches: 77, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
7 2 0.03
8 23 0.30
9 13 0.17
10 34 0.44
11 5 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTTATAT
Found at i:21420636 original size:2 final size:2
Alignment explanation
Indices: 21420624--21420707 Score: 133
Period size: 2 Copynumber: 44.5 Consensus size: 2
21420614 TTTAATTATT
21420624 TA TA T- TA TA TA TA TA TA TA T- TA TA T- TA T- 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
21420662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21420703 TA TA T
1 TA TA T
21420708 GTANAAGTGA
Statistics
Matches: 77, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
1 5 0.06
2 72 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:21421307 original size:20 final size:22
Alignment explanation
Indices: 21421271--21421320 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
21421261 ATACGGAAAG
21421271 ATTTTGAAAACACAATGC-ACTT
1 ATTTT-AAAACACAATGCAACTT
*
21421293 ATTTTAAAA-ACAATGCAATTT
1 ATTTTAAAACACAATGCAACTT
21421314 ATTTTAA
1 ATTTTAA
21421321 TTTCTTGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 14 0.54
22 5 0.19
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (22 bp):
ATTTTAAAACACAATGCAACTT
Found at i:21421647 original size:35 final size:35
Alignment explanation
Indices: 21421575--21421682 Score: 128
Period size: 35 Copynumber: 3.1 Consensus size: 35
21421565 CTTACTCAGT
*** *
21421575 TCATGTGCACTT-CCTACACGCACAAGGCAATAGCA
1 TCATGTGCA-TTCCCTACACGCACATTTCAATATCA
*
21421610 TCATGTGCATTCCCTACACGCACATTTTAATATCA
1 TCATGTGCATTCCCTACACGCACATTTCAATATCA
* * *
21421645 TCATTTGCACTCCCTACACACACATTTCAATATCA
1 TCATGTGCATTCCCTACACGCACATTTCAATATCA
21421680 TCA
1 TCA
21421683 CATGCACTCC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 2 0.03
35 61 0.97
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.29
Consensus pattern (35 bp):
TCATGTGCATTCCCTACACGCACATTTCAATATCA
Found at i:21421689 original size:35 final size:35
Alignment explanation
Indices: 21421615--21421693 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
21421605 TAGCATCATG
* * * **
21421615 TGCATTCCCTACACGCACATTTTAATATCATCATT
1 TGCACTCCCTACACACACATTTCAATATCATCACA
21421650 TGCACTCCCTACACACACATTTCAATATCATCACA
1 TGCACTCCCTACACACACATTTCAATATCATCACA
21421685 TGCACTCCC
1 TGCACTCCC
21421694 GCCCACATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.29, C:0.35, G:0.05, T:0.30
Consensus pattern (35 bp):
TGCACTCCCTACACACACATTTCAATATCATCACA
Found at i:21423323 original size:4 final size:4
Alignment explanation
Indices: 21423314--21423347 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
21423304 TACATAAATG
21423314 TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
21423348 TATATCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:21431320 original size:20 final size:20
Alignment explanation
Indices: 21431263--21431325 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
21431253 TATATACCCA
*
21431263 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
21431282 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
21431302 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
21431322 TCAT
1 TCAT
21431326 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:21431372 original size:43 final size:43
Alignment explanation
Indices: 21431324--21431442 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
21431314 TCACCAGCTC
** *
21431324 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGATT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGATT
*
21431367 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGATT
* * *
21431410 ATGCACACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
21431443 ACATAATTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGATT
Found at i:21434640 original size:192 final size:192
Alignment explanation
Indices: 21434313--21434691 Score: 661
Period size: 192 Copynumber: 2.0 Consensus size: 192
21434303 CTAACAATTC
21434313 GTGTTGATTTAATGATTTCTAAAGGGGGAGTTAATCATTGACATATATGTTTGCATGAATTCTTA
1 GTGTTGATTTAATGATTTCTAAAGGGGGAGTTAATCATTGACATATATGTTTGCATGAATTCTTA
* * *
21434378 CAGTCAAAATTGGTGTCATTAGCACTTGGTATCTTCAACAACAAATTGTGGTGAGATTCCAACAT
66 CAATCAAAATTGGTGTCATTAGCACTTGGTATCTTCAACAACAAATTATGGTGAGAATCCAACAT
21434443 TTGGTGTCCTTCATTATT-GATAATATCCTTTAACACCAAATTGATATTGTGCTTCATTATTG
131 TTGGTGTCCTTCATTATTAG-TAATATCCTTTAACACCAAATTGATATTGTGCTTCATTATTG
* * * *
21434505 GTGTTGATTTAATGATTTCTTAAGGGGGAGTTAATCATTGACATTTATGTTTGTATGAATTCTTT
1 GTGTTGATTTAATGATTTCTAAAGGGGGAGTTAATCATTGACATATATGTTTGCATGAATTCTTA
* *
21434570 CAATCAAAATTGGTGTTATTAGCACTTGGTATCTTTAACAACAAATTATGGTGAGAATCCAACAT
66 CAATCAAAATTGGTGTCATTAGCACTTGGTATCTTCAACAACAAATTATGGTGAGAATCCAACAT
21434635 TTGGTGTCCTTCATTATTAGTAATATCCTTTAACACCAAATTGATATTGTGCTTCAT
131 TTGGTGTCCTTCATTATTAGTAATATCCTTTAACACCAAATTGATATTGTGCTTCAT
21434692 GTAGATATTA
Statistics
Matches: 177, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
192 176 0.99
193 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (192 bp):
GTGTTGATTTAATGATTTCTAAAGGGGGAGTTAATCATTGACATATATGTTTGCATGAATTCTTA
CAATCAAAATTGGTGTCATTAGCACTTGGTATCTTCAACAACAAATTATGGTGAGAATCCAACAT
TTGGTGTCCTTCATTATTAGTAATATCCTTTAACACCAAATTGATATTGTGCTTCATTATTG
Found at i:21435297 original size:63 final size:63
Alignment explanation
Indices: 21435190--21435318 Score: 233
Period size: 63 Copynumber: 2.0 Consensus size: 63
21435180 TTAAAAAAGG
21435190 AATATTTGACCTTGTAACTTTAATCAAGTTTTGAACCTTTCAACTATTGAGTGGGAGTTTTCA
1 AATATTTGACCTTGTAACTTTAATCAAGTTTTGAACCTTTCAACTATTGAGTGGGAGTTTTCA
*
21435253 AATATTTGACCTTGTAGCTTTAATCAAGTTTTGAA-CTTTACAACTATTGAGTGGGAGTTTTCA
1 AATATTTGACCTTGTAACTTTAATCAAGTTTTGAACCTTT-CAACTATTGAGTGGGAGTTTTCA
21435316 AAT
1 AAT
21435319 CCTTCAAAAC
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 4 0.06
63 60 0.94
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (63 bp):
AATATTTGACCTTGTAACTTTAATCAAGTTTTGAACCTTTCAACTATTGAGTGGGAGTTTTCA
Found at i:21435565 original size:21 final size:21
Alignment explanation
Indices: 21435516--21435570 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
21435506 ATCATCAAAA
* * *
21435516 TTACTTCAATAATCTTTGAAC
1 TTACTTGAATGATCCTTGAAC
* *
21435537 TTATTTGAGTGATCCTTGAAC
1 TTACTTGAATGATCCTTGAAC
*
21435558 TTGCTTGAATGAT
1 TTACTTGAATGAT
21435571 TCTTAAAGTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (21 bp):
TTACTTGAATGATCCTTGAAC
Found at i:21436076 original size:14 final size:14
Alignment explanation
Indices: 21436047--21436076 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21436037 CAAAAATTAT
*
21436047 AACTTATAAAATAA
1 AACTTATAAAAAAA
21436061 AACTTATAAAAAAA
1 AACTTATAAAAAAA
21436075 AA
1 AA
21436077 TTTGCCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AACTTATAAAAAAA
Found at i:21440713 original size:23 final size:23
Alignment explanation
Indices: 21440679--21440738 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
21440669 TATACATATA
* *
21440679 CCCATCACCATCATGCAGACAAT
1 CCCATCATCATCATGCACACAAT
* *
21440702 CCCATCATCATCATGCACCCCAT
1 CCCATCATCATCATGCACACAAT
21440725 CCCATCATCATCAT
1 CCCATCATCATCAT
21440739 CACCAGCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.43, G:0.05, T:0.22
Consensus pattern (23 bp):
CCCATCATCATCATGCACACAAT
Found at i:21454283 original size:266 final size:268
Alignment explanation
Indices: 21454008--21454535 Score: 787
Period size: 269 Copynumber: 2.0 Consensus size: 268
21453998 AAAGTAAGAT
* *** *
21454008 AATTGATTGACACTTGTTATTATCAATTGAATTAATTTTTTTATATTTTTTATGTCTAAATTATA
1 AATTGATTGACACTTGTCATTATCAATTGAATTAATTTTTTTATATACCTTATGTCAAAATTATA
* * *
21454073 TTATTTTTTACATTGAATGG-TTTTTTTAACTTTTATTTATTTC-AACAAAAATATTTAAAAATA
66 TTATTTTTTACATTGAAGGGTTTTTTTTAACTTTTATTTATTTCAAAAAAAAATACTTAAAAATA
*
21454136 ATAATTTTTAACTTTTAATATTT-GAAAGATAGATTCATTTAATATTTATCAATTAAAATTTAAT
131 ATAATTTATAACTTTTAATATTTAGAAAG-TAGATTCATTTAATATTTATCAATTAAAATTTAAT
21454200 ATTATTTTCTG-TCAATATTTTTGTATTCTGTATGAACCTAAA-CTCATAGTATTTAGACATCTC
195 ATTATTTTCTGAT-AATATTTTTGTATTCTGTATGAACCTAAATC-CATAGTATTTAGACATCTC
21454263 TTTTTTGAGTC
258 TTTTTTGAGTC
* *
21454274 AATTGATTGATACTTGTCATTCTCAATTGAATTAATTTTTTTATATACCTTATGTCAAAATTATA
1 AATTGATTGACACTTGTCATTATCAATTGAATTAATTTTTTTATATACCTTATGTCAAAATTATA
* *
21454339 TTGTTTTTTACATTGAAGGGTTTTTTTTTTACTTTTATTTATTTCAAAAAAAAATACTTAAAAAT
66 TTATTTTTTACATTGAAGGG-TTTTTTTTAACTTTTATTTATTTCAAAAAAAAATACTTAAAAAT
** **
21454404 AATAATTTATAACTTTTAATATTTAGATTGTAGATTCATTTAATATTTATCAATTGTAATTTAAT
130 AATAATTTATAACTTTTAATATTTAGAAAGTAGATTCATTTAATATTTATCAATTAAAATTTAAT
* * * * *
21454469 ATTATTTTTTGATTATATTTTTTTATTCTGTGTGAACCTAAATCCATAGTATTTAGATATCTCTT
195 ATTATTTTCTGATAATATTTTTGTATTCTGTATGAACCTAAATCCATAGTATTTAGACATCTCTT
21454534 TT
260 TT
21454536 ATACATCTAA
Statistics
Matches: 234, Mismatches: 22, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
266 76 0.32
268 22 0.09
269 131 0.56
270 5 0.02
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.51
Consensus pattern (268 bp):
AATTGATTGACACTTGTCATTATCAATTGAATTAATTTTTTTATATACCTTATGTCAAAATTATA
TTATTTTTTACATTGAAGGGTTTTTTTTAACTTTTATTTATTTCAAAAAAAAATACTTAAAAATA
ATAATTTATAACTTTTAATATTTAGAAAGTAGATTCATTTAATATTTATCAATTAAAATTTAATA
TTATTTTCTGATAATATTTTTGTATTCTGTATGAACCTAAATCCATAGTATTTAGACATCTCTTT
TTTGAGTC
Found at i:21454804 original size:127 final size:127
Alignment explanation
Indices: 21454599--21454854 Score: 377
Period size: 127 Copynumber: 2.0 Consensus size: 127
21454589 AAATCTACCC
* * *
21454599 ATTTCTTAATATACATAACACACAGTCATTATTGAATATACAAATCAATTGAATTTGACAACTTT
1 ATTTCTCAATATACATAACACACAGTCATTATTGAATAAACAAATCAATTGAATTTGACAACCTT
* * * * * *
21454664 TAACTATTTATTTTATATATAAAAGACAGATGCTACTATAAATTAATAATTATTTTATATTG
66 TAACCATTAATTTTATATATAAAAGACAAATACTACAAGAAATTAATAATTATTTTATATTG
* *
21454726 ATTTCTCAATATACATAGCACACGGTCATTATTGAATAAACAAATCAATTGAATTTGACAACCTT
1 ATTTCTCAATATACATAACACACAGTCATTATTGAATAAACAAATCAATTGAATTTGACAACCTT
* * * *
21454791 TAGCCATTAATTTTATATATAAAAGATAAATATTACAAGAAATTAGTAATTATTTTATATTG
66 TAACCATTAATTTTATATATAAAAGACAAATACTACAAGAAATTAATAATTATTTTATATTG
21454853 AT
1 AT
21454855 AAGATCTTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
127 114 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.39
Consensus pattern (127 bp):
ATTTCTCAATATACATAACACACAGTCATTATTGAATAAACAAATCAATTGAATTTGACAACCTT
TAACCATTAATTTTATATATAAAAGACAAATACTACAAGAAATTAATAATTATTTTATATTG
Found at i:21456288 original size:17 final size:17
Alignment explanation
Indices: 21456268--21456311 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
21456258 GAATACTTTA
21456268 TTTAATTTTTCTCTCTT
1 TTTAATTTTTCTCTCTT
* *
21456285 TTTAATTTTT-TTTGTT
1 TTTAATTTTTCTCTCTT
21456301 TTT-ATTTTTCT
1 TTTAATTTTTCT
21456312 TAATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 8 0.33
17 10 0.42
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTAATTTTTCTCTCTT
Found at i:21456326 original size:17 final size:16
Alignment explanation
Indices: 21456266--21456326 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 16
21456256 TTGAATACTT
*
21456266 TATTTAATTTTTCTCTC
1 TATTTAATTTTTCT-TA
* * *
21456283 TTTTTAATTTTTTTTG
1 TATTTAATTTTTCTTA
*
21456299 T-TTTTATTTTTCTTAA
1 TATTTAATTTTTCTT-A
21456315 TATTTAATTTTT
1 TATTTAATTTTT
21456327 TTTACTAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 11 0.31
16 3 0.09
17 21 0.60
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.74
Consensus pattern (16 bp):
TATTTAATTTTTCTTA
Found at i:21460024 original size:26 final size:28
Alignment explanation
Indices: 21459985--21460043 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
21459975 TTCTAACTTA
21459985 GGAAGCACCTAAAGCAT-TT-CAAGCGT
1 GGAAGCACCTAAAGCATGTTCCAAGCGT
**
21460011 GGAAGCA-CTCAAAGGGTGTTCCAAGCGT
1 GGAAGCACCT-AAAGCATGTTCCAAGCGT
21460039 GGAAG
1 GGAAG
21460044 TGCTCTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 2 0.07
26 12 0.43
27 2 0.07
28 12 0.43
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (28 bp):
GGAAGCACCTAAAGCATGTTCCAAGCGT
Found at i:21460103 original size:27 final size:26
Alignment explanation
Indices: 21460041--21460104 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
21460031 CCAAGCGTGG
21460041 AAGTGCTCTAGGGCCTTCCCAGCGCAA
1 AAGTGC-CTAGGGCCTTCCCAGCGCAA
** * * *
21460068 AAGCACCTAGGGACGTTCCCAGTGCGA
1 AAGTGCCTAGGG-CCTTCCCAGCGCAA
21460095 AAGTGCCTAG
1 AAGTGCCTAG
21460105 ATTCCAAGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (26 bp):
AAGTGCCTAGGGCCTTCCCAGCGCAA
Found at i:21465799 original size:21 final size:21
Alignment explanation
Indices: 21465773--21465813 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
21465763 AGAATGAATC
21465773 CACACTAAGAAGTTCAATCCA
1 CACACTAAGAAGTTCAATCCA
21465794 CACACTAAGAAGTTCAATCC
1 CACACTAAGAAGTTCAATCC
21465814 GCATAAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (21 bp):
CACACTAAGAAGTTCAATCCA
Found at i:21468210 original size:3 final size:3
Alignment explanation
Indices: 21468204--21468243 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
21468194 AAATGAAATA
21468204 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21468244 AAACAAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:21495812 original size:38 final size:40
Alignment explanation
Indices: 21495769--21495872 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
21495759 GATAGTGCCC
* * *
21495769 ATGTGCACGATGTGGAGGGATGTACAC-AATG-GCACTGAT
1 ATGTGCACGATGTGGGGGGATGTACACGAAGGTGC-CGGAT
* * *
21495808 -TGTGCAAGATGTGGGGGGATGCACACGAAGGTGCCGGCT
1 ATGTGCACGATGTGGGGGGATGTACACGAAGGTGCCGGAT
21495847 ATGTGCACGATGTGGGGGGATGTACA
1 ATGTGCACGATGTGGGGGGATGTACA
21495873 TGAGCTGGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
38 23 0.43
39 6 0.11
40 25 0.46
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.21
Consensus pattern (40 bp):
ATGTGCACGATGTGGGGGGATGTACACGAAGGTGCCGGAT
Found at i:21495859 original size:40 final size:39
Alignment explanation
Indices: 21495769--21495868 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 39
21495759 GATAGTGCCC
* * * *
21495769 ATGTGCACGATGTGGAGGGATGTACACAATGGCACTGAT
1 ATGTGCACGATGTGGGGGGATGCACACAAGGGCACGGAT
* *
21495808 -TGTGCAAGATGTGGGGGGATGCACACGAAGGTGC-CGGCT
1 ATGTGCACGATGTGGGGGGATGCACAC-AAGG-GCACGGAT
21495847 ATGTGCACGATGTGGGGGGATG
1 ATGTGCACGATGTGGGGGGATG
21495869 TACATGAGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
38 23 0.45
39 6 0.12
40 22 0.43
ACGTcount: A:0.23, C:0.15, G:0.41, T:0.21
Consensus pattern (39 bp):
ATGTGCACGATGTGGGGGGATGCACACAAGGGCACGGAT
Found at i:21499317 original size:54 final size:55
Alignment explanation
Indices: 21499252--21499357 Score: 180
Period size: 54 Copynumber: 1.9 Consensus size: 55
21499242 AAGAACAAAG
21499252 GGAAAAACAAGAAAACCTAGGTGAAAATTCAAA-AAAAA-TGAAGAAATCAANAAA
1 GGAAAAACAAGAAAACCTAGGTGAAAATTCAAAGAAAAAGTGAAGAAATCAA-AAA
*
21499306 GGAAAAACAAGAAAACCTAGGTGGAAATTCAAAGAAAAAGTGAAGAAATCAA
1 GGAAAAACAAGAAAACCTAGGTGAAAATTCAAAGAAAAAGTGAAGAAATCAA
21499358 GGAAACAAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
54 32 0.65
55 5 0.10
56 12 0.24
ACGTcount: A:0.60, C:0.09, G:0.18, T:0.11
Consensus pattern (55 bp):
GGAAAAACAAGAAAACCTAGGTGAAAATTCAAAGAAAAAGTGAAGAAATCAAAAA
Found at i:21500489 original size:43 final size:43
Alignment explanation
Indices: 21500324--21500476 Score: 209
Period size: 43 Copynumber: 3.6 Consensus size: 43
21500314 TTGACTCGGC
* *
21500324 TATGTGCGAGTAGGGATTGCGCATAAGCCGAG-GATGACCCGAT
1 TATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGATGACCCGAT
* * *
21500367 TATGTGCGAGTAGGGAGTGCACATAACCCGGTGATGACCTGGT
1 TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCGAT
* * *
21500410 TATGTGCGAGTAGGGAGTGTGCATAACCCGGTGATGACCCAAC
1 TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCGAT
*
21500453 CATGTGCGAGTAGGGAGTGCGCAT
1 TATGTGCGAGTAGGGAGTGCGCAT
21500477 GAGCTGGTGA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 1 0.01
43 95 0.99
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (43 bp):
TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCGAT
Found at i:21500500 original size:20 final size:20
Alignment explanation
Indices: 21500475--21500517 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
21500465 GGGAGTGCGC
21500475 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
21500495 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
21500515 ATG
1 ATG
21500518 GGTTGTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.40, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:21504041 original size:2 final size:2
Alignment explanation
Indices: 21504036--21504074 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21504026 ACTTATTTTT
21504036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21504075 CTACCTTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21510218 original size:35 final size:35
Alignment explanation
Indices: 21510088--21510225 Score: 108
Period size: 35 Copynumber: 4.0 Consensus size: 35
21510078 TTCAGCCAAG
* * *
21510088 CTTTTACAATG-TCTTTTCACAA-ACTCAGCCATAAC
1 CTTTAACAATGAT-TTTTCACAAGA-TCAACCAAAAC
**
21510123 CTTTAACAATGATTTTTCACGGGATCAACCAAAAC
1 CTTTAACAATGATTTTTCACAAGATCAACCAAAAC
* * * * *
21510158 C--CAA-AATGACTTTCCA-AAGGCTCAACCACAAC
1 CTTTAACAATGATTTTTCACAA-GATCAACCAAAAC
*
21510190 CTTTAACAATGGTTTTTCACAAGATCAACCAAAAC
1 CTTTAACAATGATTTTTCACAAGATCAACCAAAAC
21510225 C
1 C
21510226 CAAAAACTAA
Statistics
Matches: 78, Mismatches: 18, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
32 22 0.28
33 2 0.03
34 2 0.03
35 48 0.62
36 4 0.05
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.27
Consensus pattern (35 bp):
CTTTAACAATGATTTTTCACAAGATCAACCAAAAC
Found at i:21510800 original size:74 final size:73
Alignment explanation
Indices: 21510616--21510818 Score: 203
Period size: 74 Copynumber: 2.8 Consensus size: 73
21510606 CTGGCAGTGT
* * * * * ** * * *
21510616 GCTCTTAGTCAACTAAC-ATACGTCTTATTCGATTAAGTCGCCTCTATCTTTTAACCCAAATTTT
1 GCTCTTAGTCGACTAACAATCCTTCTTAGTCGACTAAGTCTTCTCTGTCTTGTAATCCAAATTTT
*
21510680 GGCAGTAA
66 GGCAATAA
* * *
21510688 GCTCTTAGTCGACTAACAATGCTTCTTAGTTGATTAAGTTCTT-TCTGTCTTGTAATCCAAATTT
1 GCTCTTAGTCGACTAACAATCCTTCTTAGTCGACTAAG-TCTTCTCTGTCTTGTAATCCAAATTT
*
21510752 CTGGCAATAG
65 -TGGCAATAA
* * * *
21510762 GCTCTTAGTCGACTAACCATCCTTCTTGGTCGACTAAGTCTTCTCTGTTTTGCAATC
1 GCTCTTAGTCGACTAACAATCCTTCTTAGTCGACTAAGTCTTCTCTGTCTTGTAATC
21510819 TGCTCTTGAA
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
72 16 0.15
73 38 0.35
74 54 0.50
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (73 bp):
GCTCTTAGTCGACTAACAATCCTTCTTAGTCGACTAAGTCTTCTCTGTCTTGTAATCCAAATTTT
GGCAATAA
Found at i:21519317 original size:23 final size:23
Alignment explanation
Indices: 21519291--21519345 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
21519281 TCACTCTCAG
21519291 TCCTTTCTTTCTCTCTTT-TTCTT
1 TCCTTTCTTTCTC-CTTTCTTCTT
*
21519314 TCCTTTCTTTCTCCTTTCTTTTT
1 TCCTTTCTTTCTCCTTTCTTCTT
*
21519337 TCTTTTCTT
1 TCCTTTCTT
21519346 CTTAGCTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (23 bp):
TCCTTTCTTTCTCCTTTCTTCTT
Found at i:21526457 original size:35 final size:35
Alignment explanation
Indices: 21526410--21526542 Score: 119
Period size: 35 Copynumber: 3.9 Consensus size: 35
21526400 CCAAAATTTT
*
21526410 ACAATGGCTTTTCACAGGCTCAGCCACAACCTTTA
1 ACAATGGCTTTTCACAGGCTCAACCACAACCTTTA
* ** * * *
21526445 ACAATGGTTTTTCATGGGATCAACCAAAACC--CA
1 ACAATGGCTTTTCACAGGCTCAACCACAACCTTTA
* *
21526478 A-AATGGCTTTTCAAAGACTCAACCACAACCTTTA
1 ACAATGGCTTTTCACAGGCTCAACCACAACCTTTA
** * * *
21526512 ACAATGATTTTTCACGGGATCAACCAAAACC
1 ACAATGGCTTTTCACAGGCTCAACCACAACC
21526543 CAAAAACTAA
Statistics
Matches: 74, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
32 23 0.31
33 2 0.03
34 2 0.03
35 47 0.64
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (35 bp):
ACAATGGCTTTTCACAGGCTCAACCACAACCTTTA
Found at i:21526489 original size:32 final size:31
Alignment explanation
Indices: 21526447--21526547 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 31
21526437 AACCTTTAAC
21526447 AATGGTTTTTCATGGGATCAACCAAAACCCAA
1 AATGGTTTTTCA-GGGATCAACCAAAACCCAA
* ** * *
21526479 AATGGCTTTTCAAAGACTCAACCACAACCTTTAA
1 AATGGTTTTTCAGGGA-TCAACCAAAACC--CAA
*
21526513 CAATGATTTTTCACGGGATCAACCAAAACCCAA
1 -AATGGTTTTTCA-GGGATCAACCAAAACCCAA
21526546 AA
1 AA
21526548 ACTAACTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
31 2 0.04
32 24 0.45
33 2 0.04
34 2 0.04
35 21 0.40
36 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.24
Consensus pattern (31 bp):
AATGGTTTTTCAGGGATCAACCAAAACCCAA
Found at i:21526508 original size:67 final size:67
Alignment explanation
Indices: 21526412--21526547 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 67
21526402 AAAATTTTAC
* * * * *
21526412 AATGGCTTTTCACAGGCTCAGCCACAACCTTTAACAATGGTTTTTCATGGGATCAACCAAAACCC
1 AATGGCTTTTCAAAGACTCAACCACAACCTTTAACAATGATTTTTCACGGGATCAACCAAAACCC
21526477 AA
66 AA
21526479 AATGGCTTTTCAAAGACTCAACCACAACCTTTAACAATGATTTTTCACGGGATCAACCAAAACCC
1 AATGGCTTTTCAAAGACTCAACCACAACCTTTAACAATGATTTTTCACGGGATCAACCAAAACCC
21526544 AA
66 AA
21526546 AA
1 AA
21526548 ACTAACTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.24
Consensus pattern (67 bp):
AATGGCTTTTCAAAGACTCAACCACAACCTTTAACAATGATTTTTCACGGGATCAACCAAAACCC
AA
Found at i:21535073 original size:19 final size:19
Alignment explanation
Indices: 21535049--21535147 Score: 56
Period size: 19 Copynumber: 5.1 Consensus size: 19
21535039 TGCCCGTGTG
21535049 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
21535068 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
* * *
21535087 CACGATATGGAGGGATGCA
1 CACGATGTGGGGGGATGTA
* ** *
21535106 CACGATGGTGTCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
21535127 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
21535146 CA
1 CA
21535148 TGAGTCGATG
Statistics
Matches: 54, Mismatches: 22, Indels: 8
0.64 0.26 0.10
Matches are distributed among these distances:
18 3 0.06
19 32 0.59
20 9 0.17
21 10 0.19
ACGTcount: A:0.22, C:0.16, G:0.39, T:0.22
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:21535087 original size:38 final size:40
Alignment explanation
Indices: 21535045--21535147 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 40
21535035 ATAGTGCCCG
*
21535045 TGTGCACGATGTGGGGGGATGTACACGATGG-CACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTCACGGATA
* * * ** *
21535083 TGTGCACGATATGGAGGGATGCACACGATGGTGTCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTCACGGATA
21535123 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
21535148 TGAGTCGATG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 28 0.53
39 3 0.06
40 22 0.42
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTCACGGATA
Found at i:21552343 original size:9 final size:9
Alignment explanation
Indices: 21552329--21552362 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
21552319 TCTCCAACAG
21552329 CTTCTTCTC
1 CTTCTTCTC
21552338 CTTCTTCTC
1 CTTCTTCTC
*
21552347 CTTCTTCTT
1 CTTCTTCTC
21552356 CTTCTTC
1 CTTCTTC
21552363 CATCTCACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (9 bp):
CTTCTTCTC
Found at i:21552344 original size:3 final size:3
Alignment explanation
Indices: 21552329--21552362 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
21552319 TCTCCAACAG
* *
21552329 CTT CTT CTC CTT CTT CTC CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
21552363 CATCTCACGT
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:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (3 bp):
CTT
Found at i:21566591 original size:36 final size:36
Alignment explanation
Indices: 21566548--21566655 Score: 134
Period size: 35 Copynumber: 3.0 Consensus size: 36
21566538 TCTCACTAGC
21566548 TCATGTGCACTCCCACACCGCACATA-GCTAGA-ATCA
1 TCATGTGCACTCCCACACCGCACATAGGC-A-ATATCA
* *
21566584 TCCTGTGCACTCCCACACCGCACA-AGGCAATTTCA
1 TCATGTGCACTCCCACACCGCACATAGGCAATATCA
*
21566619 TCATGTGCACTCCCACATCGCACAT-GGCATATATCA
1 TCATGTGCACTCCCACACCGCACATAGGCA-ATATCA
21566655 T
1 T
21566656 TAGTGTGTGC
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
34 1 0.02
35 31 0.49
36 31 0.49
ACGTcount: A:0.28, C:0.36, G:0.14, T:0.22
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACATAGGCAATATCA
Found at i:21570696 original size:25 final size:25
Alignment explanation
Indices: 21570668--21570722 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
21570658 GGACTTCTCT
*
21570668 CATTTCTTT-TTAATTGGGTCATGCC
1 CATTTCTTTCTT-ATTGGGCCATGCC
*
21570693 CA-TTCTTTCCTTATTGGGCCATGTC
1 CATTTCTTT-CTTATTGGGCCATGCC
21570718 CATTT
1 CATTT
21570723 GTATGCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 6 0.24
25 15 0.60
26 4 0.16
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (25 bp):
CATTTCTTTCTTATTGGGCCATGCC
Found at i:21570749 original size:5 final size:5
Alignment explanation
Indices: 21570739--21570788 Score: 82
Period size: 5 Copynumber: 9.8 Consensus size: 5
21570729 ATATATATAT
*
21570739 TTTTC TTTTC TTTTC TCTTC TTTTC TTTTC TTTTC TTTTC TTTCTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC TTTT
21570789 TCTCTTCCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:21572940 original size:2 final size:2
Alignment explanation
Indices: 21572933--21572957 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21572923 AGTAAATTCC
21572933 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
21572958 AATTATCGAC
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:21580014 original size:25 final size:25
Alignment explanation
Indices: 21579960--21580032 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 25
21579950 TAATATCTTA
* *
21579960 AATAAATTATAAAAAATTAATATTT
1 AATAAATTATAAAAAACTATTATTT
*
21579985 TATAAATTACTAAAAAACTATTA-TT
1 AATAAATTA-TAAAAAACTATTATTT
*
21580010 AATAAATTATAATGAAACTATTA
1 AATAAATTATAA-AAAACTATTA
21580033 AAAATATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 3 0.07
25 27 0.66
26 11 0.27
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (25 bp):
AATAAATTATAAAAAACTATTATTT
Found at i:21580038 original size:25 final size:25
Alignment explanation
Indices: 21579986--21580043 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
21579976 TTAATATTTT
**
21579986 ATAAATTACTAAAAAACTATTATTA
1 ATAAATTACTAAAAAACTATTAAAA
*
21580011 ATAAATTA-TAATGAAACTATTAAAA
1 ATAAATTACTAA-AAAACTATTAAAA
*
21580036 ATATATTA
1 ATAAATTA
21580044 AAAATTTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 3 0.11
25 25 0.89
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAAATTACTAAAAAACTATTAAAA
Found at i:21580257 original size:22 final size:22
Alignment explanation
Indices: 21580219--21580279 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
21580209 TGTAAAAATG
*
21580219 AATTATTAATACATTTTTATTAAA
1 AATTATT-A-ACATTTTAATTAAA
*
21580243 AATTATTAACATTTTAATTATA
1 AATTATTAACATTTTAATTAAA
* *
21580265 TATTATTAATATTTT
1 AATTATTAACATTTT
21580280 CAAAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 25 0.76
23 1 0.03
24 7 0.21
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTATTAACATTTTAATTAAA
Found at i:21586561 original size:20 final size:20
Alignment explanation
Indices: 21586536--21586582 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
21586526 TTCAATCAAA
21586536 TTATATAAAATTTGAGTATC
1 TTATATAAAATTTGAGTATC
* *
21586556 TTATATTCAAATTTGGGTATC
1 TTATA-TAAAATTTGAGTATC
21586577 TTATAT
1 TTATAT
21586583 TCGAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (20 bp):
TTATATAAAATTTGAGTATC
Found at i:21586569 original size:21 final size:21
Alignment explanation
Indices: 21586543--21586592 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
21586533 AAATTATATA
21586543 AAATTTGAGTATCTTATATTC
1 AAATTTGAGTATCTTATATTC
*
21586564 AAATTTGGGTATCTTATATTC
1 AAATTTGAGTATCTTATATTC
*
21586585 GAATTTGA
1 AAATTTGA
21586593 TATGGATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (21 bp):
AAATTTGAGTATCTTATATTC
Found at i:21589538 original size:17 final size:18
Alignment explanation
Indices: 21589516--21589550 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
21589506 GCGAAACTTA
*
21589516 AAAAATTTTAA-AAAATT
1 AAAAATTTGAATAAAATT
21589533 AAAAATTTGAATAAAATT
1 AAAAATTTGAATAAAATT
21589551 GAATGAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAAATTTGAATAAAATT
Found at i:21601611 original size:25 final size:26
Alignment explanation
Indices: 21601537--21601612 Score: 129
Period size: 25 Copynumber: 3.0 Consensus size: 26
21601527 ACCCGTTTCT
*
21601537 TTTTTTGCTTTCTCACCCAAGATC-C
1 TTTTTTGCTCTCTCACCCAAGATCTC
21601562 TTTTTTGCTCTCTCACCCAAGATCTC
1 TTTTTTGCTCTCTCACCCAAGATCTC
21601588 -TTTTTGCTCTCTCACCCAAGATCTC
1 TTTTTTGCTCTCTCACCCAAGATCTC
21601613 CCCCTTCCTC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 48 0.98
26 1 0.02
ACGTcount: A:0.16, C:0.34, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTTTTGCTCTCTCACCCAAGATCTC
Found at i:21603479 original size:52 final size:52
Alignment explanation
Indices: 21603329--21603465 Score: 274
Period size: 52 Copynumber: 2.6 Consensus size: 52
21603319 TGAAAAGAAC
21603329 AAATAATAAATCAAGGTAAAATATTTTCCTAAGTCAAATGCTAGCAAAACAT
1 AAATAATAAATCAAGGTAAAATATTTTCCTAAGTCAAATGCTAGCAAAACAT
21603381 AAATAATAAATCAAGGTAAAATATTTTCCTAAGTCAAATGCTAGCAAAACAT
1 AAATAATAAATCAAGGTAAAATATTTTCCTAAGTCAAATGCTAGCAAAACAT
21603433 AAATAATAAATCAAGGTAAAATATTTTCCTAAG
1 AAATAATAAATCAAGGTAAAATATTTTCCTAAG
21603466 CTAAATATAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 85 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.28
Consensus pattern (52 bp):
AAATAATAAATCAAGGTAAAATATTTTCCTAAGTCAAATGCTAGCAAAACAT
Found at i:21603653 original size:35 final size:33
Alignment explanation
Indices: 21603614--21603698 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 33
21603604 CTTTTTATGG
*
21603614 GATCAAGCGAAACCTTCACAATAATTTTTTCACAA
1 GATCAAGCGAAACCTT-ACAA-AACTTTTTCACAA
* *
21603649 GATCAAGTGAAACCCTTATAAAACTTTTTCACAA
1 GATCAAGCGAAA-CCTTACAAAACTTTTTCACAA
21603683 GATCAAGCGAAACCTT
1 GATCAAGCGAAACCTT
21603699 TCAACAATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.09
34 23 0.51
35 14 0.31
36 4 0.09
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (33 bp):
GATCAAGCGAAACCTTACAAAACTTTTTCACAA
Found at i:21605047 original size:19 final size:19
Alignment explanation
Indices: 21605009--21605051 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
21604999 AAATTTAAAT
21605009 TTTTTTATTATGTTAATAA
1 TTTTTTATTATGTTAATAA
21605028 TATTTTTA-TAT-TTAATTAA
1 T-TTTTTATTATGTTAA-TAA
21605047 TTTTT
1 TTTTT
21605052 ATAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.36
19 8 0.36
20 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTATTATGTTAATAA
Found at i:21605049 original size:17 final size:18
Alignment explanation
Indices: 21605010--21605065 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
21605000 AATTTAAATT
21605010 TTTTTATTATGTTAATAATA
1 TTTTTA-TAT-TTAATAATA
*
21605030 TTTTTATATTTAATTA-A
1 TTTTTATATTTAATAATA
* *
21605047 TTTTTATAATTAAAAATA
1 TTTTTATATTTAATAATA
21605065 T
1 T
21605066 GATTTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 14 0.45
18 8 0.26
19 3 0.10
20 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTTATATTTAATAATA
Found at i:21618980 original size:20 final size:20
Alignment explanation
Indices: 21618951--21618990 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21618941 GTTTTAGGAC
* *
21618951 TAATAGCAAAAATGTTGACT
1 TAATAACAAAAATATTGACT
21618971 TAATAACAAAAATATTGACT
1 TAATAACAAAAATATTGACT
21618991 GAATTAAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
TAATAACAAAAATATTGACT
Found at i:21619606 original size:4 final size:4
Alignment explanation
Indices: 21619599--21619673 Score: 87
Period size: 4 Copynumber: 18.8 Consensus size: 4
21619589 ACATACATAC
* * *
21619599 TATA TATA TATA TATA TATA TATA TATA TATG TATG TATA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
21619647 TATG TATG TATG TATA TATG TATA TAT
1 TATA TATA TATA TATA TATA TATA TAT
21619674 GTATGCATGT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:21619616 original size:12 final size:12
Alignment explanation
Indices: 21619599--21619705 Score: 124
Period size: 12 Copynumber: 8.9 Consensus size: 12
21619589 ACATACATAC
*
21619599 TATATATATATA
1 TATATATGTATA
*
21619611 TATATATATATA
1 TATATATGTATA
*
21619623 TATATATGTATG
1 TATATATGTATA
21619635 TATATATGTATA
1 TATATATGTATA
* *
21619647 TATGTATGTATG
1 TATATATGTATA
21619659 TATATATGTATA
1 TATATATGTATA
* * *
21619671 TATGTATGCATG
1 TATATATGTATA
*
21619683 TATATATGCATA
1 TATATATGTATA
*
21619695 TATGTATGTAT
1 TATATATGTAT
21619706 GTATGTACAT
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 81 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (12 bp):
TATATATGTATA
Found at i:21619638 original size:24 final size:24
Alignment explanation
Indices: 21619611--21619709 Score: 162
Period size: 24 Copynumber: 4.1 Consensus size: 24
21619601 TATATATATA
* *
21619611 TATATATATATATATATATGTATG
1 TATATATGTATATATGTATGTATG
21619635 TATATATGTATATATGTATGTATG
1 TATATATGTATATATGTATGTATG
*
21619659 TATATATGTATATATGTATGCATG
1 TATATATGTATATATGTATGTATG
*
21619683 TATATATGCATATATGTATGTATG
1 TATATATGTATATATGTATGTATG
21619707 TAT
1 TAT
21619710 GTACATTGTG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.48
Consensus pattern (24 bp):
TATATATGTATATATGTATGTATG
Found at i:21619712 original size:8 final size:8
Alignment explanation
Indices: 21619603--21619709 Score: 133
Period size: 8 Copynumber: 13.4 Consensus size: 8
21619593 ACATACTATA
*
21619603 TATATATA
1 TATATATG
*
21619611 TATATATA
1 TATATATG
*
21619619 TATATATA
1 TATATATG
*
21619627 TATGTATG
1 TATATATG
21619635 TATATATG
1 TATATATG
21619643 TATATATG
1 TATATATG
*
21619651 TATGTATG
1 TATATATG
21619659 TATATATG
1 TATATATG
21619667 TATATATG
1 TATATATG
**
21619675 TATGCATG
1 TATATATG
21619683 TATATATG
1 TATATATG
*
21619691 CATATATG
1 TATATATG
*
21619699 TATGTATG
1 TATATATG
21619707 TAT
1 TAT
21619710 GTACATTGTG
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 87 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (8 bp):
TATATATG
Found at i:21625848 original size:63 final size:62
Alignment explanation
Indices: 21625781--21625948 Score: 147
Period size: 73 Copynumber: 2.5 Consensus size: 62
21625771 ATACAGAACC
21625781 TACTGAAAGAAAAGAGAATCGATATCTTGAGAAACAGAAGTCGATTCCTAAAGATACCAAAGA
1 TACTGAAAGAAAA-AGAATCGATATCTTGAGAAACAGAAGTCGATTCCTAAAGATACCAAAGA
* * * *
21625844 TACTGGAAAAGAACATAATTGATATCTTGAGATTTTTGAGAAAATATAAGTCGATTCCTAAAGAT
1 TACT-G-AAAGAA-A-AA--GA-ATC--GATA-TCTTGAG-AAACAGAAGTCGATTCCTAAAGAT
21625909 ACCAAAGA
55 ACCAAAGA
* * * *
21625917 TACTGGAAGAGAACATAATTGATATCTTGAGA
1 TACTGAAAGA-AAAAGAATCGATATCTTGAGA
21625949 TTTTTGAGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
63 5 0.06
64 7 0.08
65 9 0.11
66 2 0.02
67 3 0.04
68 3 0.04
69 3 0.04
70 1 0.01
71 8 0.10
72 8 0.10
73 34 0.41
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (62 bp):
TACTGAAAGAAAAAGAATCGATATCTTGAGAAACAGAAGTCGATTCCTAAAGATACCAAAGA
Found at i:21625905 original size:73 final size:73
Alignment explanation
Indices: 21625818--21625960 Score: 277
Period size: 73 Copynumber: 2.0 Consensus size: 73
21625808 TGAGAAACAG
21625818 AAGTCGATTCCTAAAGATACCAAAGATACTGGAAAAGAACATAATTGATATCTTGAGATTTTTGA
1 AAGTCGATTCCTAAAGATACCAAAGATACTGGAAAAGAACATAATTGATATCTTGAGATTTTTGA
21625883 GAAAATAT
66 GAAAATAT
*
21625891 AAGTCGATTCCTAAAGATACCAAAGATACTGGAAGAGAACATAATTGATATCTTGAGATTTTTGA
1 AAGTCGATTCCTAAAGATACCAAAGATACTGGAAAAGAACATAATTGATATCTTGAGATTTTTGA
21625956 GAAAA
66 GAAAA
21625961 CAGAAACAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (73 bp):
AAGTCGATTCCTAAAGATACCAAAGATACTGGAAAAGAACATAATTGATATCTTGAGATTTTTGA
GAAAATAT
Found at i:21626735 original size:31 final size:31
Alignment explanation
Indices: 21626697--21626861 Score: 149
Period size: 31 Copynumber: 5.4 Consensus size: 31
21626687 TCTAAAAAAA
*
21626697 AAAAGGTAGTGTAATGG-TATTCCTCCATTGT
1 AAAAGGTAGTGTAA-GGTTATACCTCCATTGT
* *
21626728 AAAAGGTAGTGTTAGGTTATACCTCCACTGT
1 AAAAGGTAGTGTAAGGTTATACCTCCATTGT
* *
21626759 AAAAGGTAGTGTAAGGTTATACCTTCATTGC
1 AAAAGGTAGTGTAAGGTTATACCTCCATTGT
* * * * * *
21626790 AAAAAGTAATATAATGTTATATCTCCATAG-
1 AAAAGGTAGTGTAAGGTTATACCTCCATTGT
* * **
21626820 AAAAGGTAGAT-AAAAGTTATACCTCCA-TAA
1 AAAAGGTAG-TGTAAGGTTATACCTCCATTGT
21626850 AAAAGGTAGTGT
1 AAAAGGTAGTGT
21626862 GTTAAAGGTT
Statistics
Matches: 108, Mismatches: 22, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
29 1 0.01
30 31 0.29
31 76 0.70
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (31 bp):
AAAAGGTAGTGTAAGGTTATACCTCCATTGT
Found at i:21633098 original size:54 final size:54
Alignment explanation
Indices: 21633022--21633232 Score: 318
Period size: 54 Copynumber: 3.9 Consensus size: 54
21633012 TATATCAGCA
* * *
21633022 CATCTCATCCAGCTCATGTGCATCCCACCACATTGTGCACATAGCCGGACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
*
21633076 CATCTCACCCAGCTCATGTGCATCCC-CCAACATCGTGCACATAGCCGGACATCC
1 CATCTCACCCAACTCATGTGCATCCCACC-ACATCGTGCACATAGCCGGACATCC
* *
21633130 CATCTCTCCCAACTCATGTGCATCCCACCACATCGTACACATAGCCGGACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* *
21633184 C-TCCTCACCCAACTCATGTGCATCCCACTACATCGTGCACATAACCGGA
1 CAT-CTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGA
21633233 TAGTATCACC
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
53 3 0.02
54 140 0.97
55 2 0.01
ACGTcount: A:0.25, C:0.41, G:0.13, T:0.20
Consensus pattern (54 bp):
CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
Found at i:21633347 original size:2 final size:2
Alignment explanation
Indices: 21633340--21633389 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
21633330 TATGACATAG
21633340 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
21633382 TA TA TA TA
1 TA TA TA TA
21633390 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21637664 original size:54 final size:54
Alignment explanation
Indices: 21637604--21637762 Score: 291
Period size: 54 Copynumber: 2.9 Consensus size: 54
21637594 ATGGTGATAT
* *
21637604 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGGTGGGA
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
21637658 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
*
21637712 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGATGAGATG
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
21637763 CGGTGATATA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 102 1.00
ACGTcount: A:0.18, C:0.14, G:0.42, T:0.25
Consensus pattern (54 bp):
TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
Found at i:21640711 original size:2 final size:2
Alignment explanation
Indices: 21640699--21640731 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
21640689 TGCAACAAGG
21640699 AT AT A- 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
21640732 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21640736 original size:2 final size:2
Alignment explanation
Indices: 21640731--21640767 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21640721 TATATATATA
21640731 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
21640768 AGTAGTANTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:21640817 original size:2 final size:2
Alignment explanation
Indices: 21640805--21640837 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
21640795 TGCAACAAGG
21640805 AT AT A- 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
21640838 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21640842 original size:2 final size:2
Alignment explanation
Indices: 21640837--21640873 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21640827 TATATATATA
21640837 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
21640874 TAGAGGTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:21640855 original size:106 final size:105
Alignment explanation
Indices: 21640670--21640873 Score: 399
Period size: 106 Copynumber: 1.9 Consensus size: 105
21640660 AAGTTTTAAG
21640670 TGACTCATTAAGGTCAAAATGCAACAAGGATATAATATATATATATATATATATATATATATGTG
1 TGACTCATTAAGGTCAAAATGCAACAAGGATATAATATATATATATATATATATATATATATGTG
21640735 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGTAGTA
66 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGTAGTA
21640775 NTGACTCATTAAGGTCAAAATGCAACAAGGATATAATATATATATATATATATATATATATATGT
1 -TGACTCATTAAGGTCAAAATGCAACAAGGATATAATATATATATATATATATATATATATATGT
21640840 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
65 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
21640874 TAGAGGTATG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (105 bp):
TGACTCATTAAGGTCAAAATGCAACAAGGATATAATATATATATATATATATATATATATATGTG
TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGTAGTA
Found at i:21643851 original size:42 final size:41
Alignment explanation
Indices: 21643792--21643910 Score: 157
Period size: 42 Copynumber: 2.9 Consensus size: 41
21643782 TATTGACCAG
* * *
21643792 GCTATGTGCAAGTGGGAGTGCATATAAGCCGTTGCTGACTCA
1 GCTATGTGCAAGTGGGAGTGCACATAAGCCATTGCTAACT-A
*
21643834 GCTATGTGCAAGTGGGAGTGCACATAAGCCATTGCTAACTT
1 GCTATGTGCAAGTGGGAGTGCACATAAGCCATTGCTAACTA
* * *
21643875 GACTATGTGCGAGTGGGAGTGCGCATATGCCATTGC
1 G-CTATGTGCAAGTGGGAGTGCACATAAGCCATTGC
21643911 ATATGAGATG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 68 0.99
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (41 bp):
GCTATGTGCAAGTGGGAGTGCACATAAGCCATTGCTAACTA
Found at i:21643958 original size:2 final size:2
Alignment explanation
Indices: 21643951--21643995 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
21643941 ATGATGAGTG
21643951 AT AT AT AT 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 AT
21643993 AT A
1 AT A
21643996 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21645427 original size:15 final size:15
Alignment explanation
Indices: 21645409--21645437 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21645399 AGCTGTCCAT
21645409 GAGAAAAAAAATGAA
1 GAGAAAAAAAATGAA
21645424 GAGAAAAAAAATGA
1 GAGAAAAAAAATGA
21645438 GAAAATAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (15 bp):
GAGAAAAAAAATGAA
Found at i:21645753 original size:18 final size:18
Alignment explanation
Indices: 21645701--21645766 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
21645691 GCCAAGTTGG
21645701 TAAGAAAGAATGAGATAAAGA
1 TAAGAAAGAA-GA-A-AAAGA
21645722 T--GAAAGATAG-AAAAGA
1 TAAGAAAGA-AGAAAAAGA
*
21645738 TAAGAAAGAAGAAAAAAA
1 TAAGAAAGAAGAAAAAGA
*
21645756 AAAGAAAGAAG
1 TAAGAAAGAAG
21645767 CAAAGTCGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 6 0.15
17 3 0.08
18 21 0.54
19 7 0.18
20 1 0.03
21 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (18 bp):
TAAGAAAGAAGAAAAAGA
Found at i:21645972 original size:35 final size:34
Alignment explanation
Indices: 21645933--21646041 Score: 164
Period size: 35 Copynumber: 3.1 Consensus size: 34
21645923 TGTTCAGCAC
* *
21645933 AATTTTTAGAAGGAAATAGGAAGTGTTTGGCTGTA
1 AATTTTTA-AAGGAAATAGGAAGAGTTTTGCTGTA
21645968 AATTTTTAAGAGGAAATAGGAAGAGTTTTGCTGTA
1 AATTTTTAA-AGGAAATAGGAAGAGTTTTGCTGTA
* *
21646003 AATTTTGAAAGGAAATAGAAAGAGTTTTGCTGTA
1 AATTTTTAAAGGAAATAGGAAGAGTTTTGCTGTA
21646037 AATTT
1 AATTT
21646042 GAAAGAGAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 30 0.43
35 39 0.57
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (34 bp):
AATTTTTAAAGGAAATAGGAAGAGTTTTGCTGTA
Found at i:21646067 original size:33 final size:34
Alignment explanation
Indices: 21645962--21646068 Score: 103
Period size: 34 Copynumber: 3.1 Consensus size: 34
21645952 GAAGTGTTTG
* * **
21645962 GCTGTAAATTTTTAAGAGGAAATAGGAAGAGTTTT
1 GCTGTAAATTTTGAA-AGGAAATAGAAAGAGTAGT
**
21645997 GCTGTAAATTTTGAAAGGAAATAGAAAGAGTTTT
1 GCTGTAAATTTTGAAAGGAAATAGAAAGAGTAGT
*
21646031 GCTGTAAA-TTTGAAAGAGAAA-A-CAAGAGCTAGT
1 GCTGTAAATTTTGAAAG-GAAATAGAAAGAG-TAGT
21646064 GCTGT
1 GCTGT
21646069 TAGGTTTGTG
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
32 5 0.08
33 16 0.25
34 30 0.46
35 14 0.22
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (34 bp):
GCTGTAAATTTTGAAAGGAAATAGAAAGAGTAGT
Found at i:21647516 original size:54 final size:54
Alignment explanation
Indices: 21647457--21647665 Score: 289
Period size: 54 Copynumber: 3.9 Consensus size: 54
21647447 ATGGTGATAT
* *
21647457 TGTCCGGCTAAGTGCACGATGTGGTGGGATGCACATGAGCTAGATGAGGTGGGA
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGATGAGGTGGGA
*
21647511 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGA-GAGATGGGA
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCT-GGATGAGGTGGGA
* * *
21647565 TGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTG-GGATGGGA
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGATGAGG-TGGGA
* * * *
21647619 TGTCCAGCTATGTGCATGATGTCGT-GGATGCACATGAGCTGAATGAG
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGATGAG
21647666 ATGTGGTGAT
Statistics
Matches: 137, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
53 20 0.15
54 115 0.84
55 2 0.01
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.25
Consensus pattern (54 bp):
TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGATGAGGTGGGA
Found at i:21647541 original size:29 final size:28
Alignment explanation
Indices: 21647461--21647595 Score: 88
Period size: 29 Copynumber: 5.0 Consensus size: 28
21647451 TGATATTGTC
*
21647461 CGGCTAAGTGCACGATGTGGTGGGATG-
1 CGGCTATGTGCACGATGTGGTGGGATGT
* * *
21647488 C-AC-ATGAGCTA-GATGAGGTGGGATGT
1 CGGCTATGTGC-ACGATGTGGTGGGATGT
21647514 CCGGCTATGTGCACGATGTGGTGGGATG-
1 -CGGCTATGTGCACGATGTGGTGGGATGT
* * ** * *
21647542 C-AC-ATGAGCTGGGA-GAGATGGGATGTT
1 CGGCTATGTGC-ACGATGTGGTGGGATG-T
21647569 CGGCTATGTGCACGATGTGGTGGGATG
1 CGGCTATGTGCACGATGTGGTGGGATG
21647596 CACATGAGTT
Statistics
Matches: 77, Mismatches: 19, Indels: 22
0.65 0.16 0.19
Matches are distributed among these distances:
25 31 0.40
26 5 0.06
27 4 0.05
28 5 0.06
29 32 0.42
ACGTcount: A:0.20, C:0.14, G:0.42, T:0.24
Consensus pattern (28 bp):
CGGCTATGTGCACGATGTGGTGGGATGT
Found at i:21648522 original size:8 final size:8
Alignment explanation
Indices: 21648511--21648559 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
21648501 ATACCCACTC
21648511 TCTTTTTT
1 TCTTTTTT
*
21648519 TC-TTCTT
1 TCTTTTTT
21648526 T--TTTTT
1 TCTTTTTT
*
21648532 TGTTTTTT
1 TCTTTTTT
21648540 TCTTTTTTT
1 TC-TTTTTT
21648549 TCTTTTTT
1 TCTTTTTT
21648557 TCT
1 TCT
21648560 CTCCCACCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
6 5 0.14
7 5 0.14
8 17 0.49
9 8 0.23
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (8 bp):
TCTTTTTT
Found at i:21648537 original size:9 final size:9
Alignment explanation
Indices: 21648514--21648557 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
21648504 CCCACTCTCT
21648514 TTTTTTCTTC
1 TTTTTT-TTC
21648524 TTTTTTTT-
1 TTTTTTTTC
21648532 TGTTTTTTTC
1 T-TTTTTTTC
21648542 TTTTTTTTC
1 TTTTTTTTC
21648551 TTTTTTT
1 TTTTTTT
21648558 CTCTCCCACC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 1 0.03
9 24 0.75
10 7 0.22
ACGTcount: A:0.00, C:0.09, G:0.02, T:0.89
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:21654231 original size:54 final size:54
Alignment explanation
Indices: 21654155--21654367 Score: 327
Period size: 54 Copynumber: 3.9 Consensus size: 54
21654145 TATATCACCA
* * *
21654155 CATCTCATCTAGCTCATGTGCATCCCACCACATTGTGCACATAGCCGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* *
21654209 CATTTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCAGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* * * *
21654263 CATCTCTCTCAGCTCATGTGCATCCCATCACATCGTGCACATAGCCGGACATCT
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* *
21654317 CACCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACTTAGCCGGACA
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
21654368 GTATCACCAT
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 143 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (54 bp):
CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
Found at i:21655618 original size:9 final size:10
Alignment explanation
Indices: 21655599--21655654 Score: 66
Period size: 9 Copynumber: 5.9 Consensus size: 10
21655589 ATACCCACAC
21655599 TCTTCTTTTT
1 TCTTCTTTTT
21655609 TCTT-TTTTT
1 TCTTCTTTTT
21655618 TCTTCTTTTT
1 TCTTCTTTTT
*
21655628 T-TTGTTTCTT
1 TCTTCTTT-TT
21655638 TC-TC-TTTT
1 TCTTCTTTTT
21655646 TCTTCTTTT
1 TCTTCTTTT
21655655 CCTCTTTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 4 0.10
9 18 0.46
10 17 0.44
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (10 bp):
TCTTCTTTTT
Found at i:21655623 original size:19 final size:19
Alignment explanation
Indices: 21655599--21655663 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
21655589 ATACCCACAC
21655599 TCTTCTTTTTTCTTTTTTT
1 TCTTCTTTTTTCTTTTTTT
21655618 TCTTCTTTTTT-TTGTTTCTT
1 TCTTCTTTTTTCTT-TTT-TT
*
21655638 TC-TC-TTTTTC-TTCTTT
1 TCTTCTTTTTTCTTTTTTT
*
21655654 TCCTCTTTTT
1 TCTTCTTTTT
21655664 CGTCGGTCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
16 4 0.10
17 4 0.10
18 12 0.30
19 16 0.40
20 4 0.10
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (19 bp):
TCTTCTTTTTTCTTTTTTT
Found at i:21655630 original size:16 final size:16
Alignment explanation
Indices: 21655601--21655663 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 16
21655591 ACCCACACTC
21655601 TTCTT-TTTTCTTTTTT
1 TTCTTCTTTT-TTTTTT
*
21655617 TTCTTCTTTTTTTTGT
1 TTCTTCTTTTTTTTTT
21655633 TTCTTTCTCTTTTTCTTCTT
1 TTC-TTCT-TTTTT-TT-TT
*
21655653 TTCCTCTTTTT
1 TTCTTCTTTTT
21655664 CGTCGGTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 13 0.33
17 8 0.21
18 9 0.23
19 5 0.13
20 4 0.10
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTCTTCTTTTTTTTTT
Found at i:21655648 original size:25 final size:25
Alignment explanation
Indices: 21655599--21655654 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
21655589 ATACCCACAC
*
21655599 TCTTCTTT-TTTCTTTTTTTTCTTCT
1 TCTT-TTTGTTTCTTTTCTTTCTTCT
*
21655624 TTTTTTTGTTTCTTTCTCTTT-TTCT
1 TCTTTTTGTTTCTTT-TCTTTCTTCT
21655649 TCTTTT
1 TCTTTT
21655655 CCTCTTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (25 bp):
TCTTTTTGTTTCTTTTCTTTCTTCT
Found at i:21655822 original size:34 final size:35
Alignment explanation
Indices: 21655768--21655864 Score: 126
Period size: 34 Copynumber: 2.8 Consensus size: 35
21655758 TAGCACCAGC
* ** *
21655768 TCTTATTTTCTCTTTCAAATTTGCAGCAAAACTCT
1 TCTTATTTCCTCTTAAAAATTTGTAGCAAAACTCT
*
21655803 T-TCTATTTCCTC-TCAAAATTTGTAGCAAAACTCT
1 TCT-TATTTCCTCTTAAAAATTTGTAGCAAAACTCT
21655837 TCTTATTTCCTCTTAAAAATTTGTAGCA
1 TCTTATTTCCTCTTAAAAATTTGTAGCA
21655865 CAAGGCCTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
34 30 0.56
35 24 0.44
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (35 bp):
TCTTATTTCCTCTTAAAAATTTGTAGCAAAACTCT
Found at i:21656969 original size:14 final size:14
Alignment explanation
Indices: 21656929--21656970 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
21656919 ACATTGAATA
21656929 AATATTAATATT-TT
1 AATA-TAATATTATT
* *
21656943 AATATCATTTTATT
1 AATATAATATTATT
21656957 AATATAATATTATT
1 AATATAATATTATT
21656971 TTATTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATAATATTATT
Found at i:21658485 original size:16 final size:16
Alignment explanation
Indices: 21658460--21658508 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
21658450 TTATTGTTGG
*
21658460 TTTTAATTTTAGTTAA
1 TTTTAATTTTAATTAA
*
21658476 TTTTAGTTTTAATTAA
1 TTTTAATTTTAATTAA
*
21658492 TTATTTAATTTTGATTA
1 -T-TTTAATTTTAATTA
21658509 TTTGGATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 14 0.52
17 1 0.04
18 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (16 bp):
TTTTAATTTTAATTAA
Found at i:21665818 original size:42 final size:43
Alignment explanation
Indices: 21665767--21665857 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 43
21665757 TTATGAGATA
** **
21665767 ATGATGACCCAGCTATGTGCGTGTGGG-AGTGCACATGAGTTG
1 ATGATGACCCAGCTATGTGCGAATGGGAAGTGCACATGAACTG
*
21665809 ATGATGACCCAGTTATGTGCGAATGGGAAGTGCACATGAACTG
1 ATGATGACCCAGCTATGTGCGAATGGGAAGTGCACATGAACTG
21665852 ATGATG
1 ATGATG
21665858 GTGGGATGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 24 0.56
43 19 0.44
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.25
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGAATGGGAAGTGCACATGAACTG
Found at i:21665894 original size:2 final size:2
Alignment explanation
Indices: 21665889--21665913 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21665879 TGTGTGTGTG
21665889 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 T
21665914 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21665918 original size:2 final size:2
Alignment explanation
Indices: 21665913--21666041 Score: 132
Period size: 2 Copynumber: 64.5 Consensus size: 2
21665903 TATATATATA
21665913 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * * * * * * * * *
21665955 TG TG TA NG TG TG TG TA TA TA TA TA TA TA TA TA TA TA TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
21665997 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
21666039 TG T
1 TG T
21666042 TATAGAAAGT
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 121 1.00
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (2 bp):
TG
Found at i:21668369 original size:21 final size:20
Alignment explanation
Indices: 21668343--21668382 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
21668333 ACATGCCCAT
*
21668343 ATGTATTGATACATTATGAAC
1 ATGTATCGATACATT-TGAAC
21668364 ATGTATCGATACATTTGAA
1 ATGTATCGATACATTTGAA
21668383 ATAGAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTGAAC
Found at i:21668533 original size:18 final size:18
Alignment explanation
Indices: 21668510--21668553 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
21668500 GGATTCAATA
21668510 AAAATATAAAAAAAAATC
1 AAAATATAAAAAAAAATC
* *
21668528 AAAATAT--GAAAGAATC
1 AAAATATAAAAAAAAATC
21668544 AAAATATAAA
1 AAAATATAAA
21668554 TTTGGTTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
16 14 0.67
18 7 0.33
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAATATAAAAAAAAATC
Found at i:21680643 original size:82 final size:81
Alignment explanation
Indices: 21680506--21680668 Score: 317
Period size: 82 Copynumber: 2.0 Consensus size: 81
21680496 TCACAATAGC
21680506 GGGATATTACATCGCTAATTCTACTTGCCGGTCGCTTGTTATTCCTTCGGCACACCACTATAGTG
1 GGGATATTACATCGCTAATTCTACTTGCCGGTCGCTTGTTATTCCTTCGGCACACCACTATAGTG
21680571 CACTATCTTCACTTAA
66 CACTATCTTCACTTAA
21680587 NGGGATATTACATCGCTAATTCTACTTGCCGGTCGCTTGTTATTCCTTCGGCACACCACTATAGT
1 -GGGATATTACATCGCTAATTCTACTTGCCGGTCGCTTGTTATTCCTTCGGCACACCACTATAGT
21680652 GCACTATCTTCACTTAA
65 GCACTATCTTCACTTAA
21680669 TCACTTCCAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.34
Consensus pattern (81 bp):
GGGATATTACATCGCTAATTCTACTTGCCGGTCGCTTGTTATTCCTTCGGCACACCACTATAGTG
CACTATCTTCACTTAA
Found at i:21680861 original size:15 final size:17
Alignment explanation
Indices: 21680827--21680870 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
21680817 CATTTCGTTC
*
21680827 TCTTTTTTTTTTCTCTT
1 TCTTTCTTTTTTCTCTT
21680844 TCTTTCTTTTTTC-C-T
1 TCTTTCTTTTTTCTCTT
21680859 TCTTTCTCTTTT
1 TCTTTCT-TTTT
21680871 ACACTGGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 5 0.20
17 12 0.48
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTCTTTTTTCTCTT
Found at i:21680861 original size:21 final size:21
Alignment explanation
Indices: 21680824--21680869 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 21
21680814 TTTCATTTCG
*
21680824 TTCTCTTT-TTTTTTTC-TC-
1 TTCTCTTTCTTTTTTCCTTCT
21680842 TT-TCTTTCTTTTTTCCTTCT
1 TTCTCTTTCTTTTTTCCTTCT
21680862 TTCTCTTT
1 TTCTCTTT
21680870 TACACTGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 9 0.39
19 2 0.09
20 2 0.09
21 5 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTCTCTTTCTTTTTTCCTTCT
Found at i:21680862 original size:19 final size:17
Alignment explanation
Indices: 21680827--21680870 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
21680817 CATTTCGTTC
*
21680827 TCTTTTTTTTTTCTCTT
1 TCTTTTTTTTTCCTCTT
21680844 TCTTTCTTTTTTCCTTCTT
1 TCTTT-TTTTTTCC-TCTT
21680863 TCTCTTTT
1 TCT-TTTT
21680871 ACACTGGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 9 0.39
20 2 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTTTTTTTCCTCTT
Found at i:21681075 original size:69 final size:68
Alignment explanation
Indices: 21680991--21681151 Score: 191
Period size: 69 Copynumber: 2.3 Consensus size: 68
21680981 CAGCACAAGG
* ** *
21680991 CTGCTCTCTTTTCCCT-CAAAATTGGCAGCCAAAGCCT-CTCATTTCTACCTCAAAACTCGACAG
1 CTGCTCT-TTTTCCCTAAAAAATCAGCAGCC-AAG-CTACGCATTTCTACCTCAAAACTCGACAG
21681054 CCAAAA
63 CCAAAA
* *
21681060 CTGCTCTTTTCTCCCTAAAAAATCAGCAGCCAAGCTACGCCTTTCTTCCTCAAAACTCGACAGCC
1 CTGCTCTTTT-TCCCTAAAAAATCAGCAGCCAAGCTACGCATTTCTACCTCAAAACTCGACAGCC
*
21681125 AAAG
65 AAAA
*
21681129 CTGCTCTTTTTTTCCTAAAAAAT
1 CTGCTC-TTTTTCCCTAAAAAAT
21681152 TAGCTCTTTC
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
68 5 0.06
69 60 0.75
70 15 0.19
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (68 bp):
CTGCTCTTTTTCCCTAAAAAATCAGCAGCCAAGCTACGCATTTCTACCTCAAAACTCGACAGCCA
AAA
Found at i:21681124 original size:34 final size:34
Alignment explanation
Indices: 21681032--21681127 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
21681022 AAGCCTCTCA
* * *
21681032 TTTCTACCTCAAAACTCGACAGCCAAAACTGCTCT
1 TTTCTACCTCAAAACTCGACAGCC-AAACTACGCC
* * * *
21681067 TTTCTCCCTAAAAAATC-AGCAGCCAAGCTACGCC
1 TTTCTACCTCAAAACTCGA-CAGCCAAACTACGCC
*
21681101 TTTCTTCCTCAAAACTCGACAGCCAAA
1 TTTCTACCTCAAAACTCGACAGCCAAA
21681128 GCTGCTCTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
34 28 0.58
35 20 0.42
ACGTcount: A:0.32, C:0.34, G:0.09, T:0.24
Consensus pattern (34 bp):
TTTCTACCTCAAAACTCGACAGCCAAACTACGCC
Found at i:21681144 original size:35 final size:35
Alignment explanation
Indices: 21680961--21681138 Score: 152
Period size: 35 Copynumber: 5.1 Consensus size: 35
21680951 AAGTTTCTTC
* * *
21680961 CTTTTCTCCCTCAAAA-TTGGCAGCACAAGGCTGCT
1 CTTTTCTCCCTCAAAACTCGACAGC-CAAAGCTGCT
* *
21680996 CTCTTT-TCCCTCAAAA-TTGGCAGCCAAAGCCT-CT
1 CT-TTTCTCCCTCAAAACTCGACAGCCAAAG-CTGCT
* * *
21681030 CATTTCTACCTCAAAACTCGACAGCCAAAACTGCT
1 CTTTTCTCCCTCAAAACTCGACAGCCAAAGCTGCT
* * * *
21681065 CTTTTCTCCCTAAAAAATC-AGCAGCC-AAGCTACG
1 CTTTTCTCCCTCAAAACTCGA-CAGCCAAAGCTGCT
* *
21681099 CCTTTCTTCCTCAAAACTCGACAGCCAAAGCTGCT
1 CTTTTCTCCCTCAAAACTCGACAGCCAAAGCTGCT
21681134 CTTTT
1 CTTTT
21681139 TTTCCTAAAA
Statistics
Matches: 115, Mismatches: 20, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
33 3 0.03
34 44 0.38
35 65 0.57
36 3 0.03
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.28
Consensus pattern (35 bp):
CTTTTCTCCCTCAAAACTCGACAGCCAAAGCTGCT
Found at i:21681220 original size:35 final size:36
Alignment explanation
Indices: 21681146--21681230 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 36
21681136 TTTTTTCCTA
* * *
21681146 AAAAATTAGCTCTTTCTCTCCCTTTAAAATGACAGC
1 AAAAACTAGCTCTTTCTCTCCCCTTAAAATGACAAC
*
21681182 AAAAACTAGCTCTCTT-T-TCCCCTTAAAATGGCAAC
1 AAAAACTAGCTCT-TTCTCTCCCCTTAAAATGACAAC
*
21681217 AAAAACCAGC-CTTT
1 AAAAACTAGCTCTTT
21681231 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 2 0.05
34 2 0.05
35 24 0.56
36 13 0.30
37 2 0.05
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29
Consensus pattern (36 bp):
AAAAACTAGCTCTTTCTCTCCCCTTAAAATGACAAC
Found at i:21682175 original size:18 final size:19
Alignment explanation
Indices: 21682136--21682178 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21682126 TTAATATTTT
*
21682136 AATATTATTTTATTCATAA
1 AATAATATTTTATTCATAA
*
21682155 AATAATATTTTATT-TTAA
1 AATAATATTTTATTCATAA
21682173 AATAAT
1 AATAAT
21682179 TTTCTCACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAATATTTTATTCATAA
Found at i:21684542 original size:71 final size:70
Alignment explanation
Indices: 21684453--21684647 Score: 230
Period size: 71 Copynumber: 2.8 Consensus size: 70
21684443 GAATGACATG
* * *
21684453 TTCTCCCTGCAGCCAAAATGGATTCTTGCTGCAATGAGAAAGTCTCTGACTTGGAACTGCTATTT
1 TTCTCACTGCAGCCAAAATGGATTCTGGCTGCAGTGAGAAAGTCTCTGACTTGGAACTG--ATTT
* *
21684518 T-GATGT
64 TACAAGT
* * * *
21684524 TTCTCACTGTAGCCAAAATGGATTCTGGCTGCAGTGAGAAAGTCTTTGACTTGGGATTGATTTTC
1 TTCTCACTGCAGCCAAAATGGATTCTGGCTGCAGTGAGAAAGTCTCTGACTTGGAACTGATTTT-
21684589 ACAAGT
65 ACAAGT
* * ** *
21684595 TTCTCACTACAGCCAAAATGGATTCTGGCTACAGCAAAAAAGTCTCTGACTTG
1 TTCTCACTGCAGCCAAAATGGATTCTGGCTGCAGTGAGAAAGTCTCTGACTTG
21684648 CACTGTGCAG
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
69 5 0.05
71 101 0.95
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (70 bp):
TTCTCACTGCAGCCAAAATGGATTCTGGCTGCAGTGAGAAAGTCTCTGACTTGGAACTGATTTTA
CAAGT
Found at i:21688791 original size:16 final size:17
Alignment explanation
Indices: 21688770--21688806 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
21688760 AAGACTCAGT
21688770 GAATAAAATAA-AGAAA
1 GAATAAAATAATAGAAA
*
21688786 GAATAAAATAATATAAA
1 GAATAAAATAATAGAAA
21688803 GAAT
1 GAAT
21688807 GTGTGTACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (17 bp):
GAATAAAATAATAGAAA
Done.