Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 58 of 235
Found at i:19632198 original size:46 final size:44
Alignment explanation
Indices: 19632098--19632213 Score: 126
Period size: 46 Copynumber: 2.6 Consensus size: 44
19632088 TGTCTTCGAC
** * * *
19632098 ATGGACTTACATGAATTATTCTTGTCTCCAATGATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGATATATATAAT
* *
19632142 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATA-ACTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAG--ATATATA-TAAT
*
19632188 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
19632214 CTGTCTTGTC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
44 27 0.45
45 1 0.02
46 32 0.53
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (44 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGATATATATAAT
Found at i:19634996 original size:60 final size:60
Alignment explanation
Indices: 19634903--19635020 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
19634893 CAACACCCGT
* *
19634903 TTAAAACCTTATTTTGATGATATTGATAGCAGGATTGAGAAGATTAAACTTCTCAAACGG
1 TTAAAACCTTATTTTGATGAGATTGATAGCAGGAATGAGAAGATTAAACTTCTCAAACGG
19634963 TTAAAACCTTATTTTGATGAGATTGATAGCAGGAATGAGAAGATTAAACTTCTCAAAC
1 TTAAAACCTTATTTTGATGAGATTGATAGCAGGAATGAGAAGATTAAACTTCTCAAAC
19635021 CACCATGATT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (60 bp):
TTAAAACCTTATTTTGATGAGATTGATAGCAGGAATGAGAAGATTAAACTTCTCAAACGG
Found at i:19635383 original size:55 final size:55
Alignment explanation
Indices: 19635279--19635390 Score: 129
Period size: 55 Copynumber: 2.0 Consensus size: 55
19635269 TGCGATATGG
* * * *
19635279 CCGTGGTCAACCCTGCCAAAACAACACAGGCTTGAGACACGGTCGTGTGGAAGAA
1 CCGTGGGCAACCCTGCCAAAACAACACAGGCTTCAGACACGGTCATGTGGAACAA
* * *
19635334 CCGTGGGCAAGCCTGCCAAAACAAGACGGGCGTTCA-ACAC-GTCCATGTGGAACAA
1 CCGTGGGCAACCCTGCCAAAACAACACAGGC-TTCAGACACGGT-CATGTGGAACAA
19635389 CC
1 CC
19635391 ATGGTCAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
54 2 0.04
55 43 0.90
56 3 0.06
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.13
Consensus pattern (55 bp):
CCGTGGGCAACCCTGCCAAAACAACACAGGCTTCAGACACGGTCATGTGGAACAA
Found at i:19638032 original size:24 final size:24
Alignment explanation
Indices: 19638005--19638050 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
19637995 GAATTTAACA
19638005 TTCAAAT-CAGCACACATAGTGCCT
1 TTCAAATAC-GCACACATAGTGCCT
* *
19638029 TTCAACTACGCACACGTAGTGC
1 TTCAAATACGCACACATAGTGC
19638051 TAGTATCGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.24
Consensus pattern (24 bp):
TTCAAATACGCACACATAGTGCCT
Found at i:19640782 original size:27 final size:27
Alignment explanation
Indices: 19640752--19640929 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
19640742 ATATTGAGCC
* *
19640752 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
19640779 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
19640806 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
19640834 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
19640861 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
19640888 CGCACACTTAGTGCAACATAGTCAAAC-
1 CGCACACTTAGTGCTACATAATC-AACT
19640915 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19640930 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 103 0.80
28 25 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:19640891 original size:82 final size:81
Alignment explanation
Indices: 19640773--19640928 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19640763 TGCTATATAA
* *
19640773 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAAC-CGCA
19640838 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
19640855 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAACCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCA
19640919 CACTTAGTGC
65 CACTTAGTGC
19640929 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.78
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCAC
ACTTAGTGCCGCATGG
Found at i:19644595 original size:72 final size:72
Alignment explanation
Indices: 19644473--19644615 Score: 180
Period size: 72 Copynumber: 2.0 Consensus size: 72
19644463 CTGATGGCTG
* * * *
19644473 AATATGCCAATAGCATGTTCTTGATATGTTAAACTATAAGTTCAATTAGTATGTTCCGATCTGTT
1 AATATGCCAATAGCATATTCTTGATATGTTAAACTATAAGTGCAACTAGTATGTTCCGATATGTT
19644538 TTATCTA
66 TTATCTA
* * * * * *
19644545 AATATGCCAATCA-CATATTTTTTATCTGTTAAACTATATGTGCAACTAGTATTTTCTGATATGT
1 AATATGCCAAT-AGCATATTCTTGATATGTTAAACTATAAGTGCAACTAGTATGTTCCGATATGT
19644609 TTTATCT
65 TTTATCT
19644616 GCATATGGGC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 59 0.98
73 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (72 bp):
AATATGCCAATAGCATATTCTTGATATGTTAAACTATAAGTGCAACTAGTATGTTCCGATATGTT
TTATCTA
Found at i:19646370 original size:3 final size:3
Alignment explanation
Indices: 19646362--19646393 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19646352 TTTTTCTCCT
19646362 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
19646394 TAATATTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:19647669 original size:20 final size:21
Alignment explanation
Indices: 19647644--19647685 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
19647634 ACCTGTAAAC
*
19647644 TTTAGTGTTTAAATT-ATATT
1 TTTAGTGGTTAAATTGATATT
19647664 TTTAGTGGTTAAATTGATATT
1 TTTAGTGGTTAAATTGATATT
19647685 T
1 T
19647686 AAGCTTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
TTTAGTGGTTAAATTGATATT
Found at i:19650173 original size:18 final size:18
Alignment explanation
Indices: 19650150--19650188 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
19650140 CAATACTTAA
19650150 CTTAGAATTCACCCATTT
1 CTTAGAATTCACCCATTT
19650168 CTTAGAATTCACCCATTT
1 CTTAGAATTCACCCATTT
19650186 CTT
1 CTT
19650189 CGTTACTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (18 bp):
CTTAGAATTCACCCATTT
Found at i:19650595 original size:28 final size:28
Alignment explanation
Indices: 19650455--19650774 Score: 317
Period size: 28 Copynumber: 11.4 Consensus size: 28
19650445 GTTTGGCACG
*
19650455 AGGCATTCATTTAACAGAGATAGCCACAA
1 AGGC-TTCCTTTAACAGAGATAGCCACAA
* * * *
19650484 AGACATGCTTTTAA-ATGAGGTAGCCACAA
1 AGGC-TTCCTTTAACA-GAGATAGCCACAA
**
19650513 AGGAATCCTTTTAACAGAGATAGCCACAA
1 AGGCTTCC-TTTAACAGAGATAGCCACAA
* * *
19650542 AGACTTCCTTTTAATAGAAATAGCCACAA
1 AGGCTTCC-TTTAACAGAGATAGCCACAA
* *
19650571 AGGCTTCCTTTAATAGAGATCGCCACAA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
*
19650599 AGGCTTCTTTTAACAGAGATCA-CCACAA
1 AGGCTTCCTTTAACAGAGAT-AGCCACAA
* ***
19650627 AGGCTTCCTTTAATAGAGATCTTCACAA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
* *
19650655 AAGCTTCCTTTAACAGAGATCA-CCATAA
1 AGGCTTCCTTTAACAGAGAT-AGCCACAA
* * *
19650683 AGGCTTCCTTTAATAGGGATTGCCACAA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
*
19650711 AGGCTTCCTTTAACAGAGATAGCCACGA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
*
19650739 AGGCATCCTTT--CAGAGATAGCCACAA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
*
19650765 AGGATTCCTT
1 AGGCTTCCTT
19650775 GCAAAAACTA
Statistics
Matches: 241, Mismatches: 43, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
26 22 0.09
28 145 0.60
29 73 0.30
30 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (28 bp):
AGGCTTCCTTTAACAGAGATAGCCACAA
Found at i:19666325 original size:39 final size:39
Alignment explanation
Indices: 19666240--19666328 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 39
19666230 GTACTGATTA
*
19666240 CTGATACTGTAATGGGCTAAGGCCTAATGCATGACTGCAC
1 CTGATACTG-AATGGGCTAAGGCCTAATGCATAACTGCAC
* *
19666280 CT-ATACTGAATGGGCTAAGGCCATAACTG-A-AACTGGAT
1 CTGATACTGAATGGGCTAAGGCC-TAA-TGCATAACTGCAC
19666318 CTGATACTGAA
1 CTGATACTGAA
19666329 AAAGGGCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 21 0.49
39 18 0.42
40 4 0.09
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (39 bp):
CTGATACTGAATGGGCTAAGGCCTAATGCATAACTGCAC
Found at i:19669090 original size:39 final size:39
Alignment explanation
Indices: 19669005--19669093 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 39
19668995 GTACTGATTA
*
19669005 CTGATACTGTAATGGGCTAAGGCCTAATGCATGACTGCAC
1 CTGATACTG-AATGGGCTAAGGCCTAATGCATAACTGCAC
* *
19669045 CT-ATACTGAATGGGCTAAGGCCATAACTG-A-AACTGGAT
1 CTGATACTGAATGGGCTAAGGCC-TAA-TGCATAACTGCAC
19669083 CTGATACTGAA
1 CTGATACTGAA
19669094 AAAGGGCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 21 0.49
39 18 0.42
40 4 0.09
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (39 bp):
CTGATACTGAATGGGCTAAGGCCTAATGCATAACTGCAC
Found at i:19671987 original size:27 final size:27
Alignment explanation
Indices: 19671949--19672001 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
19671939 TCTTCAGTCC
*
19671949 ACTTGAAAGGTGCACTTTTCCTCAAAA
1 ACTTGAAAGGTGCACTTTTCCACAAAA
19671976 ACTTGAAAGGTGCACTTTTCCACAAA
1 ACTTGAAAGGTGCACTTTTCCACAAA
19672002 CCTCTTATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (27 bp):
ACTTGAAAGGTGCACTTTTCCACAAAA
Found at i:19673476 original size:20 final size:21
Alignment explanation
Indices: 19673439--19673479 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19673429 AACTAGTATT
*
19673439 CTGCATCAGTGAGGGTTGTCC
1 CTGCAACAGTGAGGGTTGTCC
19673460 CTGCAACAGTG-GGGTTGTCC
1 CTGCAACAGTGAGGGTTGTCC
19673480 TAGAAACACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.15, C:0.24, G:0.34, T:0.27
Consensus pattern (21 bp):
CTGCAACAGTGAGGGTTGTCC
Found at i:19673487 original size:20 final size:21
Alignment explanation
Indices: 19673445--19673487 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
19673435 TATTCTGCAT
*
19673445 CAGTGAGGGTTGTCCCTGCAA
1 CAGTGAGGGTTGTCCCTGAAA
19673466 CAGTG-GGGTTGT-CCTAGAAA
1 CAGTGAGGGTTGTCCCT-GAAA
19673486 CA
1 CA
19673488 CCATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 12 0.60
21 5 0.25
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (21 bp):
CAGTGAGGGTTGTCCCTGAAA
Found at i:19673925 original size:16 final size:16
Alignment explanation
Indices: 19673894--19673946 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
19673884 AGTCTTGTCA
19673894 CTATAGTTTT-AGAAT
1 CTATAGTTTTCAGAAT
19673909 CTATAGTTTTCAGAAT
1 CTATAGTTTTCAGAAT
* * *
19673925 CTAGAG-TTTCACAGT
1 CTATAGTTTTCAGAAT
19673940 CTATAGT
1 CTATAGT
19673947 ATTCTATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 22 0.69
16 10 0.31
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (16 bp):
CTATAGTTTTCAGAAT
Found at i:19674107 original size:18 final size:19
Alignment explanation
Indices: 19674086--19674125 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
19674076 ATGGCATGGA
19674086 TTTTTCACAAA-ATACATT
1 TTTTTCACAAATATACATT
* *
19674104 TTTTTCTCAAATATGCATT
1 TTTTTCACAAATATACATT
19674123 TTT
1 TTT
19674126 GAAAATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTTCACAAATATACATT
Found at i:19676407 original size:34 final size:34
Alignment explanation
Indices: 19676364--19676432 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
19676354 TCACAAAGTC
19676364 AGCAGGAAAGGTAAATTATTCTACACGTACCAAT
1 AGCAGGAAAGGTAAATTATTCTACACGTACCAAT
*
19676398 AGCAGGAAAGGTAAATTTTTCTACACGTACCAAT
1 AGCAGGAAAGGTAAATTATTCTACACGTACCAAT
19676432 A
1 A
19676433 AGTCCTCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (34 bp):
AGCAGGAAAGGTAAATTATTCTACACGTACCAAT
Found at i:19692712 original size:18 final size:19
Alignment explanation
Indices: 19692686--19692722 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
19692676 AATTTTGGAA
19692686 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
19692704 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
19692723 ATGTGATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:19693653 original size:22 final size:22
Alignment explanation
Indices: 19693594--19693655 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
19693584 TAGTTTAATG
19693594 TGGTGAT-GTTACGGTGGTTGAA
1 TGGTGATGGTT-CGGTGGTTGAA
* * * *
19693616 TAGTGGTGGAGT-GGTGGTTGTA
1 TGGTGATGG-TTCGGTGGTTGAA
19693638 TGGTGATGGTTCGGTGGT
1 TGGTGATGGTTCGGTGGT
19693656 GATTTGGTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
21 1 0.03
22 27 0.90
23 1 0.03
24 1 0.03
ACGTcount: A:0.13, C:0.03, G:0.47, T:0.37
Consensus pattern (22 bp):
TGGTGATGGTTCGGTGGTTGAA
Found at i:19695327 original size:35 final size:35
Alignment explanation
Indices: 19695280--19695376 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 35
19695270 TTTATCACAG
* *
19695280 TGGCATGTTTAACATGTGAATTAGAATCAGAATAA
1 TGGCATGCTTAACATGCGAATTAGAATCAGAATAA
* * * *
19695315 TGGCATGCTTAACATACGAATCATAATCAGAATGA
1 TGGCATGCTTAACATGCGAATTAGAATCAGAATAA
* * *
19695350 TAGCATGCTCAACATGCAAATTAGAAT
1 TGGCATGCTTAACATGCGAATTAGAAT
19695377 ATCAATAAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (35 bp):
TGGCATGCTTAACATGCGAATTAGAATCAGAATAA
Found at i:19699471 original size:31 final size:32
Alignment explanation
Indices: 19699415--19699481 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
19699405 TTATTTATAT
*
19699415 AGGTTGGCCGAATGTGTGGGATCA-TTTAACA
1 AGGTTAGCCGAATGTGTGGGATCATTTTAACA
*
19699446 AGGTTAGCCGAAT-T-TGGAGATTCATTTTAGCA
1 AGGTTAGCCGAATGTGTGG-GA-TCATTTTAACA
19699478 AGGT
1 AGGT
19699482 GTATGCATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 3 0.10
31 15 0.48
32 10 0.32
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (32 bp):
AGGTTAGCCGAATGTGTGGGATCATTTTAACA
Found at i:19701542 original size:40 final size:40
Alignment explanation
Indices: 19701497--19701808 Score: 480
Period size: 40 Copynumber: 7.7 Consensus size: 40
19701487 GCAAACACAT
* * *
19701497 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCATCTCGCATAA
*
19701537 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCATCTCGCATAA
** *
19701577 TTGCCTTCGGGTTTTAGCCCGGATATATCATCTCGCTTAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCATCTCGCATAA
* *
19701617 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCTTAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCATCTCGCATAA
19701657 TTGCCTTCGGGTCATAGCCCGGACGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCATAG-CC---CGGATATATCATCTCGCATAA
*
19701701 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCATCTCGCATAA
* *
19701741 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCATCTCGCATAA
19701781 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCATAGCCCGGATATAT
19701809 TCCAATGCTC
Statistics
Matches: 256, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
40 216 0.84
41 2 0.01
43 2 0.01
44 36 0.14
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCATAGCCCGGATATATCATCTCGCATAA
Found at i:19701764 original size:164 final size:160
Alignment explanation
Indices: 19701497--19701809 Score: 527
Period size: 164 Copynumber: 1.9 Consensus size: 160
19701487 GCAAACACAT
* *
19701497 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAGCCCGGACATATCAACTCGCATAATTGCCTTCGGGTCATAGCCCGGATA
* * * *
19701562 TATCATCTCGCATAATTGCCTTCGGGTTTTAGCCCGGATATATCATCTCGCTTAATTGCCTTCGG
66 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGG
19701627 GTCATAGCCCGGATATATTATCTCGCTTAA
131 GTCATAGCCCGGATATATTATCTCGCTTAA
*
19701657 TTGCCTTCGGGTCATAGCCCGGACGGATATATCATCTCGCATAATTGCCTTCGGGTCATAGCCCG
1 TTGCCTTCGGGTCATAGCCCGGAC----ATATCAACTCGCATAATTGCCTTCGGGTCATAGCCCG
19701722 GATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCT
62 GATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCT
19701787 TCGGGTCATAGCCCGGATATATT
127 TCGGGTCATAGCCCGGATATATT
19701810 CCAATGCTCA
Statistics
Matches: 142, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
160 23 0.16
164 119 0.84
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (160 bp):
TTGCCTTCGGGTCATAGCCCGGACATATCAACTCGCATAATTGCCTTCGGGTCATAGCCCGGATA
TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGG
GTCATAGCCCGGATATATTATCTCGCTTAA
Found at i:19710168 original size:40 final size:40
Alignment explanation
Indices: 19710123--19710390 Score: 455
Period size: 40 Copynumber: 6.7 Consensus size: 40
19710113 GCAAACACAT
*
19710123 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
19710163 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
19710203 TTGCCTTCGGGTTTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
19710243 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
19710283 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
19710323 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
19710363 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
19710391 TCCAATGCTC
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:19718619 original size:49 final size:51
Alignment explanation
Indices: 19718547--19718679 Score: 159
Period size: 50 Copynumber: 2.7 Consensus size: 51
19718537 AGGTTATAAT
* * *
19718547 GCCGATGCCATTTCCCAGACATGGTCTTACACTGA-CTATTGA-A-ATT-GAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCT-CTCACATATTCG-G
* *
19718596 GCCGATGCTATGTCCCAGACATGGTTTTACACT-AGCTCTCACATATTCGG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCTCTCACATATTCGG
*
19718646 GCCGATGCCATGTCCTAGACATGGTCTTACACTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTG
19718680 GCACATCTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
48 3 0.04
49 33 0.46
50 34 0.48
51 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (51 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCTCTCACATATTCGG
Found at i:19718758 original size:46 final size:46
Alignment explanation
Indices: 19718695--19718816 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
19718685 TCTTGTAACC
* *
19718695 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATTCCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGATTACATTCCGAGGCT
* * * * *
19718741 GATTCATGTCCCTGACATGTCTTGCACTAGATTACATTCTGAGGTT
1 GATGCATGTCCCAGACATGTCTTACACTAGATTACATTCCGAGGCT
19718787 GATGCATGTCCCAGACATGTCTTACACTAG
1 GATGCATGTCCCAGACATGTCTTACACTAG
19718817 CACACAAATG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.31
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGATTACATTCCGAGGCT
Found at i:19719539 original size:13 final size:13
Alignment explanation
Indices: 19719521--19719545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19719511 CCAAAAATGT
19719521 AAAAATCATCAAG
1 AAAAATCATCAAG
19719534 AAAAATCATCAA
1 AAAAATCATCAA
19719546 AATCACTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:19729307 original size:47 final size:47
Alignment explanation
Indices: 19729238--19729327 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
19729228 AATGCATATG
* **
19729238 AAAATTCGCGCCTATACAAGGAAGCAACGAAGTGCTGCCACGACGCT
1 AAAATTCACGCCTATACAAGGAAGCAACGAAGCACTGCCACGACGCT
* *
19729285 AAAATTCATGCCTATACAAGGAAGCAATGAAGCACTGCCACGA
1 AAAATTCACGCCTATACAAGGAAGCAACGAAGCACTGCCACGA
19729328 TGCTCGTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.16
Consensus pattern (47 bp):
AAAATTCACGCCTATACAAGGAAGCAACGAAGCACTGCCACGACGCT
Found at i:19730134 original size:5 final size:5
Alignment explanation
Indices: 19730121--19730166 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
19730111 ACACCTATTA
*
19730121 TTTAT TTTAC TTTAT TTTAT TTTATT TTTAT CTTTAT TTATAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT -TTTAT TT-TAT TTT
19730167 GAAATTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 21 0.58
6 15 0.42
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:19736975 original size:46 final size:46
Alignment explanation
Indices: 19736908--19737036 Score: 197
Period size: 46 Copynumber: 2.8 Consensus size: 46
19736898 TGTAACCCGG
* * *
19736908 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCAG-AT
*
19736954 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGACATTCAGAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCAGAT
*
19737000 CCATAAGTGAACTCGGACTCAACTCAACGAACTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
19737037 TGCCCAAATA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
46 75 0.99
47 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCAGAT
Found at i:19738715 original size:70 final size:70
Alignment explanation
Indices: 19738629--19738764 Score: 263
Period size: 70 Copynumber: 1.9 Consensus size: 70
19738619 TACTCACAAC
*
19738629 ATGGTTATACTTTTCTTGTTTAACTTATACTATATCTCTCATCGTTGAACCATTTGGAAAGCTAT
1 ATGGTTATACTTTTCTTGTTTAACTTAAACTATATCTCTCATCGTTGAACCATTTGGAAAGCTAT
19738694 CAGAT
66 CAGAT
19738699 ATGGTTATACTTTTCTTGTTTAACTTAAACTATATCTCTCATCGTTGAACCATTTGGAAAGCTAT
1 ATGGTTATACTTTTCTTGTTTAACTTAAACTATATCTCTCATCGTTGAACCATTTGGAAAGCTAT
19738764 C
66 C
19738765 GAATATTCAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (70 bp):
ATGGTTATACTTTTCTTGTTTAACTTAAACTATATCTCTCATCGTTGAACCATTTGGAAAGCTAT
CAGAT
Found at i:19748780 original size:14 final size:15
Alignment explanation
Indices: 19748750--19748780 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
19748740 TTATGAAGAC
19748750 ATCATTTATACAAAAA
1 ATCATTTATA-AAAAA
19748766 ATCATTTATAAAAAA
1 ATCATTTATAAAAAA
19748781 GCTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (15 bp):
ATCATTTATAAAAAA
Found at i:19750026 original size:32 final size:32
Alignment explanation
Indices: 19749968--19750087 Score: 143
Period size: 32 Copynumber: 3.8 Consensus size: 32
19749958 TTAGTATAGT
** *
19749968 TTGCATAGATACAGTTTGCAT-TTCATTCAGC
1 TTGCATAGATACAGTTCACATAATCATTCAGC
* * *
19749999 TTGCACAAATATAGTTCACATAATCATTCAGC
1 TTGCATAGATACAGTTCACATAATCATTCAGC
* * *
19750031 TTGCGTAGATACAATTCACATATTCATTCAGC
1 TTGCATAGATACAGTTCACATAATCATTCAGC
*
19750063 TTGCATAGATACAGTTTACATAATC
1 TTGCATAGATACAGTTCACATAATC
19750088 CTACAACACG
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
31 16 0.22
32 56 0.78
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (32 bp):
TTGCATAGATACAGTTCACATAATCATTCAGC
Found at i:19750294 original size:55 final size:55
Alignment explanation
Indices: 19750220--19750340 Score: 136
Period size: 55 Copynumber: 2.2 Consensus size: 55
19750210 AGACTCATAA
* * * *
19750220 ACAGACATATCGTAGATAGTTCC-AAAGGCAGTCATACTACGAATAGTCTCTACGT
1 ACAGACATATGGCAAATAG-TCCTAAAGACAGTCATACTACGAATAGTCTCTACGT
* ** * *
19750275 ACAGACCTATGGCAAATAGTCCTGCAGATAGTCATACTACGGATAGTCTCTACGT
1 ACAGACATATGGCAAATAGTCCTAAAGACAGTCATACTACGAATAGTCTCTACGT
*
19750330 ATAGACATATG
1 ACAGACATATG
19750341 ACGGATAGTC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 3 0.06
55 51 0.94
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (55 bp):
ACAGACATATGGCAAATAGTCCTAAAGACAGTCATACTACGAATAGTCTCTACGT
Found at i:19750321 original size:15 final size:15
Alignment explanation
Indices: 19750301--19750350 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
19750291 TAGTCCTGCA
19750301 GATAGTCATACTACG
1 GATAGTCATACTACG
19750316 GATAGTC-T-CTACG
1 GATAGTCATACTACG
* *
19750329 TATAGACATA-TGACG
1 GATAGTCATACT-ACG
19750344 GATAGTC
1 GATAGTC
19750351 CTGTGAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 10 0.36
14 3 0.11
15 15 0.54
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (15 bp):
GATAGTCATACTACG
Found at i:19750349 original size:55 final size:55
Alignment explanation
Indices: 19750249--19750353 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
19750239 TTCCAAAGGC
* *
19750249 AGTCATACTACGAATAGTCTCTACGTACAGACCTATGGCAAATAGTCCTGCAGAT
1 AGTCATACTACGAATAGTCTCTACGTACAGACATATGACAAATAGTCCTGCAGAT
* * **
19750304 AGTCATACTACGGATAGTCTCTACGTATAGACATATGACGGATAGTCCTG
1 AGTCATACTACGAATAGTCTCTACGTACAGACATATGACAAATAGTCCTG
19750354 TGAACAGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (55 bp):
AGTCATACTACGAATAGTCTCTACGTACAGACATATGACAAATAGTCCTGCAGAT
Found at i:19759608 original size:42 final size:42
Alignment explanation
Indices: 19759496--19759641 Score: 145
Period size: 42 Copynumber: 3.4 Consensus size: 42
19759486 TTTCGTTATG
*
19759496 TGATTTCATGTAAGACCAC-GTCTGGGACGTTGGCATCG-ACTTC
1 TGATTTCATGTAAGACC-CTGTCTGGGACATTGGCATCGTA--TC
* * *
19759539 T-ATATTACGTGTAAGACCATGTATGGGACATTGGCATCGTATC
1 TGAT-TT-CATGTAAGACCCTGTCTGGGACATTGGCATCGTATC
* * *
19759582 TGATTTCATGTAAGACCCTGTCTGGGACAGTGGCATCGATGTT
1 TGATTTCATGTAAGACCCTGTCTGGGACATTGGCATCG-TATC
*
19759625 TGATTACATGTAAGACC
1 TGATTTCATGTAAGACC
19759642 ACGTCTAGGA
Statistics
Matches: 86, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
42 30 0.35
43 26 0.30
44 29 0.34
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (42 bp):
TGATTTCATGTAAGACCCTGTCTGGGACATTGGCATCGTATC
Found at i:19759883 original size:20 final size:21
Alignment explanation
Indices: 19759854--19759893 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
19759844 GTATAAATGA
19759854 TTTGATGATA-C-TTATTTGC
1 TTTGATGATATCTTTATTTGC
19759873 TTTGAATGATATCTTTATTTG
1 TTTG-ATGATATCTTTATTTG
19759894 TATATGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 1 0.06
22 7 0.39
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (21 bp):
TTTGATGATATCTTTATTTGC
Found at i:19768761 original size:27 final size:27
Alignment explanation
Indices: 19768723--19768776 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
19768713 AATACAATGG
19768723 ATGAAGGAATACCATGTAATCGTACTA
1 ATGAAGGAATACCATGTAATCGTACTA
*
19768750 ATGAAGGAATACCATGTAATTGTACTA
1 ATGAAGGAATACCATGTAATCGTACTA
19768777 TCTTGACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (27 bp):
ATGAAGGAATACCATGTAATCGTACTA
Found at i:19771502 original size:29 final size:29
Alignment explanation
Indices: 19771470--19771545 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
19771460 ATCATATTCG
*
19771470 TATGGCCTATTAGGCCCAAATCACCTGTA
1 TATGGCCTATTAGGCCCAAATCACATGTA
* *
19771499 TATGGCCCATTAGGCCCAAATCACATTTA
1 TATGGCCTATTAGGCCCAAATCACATGTA
* *
19771528 TATGGCTTGTTAGGCCCA
1 TATGGCCTATTAGGCCCA
19771546 GTCACATTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (29 bp):
TATGGCCTATTAGGCCCAAATCACATGTA
Found at i:19782214 original size:27 final size:26
Alignment explanation
Indices: 19782184--19782298 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
19782174 GGCAAAATTC
19782184 TCATTTTACCTCATAAGGGCAAAACAA
1 TCATTTTACC-CATAAGGGCAAAACAA
*
19782211 TCATTTTAACCCATAAGGGTAAAACAA
1 TCATTTT-ACCCATAAGGGCAAAACAA
* *
19782238 TCATTTTACCCCAAAAGGGCAAAACAG
1 TCATTTTA-CCCATAAGGGCAAAACAA
* * * *
19782265 TCATTTTGCCACATGAGGGAAAAATAA
1 TCATTTTACC-CATAAGGGCAAAACAA
19782292 TCATTTT
1 TCATTTT
19782299 TTCGATTAGG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.04
27 69 0.92
28 3 0.04
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (26 bp):
TCATTTTACCCATAAGGGCAAAACAA
Found at i:19782256 original size:54 final size:54
Alignment explanation
Indices: 19782184--19782298 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
19782174 GGCAAAATTC
* * *
19782184 TCATTTTACCTCATAAGGGCAAAACAATCATTTTAACC-CATAAGGGTAAAACAA
1 TCATTTTACCCCAAAAGGGCAAAACAATCATTTT-ACCACATAAGGGAAAAACAA
* * * *
19782238 TCATTTTACCCCAAAAGGGCAAAACAGTCATTTTGCCACATGAGGGAAAAATAA
1 TCATTTTACCCCAAAAGGGCAAAACAATCATTTTACCACATAAGGGAAAAACAA
19782292 TCATTTT
1 TCATTTT
19782299 TTCGATTAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
53 2 0.04
54 51 0.96
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (54 bp):
TCATTTTACCCCAAAAGGGCAAAACAATCATTTTACCACATAAGGGAAAAACAA
Found at i:19787513 original size:16 final size:16
Alignment explanation
Indices: 19787484--19787516 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19787474 CTAGCTCGAG
19787484 TGCATTTTATTTTCTT
1 TGCATTTTATTTTCTT
19787500 TGCATGTTTA-TTTCTT
1 TGCAT-TTTATTTTCTT
19787516 T
1 T
19787517 TTTTTTCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.67
Consensus pattern (16 bp):
TGCATTTTATTTTCTT
Found at i:19787543 original size:16 final size:16
Alignment explanation
Indices: 19787518--19787566 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
19787508 TATTTCTTTT
19787518 TTTTTCAGTTTAGTTTG
1 TTTTT-AGTTTAGTTTG
*
19787535 TTTTTAGTTTTATTTTG
1 TTTTTAG-TTTAGTTTG
*
19787552 -TTTTCGTTTAGTTTG
1 TTTTTAGTTTAGTTTG
19787567 CTTGAAGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 13 0.46
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.69
Consensus pattern (16 bp):
TTTTTAGTTTAGTTTG
Found at i:19792278 original size:5 final size:5
Alignment explanation
Indices: 19792257--19792293 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
19792247 TTTATGGAAC
19792257 TTTCT TTGT-T TTT-T TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TT-TCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
19792294 TTTCTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 5 0.17
5 24 0.80
6 1 0.03
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (5 bp):
TTTCT
Found at i:19792288 original size:15 final size:13
Alignment explanation
Indices: 19792257--19792296 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
19792247 TTTATGGAAC
19792257 TTTCTTTGTTTTTT
1 TTTCTTT-TTTTTT
19792271 TTTCTTTTCTTTTCT
1 TTTCTTTT-TTTT-T
19792286 TTTCTTTTTTT
1 TTTCTTTTTTT
19792297 CTATAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.04
14 14 0.58
15 9 0.38
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:19795636 original size:17 final size:17
Alignment explanation
Indices: 19795614--19795647 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19795604 CATGGGTTTA
19795614 TTGTGAATTTCAGTAAT
1 TTGTGAATTTCAGTAAT
* *
19795631 TTGTGATTTTGAGTAAT
1 TTGTGAATTTCAGTAAT
19795648 AAGGACTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (17 bp):
TTGTGAATTTCAGTAAT
Found at i:19799789 original size:21 final size:20
Alignment explanation
Indices: 19799763--19799804 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
19799753 TGTGTCCCCT
19799763 GTTTTGAGTAAAATTTTCAAA
1 GTTTTGAG-AAAATTTTCAAA
* *
19799784 GTTTTGTGAAAATTTTTAAA
1 GTTTTGAGAAAATTTTCAAA
19799804 G
1 G
19799805 ATATTGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (20 bp):
GTTTTGAGAAAATTTTCAAA
Found at i:19802457 original size:85 final size:85
Alignment explanation
Indices: 19802279--19802447 Score: 320
Period size: 85 Copynumber: 2.0 Consensus size: 85
19802269 CTTACCTCTC
*
19802279 TCCATAGCTAGGATTTCTTCAACTTCCAAGCTTCATAGTAAGTGATTTCAAGCCTCGTTTTTAAT
1 TCCATAGCTAGGATTTCTTCAACTTCAAAGCTTCATAGTAAGTGATTTCAAGCCTCGTTTTTAAT
19802344 GATTTTTATATTTTTGAAAA
66 GATTTTTATATTTTTGAAAA
*
19802364 TCCATAGCTAGGGTTTCTTCAACTTCAAAGCTTCATAGTAAGTGATTTCAAGCCTCGTTTTTAAT
1 TCCATAGCTAGGATTTCTTCAACTTCAAAGCTTCATAGTAAGTGATTTCAAGCCTCGTTTTTAAT
19802429 GATTTTTATATTTTTGAAA
66 GATTTTTATATTTTTGAAA
19802448 TCCGGTAGCT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (85 bp):
TCCATAGCTAGGATTTCTTCAACTTCAAAGCTTCATAGTAAGTGATTTCAAGCCTCGTTTTTAAT
GATTTTTATATTTTTGAAAA
Found at i:19813759 original size:73 final size:74
Alignment explanation
Indices: 19813672--19813820 Score: 255
Period size: 74 Copynumber: 2.0 Consensus size: 74
19813662 TAGGTTCAGG
*
19813672 CTTGAATTGGGTG-AAAAAATGGCTTGGTTTTGGCCTATTCCTTGTCCACAAGGCCAAATACACG
1 CTTGAATTGGGTGAAAAAAATGGCTTGGTTTTGGCCTATTCCTTGTCCACAAGGCCAAAAACACG
19813736 GGTGTGTGT
66 GGTGTGTGT
* * *
19813745 CTTGAATTGGGTGAAAAAAATGGCTTGGTTTTGGCCTATTTCTTGTCTACAAGGCCAAAAACACT
1 CTTGAATTGGGTGAAAAAAATGGCTTGGTTTTGGCCTATTCCTTGTCCACAAGGCCAAAAACACG
19813810 GGTGTGTGT
66 GGTGTGTGT
19813819 CT
1 CT
19813821 CAGCCATGTG
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 13 0.18
74 58 0.82
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (74 bp):
CTTGAATTGGGTGAAAAAAATGGCTTGGTTTTGGCCTATTCCTTGTCCACAAGGCCAAAAACACG
GGTGTGTGT
Found at i:19816741 original size:21 final size:21
Alignment explanation
Indices: 19816715--19816756 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19816705 ATGATGCCTT
*
19816715 GATCCAAAGTCAAGCAGCAAC
1 GATCCAAAGCCAAGCAGCAAC
*
19816736 GATCCAAAGCCAAGCATCAAC
1 GATCCAAAGCCAAGCAGCAAC
19816757 ACTAAAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.31, G:0.17, T:0.10
Consensus pattern (21 bp):
GATCCAAAGCCAAGCAGCAAC
Found at i:19819521 original size:26 final size:26
Alignment explanation
Indices: 19819492--19819700 Score: 309
Period size: 26 Copynumber: 8.2 Consensus size: 26
19819482 GAGGAAGTGC
19819492 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
19819518 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
19819544 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
19819570 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
19819596 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
19819622 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
19819648 AAAAGGGCTT-TGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
19819673 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
19819696 AAAAG
1 AAAAG
19819701 AGGGTAGGCC
Statistics
Matches: 165, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
23 5 0.03
24 3 0.02
25 29 0.18
26 128 0.78
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:19819949 original size:31 final size:31
Alignment explanation
Indices: 19819911--19819989 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
19819901 CGTTTACAGT
19819911 AAAGGCTTCAGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCAGCCCAGTGAAATGATTTATGA
** * *
19819942 AAAGGCTTTGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCAGCCCAGTGAAATGATTTATGA
19819973 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCAGCCCAGT
19819990 AACCGTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTGAAATGATTTATGA
Found at i:19823472 original size:49 final size:47
Alignment explanation
Indices: 19823204--19823659 Score: 750
Period size: 47 Copynumber: 9.6 Consensus size: 47
19823194 CCCTTCGGGA
* * * * * *
19823204 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19823251 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19823298 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19823345 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19823392 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19823439 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19823488 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19823535 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19823584 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19823633 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
19823660 TATTCAAATA
Statistics
Matches: 387, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
47 247 0.64
49 140 0.36
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19823489 original size:96 final size:94
Alignment explanation
Indices: 19823204--19823659 Score: 750
Period size: 96 Copynumber: 4.8 Consensus size: 94
19823194 CCCTTCGGGA
* * * * * * * *
19823204 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
19823269 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
19823298 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
19823363 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
19823392 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
19823457 ACTTTCACATTCATCACATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
19823488 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
19823553 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
19823584 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
19823649 ACTTTCACATT
64 ACTTTCACATT
19823660 TATTCAAATA
Statistics
Matches: 342, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
94 140 0.41
96 156 0.46
98 46 0.13
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:19827057 original size:27 final size:27
Alignment explanation
Indices: 19827027--19827232 Score: 144
Period size: 27 Copynumber: 7.6 Consensus size: 27
19827017 CAAATTGTAA
*
19827027 AATTACCAAAGTACCCTCGATTTATAG
1 AATTACCAAATTACCCTCGATTTATAG
***
19827054 AATTACCGTTTTACCCTCGATTTATAG
1 AATTACCAAATTACCCTCGATTTATAG
***
19827081 AATTACCGTTTTACCCTCGATTTATAG
1 AATTACCAAATTACCCTCGATTTATAG
* ** * *
19827108 AATTACTATTTTACCCTTGATTTACAG
1 AATTACCAAATTACCCTCGATTTATAG
**** * *
19827135 AATTACTGTTTTACCCTCGATTTACAA
1 AATTACCAAATTACCCTCGATTTATAG
* * * * * *
19827162 AATTACTAAAATGCCCTCGGTTTACAA
1 AATTACCAAATTACCCTCGATTTATAG
* * *
19827189 AATTACCAAAATACCCTCGA-TCAGTAA
1 AATTACCAAATTACCCTCGATTTA-TAG
*
19827216 AATTACCAAAATACCCT
1 AATTACCAAATTACCCT
19827233 AGTCTGTAAA
Statistics
Matches: 156, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 2 0.01
27 154 0.99
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (27 bp):
AATTACCAAATTACCCTCGATTTATAG
Found at i:19827069 original size:54 final size:54
Alignment explanation
Indices: 19827011--19827124 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
19827001 ATTACTGAAA
* *
19827011 TACCCTCAAATTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCAAATTATAAAATTACCAAAGTACCCTCGATTTATAGAATTACCATTT
* * * **** *
19827065 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTATAGAATTACTATTT
1 TACCCTCAAATTATAAAATTACCAAAGTACCCTCGATTTATAGAATTACCATTT
19827119 TACCCT
1 TACCCT
19827125 TGATTTACAG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.38
Consensus pattern (54 bp):
TACCCTCAAATTATAAAATTACCAAAGTACCCTCGATTTATAGAATTACCATTT
Found at i:19827130 original size:54 final size:54
Alignment explanation
Indices: 19827038--19827169 Score: 201
Period size: 54 Copynumber: 2.4 Consensus size: 54
19827028 ATTACCAAAG
** *
19827038 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTT
* *
19827092 TACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTT
* *
19827146 TACCCTCGATTTACAAAATTACTA
1 TACCCTCGATTTATAGAATTACTA
19827170 AAATGCCCTC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (54 bp):
TACCCTCGATTTATAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTT
Found at i:19827186 original size:54 final size:54
Alignment explanation
Indices: 19827065--19827195 Score: 163
Period size: 54 Copynumber: 2.4 Consensus size: 54
19827055 ATTACCGTTT
* * * ***
19827065 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAA
* *
19827119 TACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAA
* * *
19827173 TGCCCTCGGTTTACAAAATTACC
1 TACCCTCGATTTACAGAATTACC
19827196 AAAATACCCT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (54 bp):
TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAA
Found at i:19827204 original size:81 final size:81
Alignment explanation
Indices: 19826993--19827209 Score: 200
Period size: 81 Copynumber: 2.7 Consensus size: 81
19826983 AATACTTTAG
* ** * * ** * *
19826993 TTTACCAAATTACTGAAATACCCTCAAATTGTAAAATTACCAAAGTACCCTCGATTTATAGAATT
1 TTTACAAAATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTACAGAATT
19827058 ACCGTTTTACCCTCGA
66 ACCGTTTTACCCTCGA
* * **** * * * *** *
19827074 TTTATAGAATTACCGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATT
1 TTTACAAAATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTACAGAATT
*
19827139 ACTGTTTTACCCTCGA
66 ACCGTTTTACCCTCGA
* * *
19827155 TTTACAAAATTACTAAAATGCCCTCGGTTTACAAAATTACCAAAATACCCTCGAT
1 TTTACAAAATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCTCGAT
19827210 CAGTAAAATT
Statistics
Matches: 102, Mismatches: 34, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
81 102 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (81 bp):
TTTACAAAATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTACAGAATT
ACCGTTTTACCCTCGA
Found at i:19827231 original size:81 final size:81
Alignment explanation
Indices: 19827146--19827422 Score: 292
Period size: 81 Copynumber: 3.4 Consensus size: 81
19827136 ATTACTGTTT
* * ** * * *
19827146 TACCCTCGATTTACAAAATTACTAAAATGCCCTCGGTTTACAAAATTACCAAAATACCCTCGATC
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATT
*
19827211 AGTAAAATTACCAAAA
66 TGTAAAATTACCAAAA
* * ** * * *
19827227 TACCCTAG-TCTGTAAAATTGCTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCATTAATT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATT
19827291 TGTAAAATTACCAAAA
66 TGTAAAATTACCAAAA
* * ** * * *
19827307 TTCCCT-TAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTGAAATTACTGAAATACCCTCAAT
1 TACCCTCGA-TTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAAT
19827371 TTGTAAAATTACCAAAA
65 TTGTAAAATTACCAAAA
*
19827388 TACCC-CTGATTTACAAAGTTAC-AGAAATACCCTTG
1 TACCCTC-GATTTACAAAATTACTA-AAATACCCTTG
19827423 ACTTTCTAAA
Statistics
Matches: 162, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
80 64 0.40
81 97 0.60
82 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATT
TGTAAAATTACCAAAA
Found at i:19827280 original size:27 final size:27
Alignment explanation
Indices: 19827160--19827505 Score: 257
Period size: 27 Copynumber: 12.8 Consensus size: 27
19827150 CTCGATTTAC
* * * **
19827160 AAAATTACTAAAATGCCCTCGGTTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
* * **
19827187 AAAATTACCAAAATACCCTCGATCAGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
19827214 AAAATTACCAAAATACCC-TAGTCTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
19827240 AAAATTGCTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * **
19827267 AAAATTACCGAAATACCATTAATTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
19827294 AAAATTACCAAAATTCCCTTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
19827321 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* ** ***
19827348 GAAATTACTGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * **
19827375 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
19827402 AAAGTTA-CAGAAATACCCTTGACTTTCT
1 AAAATTACCA-AAATACCCTTG-GTTTGT
* * **
19827430 AAAAATTA-TAGAAATACCATTGGTTTAC
1 -AAAATTACCA-AAATACCCTTGGTTTGT
** *
19827458 AAAATTACTGAAATACCTTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
19827485 AGATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
19827506 TAGGATGAAA
Statistics
Matches: 252, Mismatches: 62, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
26 22 0.09
27 205 0.81
28 7 0.03
29 18 0.07
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGGTTTGT
Found at i:19827566 original size:27 final size:27
Alignment explanation
Indices: 19827536--19827627 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
19827526 ACCCCTATTA
*
19827536 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
*
19827563 GGTAAAGTGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
19827590 GGTAAAGTGATCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
19827617 GGTAAAATGAC
1 GGTAAAATGAC
19827628 AAATATGCCC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:19828457 original size:26 final size:26
Alignment explanation
Indices: 19828428--19828652 Score: 328
Period size: 26 Copynumber: 8.7 Consensus size: 26
19828418 GAGGAAGTGC
**
19828428 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
19828454 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
19828480 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
19828506 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
19828532 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
19828558 AAAAGGGCTTATGTCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
19828584 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
19828610 AAAAGGGCTT-TGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
19828635 AAAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTATGCCCCAG
19828653 CTATTAAAAG
Statistics
Matches: 177, Mismatches: 22, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
25 29 0.16
26 148 0.84
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:19828506 original size:52 final size:52
Alignment explanation
Indices: 19828428--19828652 Score: 402
Period size: 52 Copynumber: 4.4 Consensus size: 52
19828418 GAGGAAGTGC
19828428 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
19828480 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
19828532 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGTCCC-AGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG-CCCTAGTTTACCG
* *
19828584 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
19828635 AAAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTATGCCCCAG
19828653 CTATTAAAAG
Statistics
Matches: 170, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
50 11 0.06
51 20 0.12
52 136 0.80
53 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
Found at i:19828908 original size:31 final size:31
Alignment explanation
Indices: 19828873--19828951 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
19828863 CGTTTACAGT
*
19828873 AAAGGCTTCAGCCTAGTGAAATGATTTATGA
1 AAAGGCTTCAGCCCAGTGAAATGATTTATGA
* *
19828904 AAAGGC-TCTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTC-AGCCCAGTGAAATGATTTATGA
19828935 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCAGCCCAGT
19828952 AACCGTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 2 0.05
31 38 0.90
32 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTGAAATGATTTATGA
Found at i:19832910 original size:36 final size:37
Alignment explanation
Indices: 19832841--19832913 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
19832831 GAACTGGACT
*
19832841 CGGCATTCAGAGAATCAACTTGGACCTCGGATTATTA
1 CGGCATTCAGAGAATCAACTTGGACCTCAGATTATTA
19832878 CGGCATTCCA-AGAATCAACTT-GACCTCAGATTATTA
1 CGGCATT-CAGAGAATCAACTTGGACCTCAGATTATTA
19832914 TTTTTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 14 0.41
37 18 0.53
38 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (37 bp):
CGGCATTCAGAGAATCAACTTGGACCTCAGATTATTA
Found at i:19845928 original size:21 final size:19
Alignment explanation
Indices: 19845893--19845931 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
19845883 TAAACACCTA
19845893 TTATTTTTATTTATTTATT
1 TTATTTTTATTTATTTATT
19845912 TTATTTTTATCTTTATTTAT
1 TTATTTTTA--TTTATTTAT
19845932 ATTTTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (19 bp):
TTATTTTTATTTATTTATT
Found at i:19867384 original size:30 final size:30
Alignment explanation
Indices: 19867348--19867408 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
19867338 CATTTAATAA
*
19867348 AAAC-TTTGAAAAAATTACATTTTTGCCCCT
1 AAACTTTTG-AAAAATTACACTTTTGCCCCT
* *
19867378 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACACTTTTGCCCCT
19867408 A
1 A
19867409 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACACTTTTGCCCCT
Found at i:19872663 original size:21 final size:21
Alignment explanation
Indices: 19872639--19872680 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19872629 TCATCAGATC
19872639 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGCATCGGGGG
**
19872660 TACAGGTTGAGGCATCGGGGG
1 TACACCTTGAGGCATCGGGGG
19872681 AGGTGGGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (21 bp):
TACACCTTGAGGCATCGGGGG
Found at i:19882613 original size:23 final size:23
Alignment explanation
Indices: 19882571--19882614 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19882561 CTGACCTCTG
* *
19882571 TGTATTACGAATATAGAATTTTT
1 TGTATTACGAATACAAAATTTTT
*
19882594 TGTATTACGAATGCAAAATTT
1 TGTATTACGAATACAAAATTT
19882615 CAATGACTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (23 bp):
TGTATTACGAATACAAAATTTTT
Found at i:19888813 original size:32 final size:32
Alignment explanation
Indices: 19888777--19888842 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
19888767 AAATCTCGAG
19888777 TTCCCTACACTGGCTGCAAAAGTATTCTGAGA
1 TTCCCTACACTGGCTGCAAAAGTATTCTGAGA
19888809 TTCCCTACACTGGCTGCAAAAGTATTCTGAGA
1 TTCCCTACACTGGCTGCAAAAGTATTCTGAGA
19888841 TT
1 TT
19888843 TAGGACCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (32 bp):
TTCCCTACACTGGCTGCAAAAGTATTCTGAGA
Found at i:19898872 original size:15 final size:15
Alignment explanation
Indices: 19898852--19898889 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
19898842 CACAATCGCA
19898852 ACAAGTAATAAAGTG
1 ACAAGTAATAAAGTG
19898867 ACAAGTAATAAAGTG
1 ACAAGTAATAAAGTG
19898882 ACAAGTAA
1 ACAAGTAA
19898890 ATGTCGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.18
Consensus pattern (15 bp):
ACAAGTAATAAAGTG
Found at i:19904702 original size:29 final size:29
Alignment explanation
Indices: 19904644--19904703 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
19904634 GCCTTTTGAC
* * **
19904644 AATATTTACAAAAAGAGGCATCTAGTTTT
1 AATATTTACAAAAAGAGGCACCAAAATTT
19904673 AATATTTACAAAAAGA-GCAACCAAAATTT
1 AATATTTACAAAAAGAGGC-ACCAAAATTT
19904702 AA
1 AA
19904704 AAATAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (29 bp):
AATATTTACAAAAAGAGGCACCAAAATTT
Found at i:19907770 original size:27 final size:27
Alignment explanation
Indices: 19907740--19907917 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
19907730 ATATTGAGCC
* * * *
19907740 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
19907767 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19907794 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
19907822 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
19907849 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
19907876 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19907903 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19907918 GTAGAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:19907879 original size:82 final size:81
Alignment explanation
Indices: 19907761--19907916 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19907751 TGCTATATAA
* *
19907761 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
19907826 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
19907843 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
19907907 CACTTAGTGC
65 CACTTAGTGC
19907917 TGTAGAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19917085 original size:27 final size:27
Alignment explanation
Indices: 19917055--19917232 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
19917045 ATATTGAGTC
* * * *
19917055 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
19917082 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19917109 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
19917137 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
19917164 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
19917191 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19917218 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19917233 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:19917194 original size:82 final size:81
Alignment explanation
Indices: 19917076--19917231 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19917066 TGCTATATAA
* *
19917076 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
19917141 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
19917158 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
19917222 CACTTAGTGC
65 CACTTAGTGC
19917232 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19930895 original size:19 final size:19
Alignment explanation
Indices: 19930863--19930909 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
19930853 AACTAAACAC
*
19930863 AAATAATATTAATAAAAATA
1 AAATAATATGAAT-AAAATA
19930883 AAATAA-ATGAATAAAATA
1 AAATAATATGAATAAAATA
19930901 ATAATAATA
1 A-AATAATA
19930910 AACTATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.29
19 10 0.42
20 7 0.29
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAATAATATGAATAAAATA
Found at i:19943721 original size:37 final size:37
Alignment explanation
Indices: 19943665--19943743 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
19943655 CCGAGCTCTA
* * *
19943665 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
19943702 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
19943739 AAGAC
1 AAGAC
19943744 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:19945695 original size:43 final size:43
Alignment explanation
Indices: 19945647--19945749 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
19945637 TTGGTTTTCA
*
19945647 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTCTGAGATTG
19945690 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTCTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTCTGAGATTG
19945733 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
19945750 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTCTGAGATTG
Found at i:19945766 original size:29 final size:29
Alignment explanation
Indices: 19945731--19945804 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
19945721 GTTCTGAGAT
* *
19945731 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
19945760 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
19945789 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
19945805 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:19946240 original size:40 final size:40
Alignment explanation
Indices: 19946117--19946308 Score: 167
Period size: 40 Copynumber: 4.8 Consensus size: 40
19946107 TCGAATGATG
** *
19946117 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAA-TGA-TATA
* ** * * * *
19946157 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAATGA-TATA
*
19946197 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAATGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAATGATATA
* *
19946237 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAATGATATA
** * *
19946277 TCCATGCTAAATCCCGAAGAGCAATCATGCTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTA
19946309 GTGACGTGTA
Statistics
Matches: 125, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 105 0.84
41 19 0.15
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAATGATATA
Found at i:19946254 original size:80 final size:82
Alignment explanation
Indices: 19946117--19946313 Score: 210
Period size: 80 Copynumber: 2.5 Consensus size: 82
19946107 TCGAATGATG
**
19946117 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAAGTGACCATATCCGGACTAAGATCCGAAGAGCA
* *
19946179 TTGGTGCGAGTTACTAAA
66 TTCGTGCGAGTGA-TAAA
** *
19946197 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAA-TGA-TGTATCCGGGCTAAG-TCCCGAAGAGC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGAGC
* *
19946259 ATTCGTGCTAGTGATATA
65 ATTCGTGCGAGTGATAAA
** * *
19946277 TCCATGCTAAATCCCGAAGAGCAATCATGCT-AGTGAC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAAGTGAC
19946314 GTGTATTCGG
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
79 2 0.02
80 70 0.71
81 18 0.18
82 8 0.08
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAAGTGACCATATCCGGACTAAGATCCGAAGAGCA
TTCGTGCGAGTGATAAA
Found at i:19950245 original size:37 final size:37
Alignment explanation
Indices: 19950189--19950267 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
19950179 CCGAGCTCTA
* * *
19950189 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
19950226 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
19950263 AAGAC
1 AAGAC
19950268 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:19952430 original size:23 final size:23
Alignment explanation
Indices: 19952404--19952448 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
19952394 CATGTCCAAG
19952404 TGATTTGACCACATTCCATATGT
1 TGATTTGACCACATTCCATATGT
* *
19952427 TGATTTGACCATATTTCATATG
1 TGATTTGACCACATTCCATATG
19952449 CCCATTCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (23 bp):
TGATTTGACCACATTCCATATGT
Found at i:19955411 original size:41 final size:41
Alignment explanation
Indices: 19955349--19955449 Score: 159
Period size: 41 Copynumber: 2.5 Consensus size: 41
19955339 TGGAGATAGC
* * *
19955349 GATTTAGGCTTTGTACCTAGCA-GTTTTAGTGCTGGTGTATT
1 GATTCAGGCTTTGTGCCTAGCAGGTTTT-GTGCCGGTGTATT
19955390 GATTCAGGCTTTGTGCCTAGCAGGTTTTGTGCCGGTGTATT
1 GATTCAGGCTTTGTGCCTAGCAGGTTTTGTGCCGGTGTATT
19955431 GATTCAGGCTTTGTGCCTA
1 GATTCAGGCTTTGTGCCTA
19955450 CCAAGCTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 51 0.91
42 5 0.09
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.41
Consensus pattern (41 bp):
GATTCAGGCTTTGTGCCTAGCAGGTTTTGTGCCGGTGTATT
Found at i:19964087 original size:34 final size:35
Alignment explanation
Indices: 19964040--19964107 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 35
19964030 ACTAGTTAAT
19964040 AGGGTATTCCATATTAC-TTTTCAATTTCAATTTC
1 AGGGTATTCCATATTACTTTTTCAATTTCAATTTC
*
19964074 AGGGTATTTCATATTACTTTTTCAATTTCAATTT
1 AGGGTATTCCATATTACTTTTTCAATTTCAATTT
19964108 TATTCTCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (35 bp):
AGGGTATTCCATATTACTTTTTCAATTTCAATTTC
Found at i:19964481 original size:17 final size:18
Alignment explanation
Indices: 19964451--19964484 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19964441 AATTTCTATT
19964451 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
19964469 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
19964485 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:19964759 original size:22 final size:20
Alignment explanation
Indices: 19964725--19964765 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
19964715 CTCTATTTCT
19964725 TTTTAGCTTTGTTTCTTTTG
1 TTTTAGCTTTGTTTCTTTTG
19964745 TTTTATGCTATTGTTTCTTTT
1 TTTTA-GCT-TTGTTTCTTTT
19964766 ATTTCATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 3 0.16
22 11 0.58
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.71
Consensus pattern (20 bp):
TTTTAGCTTTGTTTCTTTTG
Found at i:19964996 original size:16 final size:16
Alignment explanation
Indices: 19964977--19965018 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
19964967 AATCTCGTAA
19964977 TATAATTAATATAAAT
1 TATAATTAATATAAAT
*
19964993 TATAATTTA-ATAAAT
1 TATAATTAATATAAAT
19965008 TAATAA-TAATA
1 T-ATAATTAATA
19965019 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATTAATATAAAT
Found at i:19965022 original size:25 final size:26
Alignment explanation
Indices: 19964974--19965023 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
19964964 AAAAATCTCG
*
19964974 TAATATAATTAATATAAATTATAATT
1 TAATATAATTAATATAAATAATAATT
19965000 TAATA-AATTAATA-ATAATAATAAT
1 TAATATAATTAATATA-AATAATAAT
19965024 AATAATACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 16 0.73
26 5 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TAATATAATTAATATAAATAATAATT
Found at i:19965200 original size:19 final size:19
Alignment explanation
Indices: 19965176--19965228 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 19
19965166 ATAATTATTT
19965176 AATTAATAAATATATTTTA
1 AATTAATAAATATATTTTA
**
19965195 AATTAAT-AAT-TATAATA
1 AATTAATAAATATATTTTA
19965212 AA-TAATAAATATATTTT
1 AATTAATAAATATATTTT
19965229 TACTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
18 7 0.25
19 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTAATAAATATATTTTA
Found at i:19965219 original size:16 final size:17
Alignment explanation
Indices: 19965176--19965224 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
19965166 ATAATTATTT
*
19965176 AATTAATAAATATATTTTA
1 AATTAATAAATATA--ATA
*
19965195 AATTAATAATTATAATA
1 AATTAATAAATATAATA
19965212 AA-TAATAAATATA
1 AATTAATAAATATA
19965225 TTTTTACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 10 0.37
17 4 0.15
19 13 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTAATAAATATAATA
Found at i:19974878 original size:23 final size:21
Alignment explanation
Indices: 19974836--19974894 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
19974826 ACATGAAACA
* *
19974836 ACACACGAGGTGCCTGATATG
1 ACACACAAGGTGCCTAATATG
19974857 ACACACAAGGTGCCTCAAATATG
1 ACACACAAGGTGCCT--AATATG
* *
19974880 ACACATAAAGTGCCT
1 ACACACAAGGTGCCT
19974895 GATCAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 14 0.44
23 18 0.56
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (21 bp):
ACACACAAGGTGCCTAATATG
Found at i:19975383 original size:17 final size:18
Alignment explanation
Indices: 19975353--19975386 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19975343 AATTTCTATT
19975353 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
19975371 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
19975387 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:19976146 original size:22 final size:20
Alignment explanation
Indices: 19976111--19976151 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
19976101 CTTTGTTTCT
19976111 TTTTAGCTTTGTTTCTTTTG
1 TTTTAGCTTTGTTTCTTTTG
19976131 TTTTATGCTTTTGTTTCTTTT
1 TTTTA-GC-TTTGTTTCTTTT
19976152 ATTTCATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.73
Consensus pattern (20 bp):
TTTTAGCTTTGTTTCTTTTG
Found at i:19978609 original size:25 final size:24
Alignment explanation
Indices: 19978581--19978648 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 24
19978571 AGCTCTTCAT
19978581 GAGCGTCCTATTATATGGCTCCCCG
1 GAGC-TCCTATTATATGGCTCCCCG
* * **
19978606 GAGCTTCT-TGATATGGCTCGCTTG
1 GAGCTCCTATTATATGGCTC-CCCG
* *
19978630 AACCTCCTATTATATGGCT
1 GAGCTCCTATTATATGGCT
19978649 ATTTAGAGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
23 10 0.30
24 10 0.30
25 13 0.39
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (24 bp):
GAGCTCCTATTATATGGCTCCCCG
Found at i:19978726 original size:25 final size:24
Alignment explanation
Indices: 19978693--19978744 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
19978683 GCCTGTTAAA
*
19978693 CTCAATGAGCTTCCTATTACATGG
1 CTCAATGAGCATCCTATTACATGG
* *
19978717 CTCACATGAGCATCCTGTTATATGG
1 CTCA-ATGAGCATCCTATTACATGG
19978742 CTC
1 CTC
19978745 GAGATTGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (24 bp):
CTCAATGAGCATCCTATTACATGG
Found at i:19979436 original size:25 final size:26
Alignment explanation
Indices: 19979408--19979459 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
19979398 AGCATTAAAA
*
19979408 TATATATGT-ATTAATGCTTA-ATTAT
1 TATATATGTGATAAATG-TTATATTAT
*
19979433 TATATTTGTGATAAATGTTATATTAT
1 TATATATGTGATAAATGTTATATTAT
19979459 T
1 T
19979460 GAAATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.54
Consensus pattern (26 bp):
TATATATGTGATAAATGTTATATTAT
Found at i:19983566 original size:49 final size:49
Alignment explanation
Indices: 19983504--19983603 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
19983494 GTGATTATCC
*
19983504 AAGTATCCTCTTCAATTCCGAATGGTTCTGCAGGCAATGATATGTTGTG
1 AAGTATCCGCTTCAATTCCGAATGGTTCTGCAGGCAATGATATGTTGTG
*
19983553 AAGTATCCGCTTCAATTCCGAATGGTTCTTCAGGCAATGATATGTTGTG
1 AAGTATCCGCTTCAATTCCGAATGGTTCTGCAGGCAATGATATGTTGTG
19983602 AA
1 AA
19983604 CAAAGGTGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (49 bp):
AAGTATCCGCTTCAATTCCGAATGGTTCTGCAGGCAATGATATGTTGTG
Found at i:19997442 original size:43 final size:43
Alignment explanation
Indices: 19997389--19997510 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
19997379 ACATAGGATT
*
19997389 TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGACA
1 TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACAGTGACA
* *
19997432 TCGATTTGTGATTTCGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGATATGTGATTTCGTGTAAGACCAC-GTCTGGGACAGTGACA
* * *
19997475 TCGATATGTTATTACATGTAAGACCACGTCTGGGAC
1 TCGATATGTGATTTCGTGTAAGACCACGTCTGGGAC
19997511 GTTTTCGTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.01
43 68 0.97
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACAGTGACA
Found at i:20008356 original size:22 final size:22
Alignment explanation
Indices: 20008331--20008372 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
20008321 AGTCATGAAG
20008331 AAGGTCAAATCAATCCAATTGA
1 AAGGTCAAATCAATCCAATTGA
*
20008353 AAGGTTAAATCAATCCAATT
1 AAGGTCAAATCAATCCAATT
20008373 AACTCCCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (22 bp):
AAGGTCAAATCAATCCAATTGA
Found at i:20010349 original size:40 final size:40
Alignment explanation
Indices: 20010284--20010395 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
20010274 TTCATAGTCT
20010284 AAGCTATTTT-AATCTAGCACACTAAGTGTCACATATAGCCG
1 AAGCTATTTTGAATC--GCACACTAAGTGTCACATATAGCCG
* *
20010325 AAGCTATTTTGAATCGCACACTAAGTGCCATATATAGCCG
1 AAGCTATTTTGAATCGCACACTAAGTGTCACATATAGCCG
* * *
20010365 AAGCTATCTCGAATCGTACACTAAGTGTCAC
1 AAGCTATTTTGAATCGCACACTAAGTGTCAC
20010396 CTGTATATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 49 0.78
41 10 0.16
42 4 0.06
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (40 bp):
AAGCTATTTTGAATCGCACACTAAGTGTCACATATAGCCG
Found at i:20011964 original size:19 final size:20
Alignment explanation
Indices: 20011942--20011989 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
20011932 TTATTACATT
20011942 TTATTTTT-TTTCATCTTAA
1 TTATTTTTATTTCATCTTAA
* *
20011961 TTATATTTTATTTGATCTTTA
1 TTAT-TTTTATTTCATCTTAA
*
20011982 TCATTTTT
1 TTATTTTT
20011990 CGAGATAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 8 0.33
21 12 0.50
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (20 bp):
TTATTTTTATTTCATCTTAA
Found at i:20021740 original size:50 final size:50
Alignment explanation
Indices: 20021665--20021764 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
20021655 AAAAAGATAG
20021665 TGATTTCGAGGTCATAAATGGAGTGCTCCCCCACCTTAATAATCATTCCT
1 TGATTTCGAGGTCATAAATGGAGTGCTCCCCCACCTTAATAATCATTCCT
* *
20021715 TGATTTCGAGGTCATAAATGGAGTGCTTCCCCACCTTAATAATTATTCCT
1 TGATTTCGAGGTCATAAATGGAGTGCTCCCCCACCTTAATAATCATTCCT
20021765 GCTTTTAGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (50 bp):
TGATTTCGAGGTCATAAATGGAGTGCTCCCCCACCTTAATAATCATTCCT
Found at i:20028294 original size:10 final size:10
Alignment explanation
Indices: 20028279--20028306 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
20028269 TAAAACTATT
20028279 AAAGTTTCTA
1 AAAGTTTCTA
20028289 AAAGTTTCTA
1 AAAGTTTCTA
20028299 AAAGTTTC
1 AAAGTTTC
20028307 CATTGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (10 bp):
AAAGTTTCTA
Found at i:20036741 original size:290 final size:290
Alignment explanation
Indices: 20036221--20036800 Score: 1160
Period size: 290 Copynumber: 2.0 Consensus size: 290
20036211 ATACGGGTTG
20036221 ATTTTACGTATTAATTAAAATAATATAACGAAGAAAACAAAAATAGAATAATATAAAATGTTTAA
1 ATTTTACGTATTAATTAAAATAATATAACGAAGAAAACAAAAATAGAATAATATAAAATGTTTAA
20036286 TTTCATGGTGAGTTCATCAAATTAAAAGTAAACTAACTTTCACAATGCACGGATTTATCTTGTTA
66 TTTCATGGTGAGTTCATCAAATTAAAAGTAAACTAACTTTCACAATGCACGGATTTATCTTGTTA
20036351 GATTTTAAAAATAAATTTCACAAATTCATAATTTTTTAATATATATAATATATTTATACATAATA
131 GATTTTAAAAATAAATTTCACAAATTCATAATTTTTTAATATATATAATATATTTATACATAATA
20036416 TAAACTTAGAAATTGAAAATAATAATAGATAAAAGAAATAGTAAACGTACAAAATCATTACTTCA
196 TAAACTTAGAAATTGAAAATAATAATAGATAAAAGAAATAGTAAACGTACAAAATCATTACTTCA
20036481 ATTTAATCAGGGGAGAGGTAGGTTAAAACA
261 ATTTAATCAGGGGAGAGGTAGGTTAAAACA
20036511 ATTTTACGTATTAATTAAAATAATATAACGAAGAAAACAAAAATAGAATAATATAAAATGTTTAA
1 ATTTTACGTATTAATTAAAATAATATAACGAAGAAAACAAAAATAGAATAATATAAAATGTTTAA
20036576 TTTCATGGTGAGTTCATCAAATTAAAAGTAAACTAACTTTCACAATGCACGGATTTATCTTGTTA
66 TTTCATGGTGAGTTCATCAAATTAAAAGTAAACTAACTTTCACAATGCACGGATTTATCTTGTTA
20036641 GATTTTAAAAATAAATTTCACAAATTCATAATTTTTTAATATATATAATATATTTATACATAATA
131 GATTTTAAAAATAAATTTCACAAATTCATAATTTTTTAATATATATAATATATTTATACATAATA
20036706 TAAACTTAGAAATTGAAAATAATAATAGATAAAAGAAATAGTAAACGTACAAAATCATTACTTCA
196 TAAACTTAGAAATTGAAAATAATAATAGATAAAAGAAATAGTAAACGTACAAAATCATTACTTCA
20036771 ATTTAATCAGGGGAGAGGTAGGTTAAAACA
261 ATTTAATCAGGGGAGAGGTAGGTTAAAACA
20036801 GAAAATTTTT
Statistics
Matches: 290, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
290 290 1.00
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (290 bp):
ATTTTACGTATTAATTAAAATAATATAACGAAGAAAACAAAAATAGAATAATATAAAATGTTTAA
TTTCATGGTGAGTTCATCAAATTAAAAGTAAACTAACTTTCACAATGCACGGATTTATCTTGTTA
GATTTTAAAAATAAATTTCACAAATTCATAATTTTTTAATATATATAATATATTTATACATAATA
TAAACTTAGAAATTGAAAATAATAATAGATAAAAGAAATAGTAAACGTACAAAATCATTACTTCA
ATTTAATCAGGGGAGAGGTAGGTTAAAACA
Found at i:20042808 original size:111 final size:111
Alignment explanation
Indices: 20042614--20042836 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
20042604 GTATTGGGTT
20042614 AGTTTCTTACCAAATTCCAACAGCTGAGACCATTTGAAGCAGCGAAAAAGAAATTGGGTCTTAAA
1 AGTTTCTTACCAAATTCCAACAGCTGAGACCATTTGAAGCAGCGAAAAAGAAATTGGGTCTTAAA
20042679 ACTTCAGCCCAATGAAGAAAACAACAAAAATATGTTAAAGACCCAA
66 ACTTCAGCCCAATGAAGAAAACAACAAAAATATGTTAAAGACCCAA
20042725 AGTTTCTTACCAAATTCCAACAGCTGAGACCATTTGAAGCAGCGAAAAAGAAATTGGGTCTTAAA
1 AGTTTCTTACCAAATTCCAACAGCTGAGACCATTTGAAGCAGCGAAAAAGAAATTGGGTCTTAAA
20042790 ACTTCAGCCCAATGAAGAAAACAACAAAAATATGTTAAAGACCCAA
66 ACTTCAGCCCAATGAAGAAAACAACAAAAATATGTTAAAGACCCAA
20042836 A
1 A
20042837 AAAGAGGAAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (111 bp):
AGTTTCTTACCAAATTCCAACAGCTGAGACCATTTGAAGCAGCGAAAAAGAAATTGGGTCTTAAA
ACTTCAGCCCAATGAAGAAAACAACAAAAATATGTTAAAGACCCAA
Found at i:20044162 original size:28 final size:28
Alignment explanation
Indices: 20044129--20044186 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
20044119 TGCTCATGTC
20044129 CTTTCATTTTCTTCTTTTTTCTTTATAG
1 CTTTCATTTTCTTCTTTTTTCTTTATAG
20044157 CTTTCATTTTCTTCTTTTTTCTTTATAG
1 CTTTCATTTTCTTCTTTTTTCTTTATAG
20044185 CT
1 CT
20044187 CTGTTATCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.10, C:0.19, G:0.03, T:0.67
Consensus pattern (28 bp):
CTTTCATTTTCTTCTTTTTTCTTTATAG
Found at i:20045391 original size:39 final size:39
Alignment explanation
Indices: 20045339--20045424 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
20045329 GACTTTAGCT
* * *
20045339 CGGACATATTTCCAGCACATAGCCTGCGGACCTTAAGTC
1 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
20045378 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
1 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
20045417 CGGATATA
1 CGGATATA
20045425 CATCAATATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (39 bp):
CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
Found at i:20051883 original size:5 final size:5
Alignment explanation
Indices: 20051873--20051906 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
20051863 ATCGATATTA
20051873 AATTG AATTG AATTG AATTG AATTG AATTG AATT
1 AATTG AATTG AATTG AATTG AATTG AATTG AATT
20051907 ATGAATTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
AATTG
Found at i:20052950 original size:118 final size:118
Alignment explanation
Indices: 20052792--20053028 Score: 474
Period size: 118 Copynumber: 2.0 Consensus size: 118
20052782 ATTTGAATAT
20052792 ACATATTTTATTGAATTGGTAATTAAAATTGATATTTAATGTGTTTGAATTAAGTGACCCGAACC
1 ACATATTTTATTGAATTGGTAATTAAAATTGATATTTAATGTGTTTGAATTAAGTGACCCGAACC
20052857 CTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATCCATATAG
66 CTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATCCATATAG
20052910 ACATATTTTATTGAATTGGTAATTAAAATTGATATTTAATGTGTTTGAATTAAGTGACCCGAACC
1 ACATATTTTATTGAATTGGTAATTAAAATTGATATTTAATGTGTTTGAATTAAGTGACCCGAACC
20052975 CTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATCCATATAG
66 CTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATCCATATAG
20053028 A
1 A
20053029 ACTACACTTC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (118 bp):
ACATATTTTATTGAATTGGTAATTAAAATTGATATTTAATGTGTTTGAATTAAGTGACCCGAACC
CTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGTAAAATCCATATAG
Found at i:20061279 original size:19 final size:18
Alignment explanation
Indices: 20061254--20061298 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
20061244 GTATATGAGT
**
20061254 TAATTGAATATAATCTTA
1 TAATTGAATATAAAATTA
*
20061272 TGAATTGATTATAAAATTA
1 T-AATTGAATATAAAATTA
20061291 TAATTGAA
1 TAATTGAA
20061299 ATATGTTGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (18 bp):
TAATTGAATATAAAATTA
Found at i:20061665 original size:74 final size:74
Alignment explanation
Indices: 20061544--20061692 Score: 271
Period size: 74 Copynumber: 2.0 Consensus size: 74
20061534 TATTGTAAGT
*
20061544 AAAATGGTACTAAGATTAAAATGTGCATGTTTATTGTTTTTAACTTAAGTATTTGAATTATAGTA
1 AAAATGGTACTAAGATTAAAATGTGCATGTTTATTATTTTTAACTTAAGTATTTGAATTATAGTA
20061609 ATACCACTG
66 ATACCACTG
* *
20061618 AAAATGGTAGTAAGATTAAAATGTGCATGTTTATTATTTTTACCTTAAGTATTTGAATTATAGTA
1 AAAATGGTACTAAGATTAAAATGTGCATGTTTATTATTTTTAACTTAAGTATTTGAATTATAGTA
20061683 ATACCACTG
66 ATACCACTG
20061692 A
1 A
20061693 GTGCATACTC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (74 bp):
AAAATGGTACTAAGATTAAAATGTGCATGTTTATTATTTTTAACTTAAGTATTTGAATTATAGTA
ATACCACTG
Found at i:20062849 original size:20 final size:20
Alignment explanation
Indices: 20062819--20062866 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
20062809 ATTTTAGAGT
*
20062819 TTTAT-TTTAATT-ATCTTTA
1 TTTATCTTTAATTAAT-TGTA
20062838 TTTATCTTTAATTAATTGTA
1 TTTATCTTTAATTAATTGTA
20062858 TTTATCTTT
1 TTTATCTTT
20062867 TTAGAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 19 0.73
21 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATCTTTAATTAATTGTA
Found at i:20064486 original size:29 final size:29
Alignment explanation
Indices: 20064426--20064491 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
20064416 TAATCAACCA
*
20064426 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
**
20064455 CGCACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
20064484 CGCACACT
1 CGCACACT
20064492 CGCACATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:20064558 original size:28 final size:27
Alignment explanation
Indices: 20064491--20064587 Score: 113
Period size: 27 Copynumber: 3.6 Consensus size: 27
20064481 GTTCGCACAC
* * *
20064491 TCGCACATTTAGTGCCACGTAATCAAA
1 TCGCACACTTAGTGCCACATAGTCAAA
*
20064518 TCGCACACTTAGTGCTACATAGTCAAA
1 TCGCACACTTAGTGCCACATAGTCAAA
* * * *
20064545 CCCGCACACTTAGTGCCGCATGGTCAAT
1 -TCGCACACTTAGTGCCACATAGTCAAA
20064573 TCGCACACTTAGTGC
1 TCGCACACTTAGTGC
20064588 ATCATATAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 37 0.63
28 22 0.37
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (27 bp):
TCGCACACTTAGTGCCACATAGTCAAA
Done.