Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1929
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: 264168
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:1302 original size:13 final size:13
Alignment explanation
Indices: 1284--1309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1274 CAATTTTTTG
1284 TGTATCGATACAT
1 TGTATCGATACAT
1297 TGTATCGATACAT
1 TGTATCGATACAT
1310 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1999 original size:38 final size:40
Alignment explanation
Indices: 1933--2012 Score: 101
Period size: 38 Copynumber: 2.0 Consensus size: 40
1923 TTTTATTTCT
* **
1933 CCCTTAATCAAAATAATTTTAACAAATTTGTACATTCTCC
1 CCCTTAATCAAAATAATTGTAACAAATTTACACATTCTCC
* *
1973 CCCTTAAT-AAGATAATTGTAGC-AATTTACACATTCTCC
1 CCCTTAATCAAAATAATTGTAACAAATTTACACATTCTCC
2011 CC
1 CC
2013 TTTATCTCCC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 16 0.46
39 11 0.31
40 8 0.23
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (40 bp):
CCCTTAATCAAAATAATTGTAACAAATTTACACATTCTCC
Found at i:2058 original size:21 final size:21
Alignment explanation
Indices: 2017--2060 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2007 CTCCCCTTTA
* *
2017 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2038 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2059 TC
1 TC
2061 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:3883 original size:13 final size:13
Alignment explanation
Indices: 3865--3890 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3855 ATAATCACCC
3865 TGTATCGATACAA
1 TGTATCGATACAA
3878 TGTATCGATACAA
1 TGTATCGATACAA
3891 AGGAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5989 original size:15 final size:15
Alignment explanation
Indices: 5969--5999 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5959 ATTTCGTTTG
*
5969 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5984 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5999 G
1 G
6000 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:7847 original size:21 final size:21
Alignment explanation
Indices: 7801--7845 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
7791 AAGTTTTCAT
7801 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
7821 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
7843 TTT
1 TTT
7846 CAACTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:10079 original size:13 final size:13
Alignment explanation
Indices: 10061--10086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10051 CAATTTTTTG
10061 TGTATCGATACAT
1 TGTATCGATACAT
10074 TGTATCGATACAT
1 TGTATCGATACAT
10087 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11353 original size:43 final size:43
Alignment explanation
Indices: 11305--11406 Score: 129
Period size: 43 Copynumber: 2.3 Consensus size: 43
11295 AGCTTGTAGG
*
11305 TTTTTTTTTTTCTTACAAAAAAC-TTTTTTATCACTTTTAGGGC
1 TTTTTTTTTTCCTTA-AAAAAACTTTTTTTATCACTTTTAGGGC
11348 --TTTTTTTTCCTTAAAAAAACTTTTTTTTTATCACTTTTAGGGC
1 TTTTTTTTTTCCTTAAAAAAAC--TTTTTTTATCACTTTTAGGGC
11391 TTTTTCTTTTGTCCTT
1 TTTTT-TTTT-TCCTT
11407 TTCCTTTTCC
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
40 7 0.14
41 12 0.24
43 20 0.39
45 3 0.06
46 4 0.08
47 5 0.10
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.59
Consensus pattern (43 bp):
TTTTTTTTTTCCTTAAAAAAACTTTTTTTATCACTTTTAGGGC
Found at i:11366 original size:41 final size:41
Alignment explanation
Indices: 11307--11395 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 41
11297 CTTGTAGGTT
*
11307 TTTTTTTTTCTTACAAAAAAC-TTTTTTATCACTTTTAGGGC
1 TTTTTTTTCCTTA-AAAAAACTTTTTTTATCACTTTTAGGGC
11348 TTTTTTTTCCTTAAAAAAACTTTTTTTTTATCACTTTTAGGGC
1 TTTTTTTTCCTTAAAAAAAC--TTTTTTTATCACTTTTAGGGC
11391 TTTTT
1 TTTTT
11396 CTTTTGTCCT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 7 0.16
41 12 0.27
43 25 0.57
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.57
Consensus pattern (41 bp):
TTTTTTTTCCTTAAAAAAACTTTTTTTATCACTTTTAGGGC
Found at i:16470 original size:17 final size:14
Alignment explanation
Indices: 16438--16479 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 14
16428 CTTGGGAATC
16438 AAGAAAAAAAATAA
1 AAGAAAAAAAATAA
16452 AAGAAAAGAAAAGTGAA
1 AAGAAAA-AAAA-T-AA
16469 AAGAAAAAAAA
1 AAGAAAAAAAA
16480 ATCCAAGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.28
15 4 0.16
16 5 0.20
17 9 0.36
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (14 bp):
AAGAAAAAAAATAA
Found at i:16480 original size:17 final size:15
Alignment explanation
Indices: 16441--16481 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
16431 GGGAATCAAG
16441 AAAAAAAATAAAAGA
1 AAAAAAAATAAAAGA
*
16456 AAAGAAAAGTGAAAAGA
1 AAA-AAAAAT-AAAAGA
16473 AAAAAAAAT
1 AAAAAAAAT
16482 CCAAGATCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 10 0.45
17 9 0.41
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAAAAAATAAAAGA
Found at i:19213 original size:89 final size:90
Alignment explanation
Indices: 19074--19285 Score: 335
Period size: 90 Copynumber: 2.4 Consensus size: 90
19064 AGTTTTCTCG
*
19074 AGGATAAAA-T-TAC-AAGG-AATATTTGATTTTTTTTAAAAAAAGTGAGTTTGAAGTATCCCCT
1 AGGATAAAATTATACGAAGGAAAT-TTTGA-ATTTTTTAAAAAAAGTGAGTTTGAAGTATCCCCT
19135 CAAAGGAGT-AGGATAGAGTTTCCCTA
64 CAAAGGAGTAAGGATAGAGTTTCCCTA
19161 AGGATAAAATTATACGAAGGAAATTTTGAATTTTTTAAAAAAAGTGAGTTTGAAGTATCCCCTCA
1 AGGATAAAATTATACGAAGGAAATTTTGAATTTTTTAAAAAAAGTGAGTTTGAAGTATCCCCTCA
* *
19226 GAGGAGTAAGGATAGAGTTTCTCTA
66 AAGGAGTAAGGATAGAGTTTCCCTA
*
19251 AGGATAAAATTATACGAAGGAAAATTTGAATTTTT
1 AGGATAAAATTATACGAAGGAAATTTTGAATTTTT
19286 ATTAGAGCAG
Statistics
Matches: 116, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
87 9 0.08
88 1 0.01
89 44 0.38
90 59 0.51
91 3 0.03
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (90 bp):
AGGATAAAATTATACGAAGGAAATTTTGAATTTTTTAAAAAAAGTGAGTTTGAAGTATCCCCTCA
AAGGAGTAAGGATAGAGTTTCCCTA
Found at i:19366 original size:88 final size:88
Alignment explanation
Indices: 19264--19424 Score: 250
Period size: 88 Copynumber: 1.8 Consensus size: 88
19254 ATAAAATTAT
* * *
19264 ACGAAGGAAAATTTGAATTTTTATTAGAGCAGGGTTGGAGTATCCCCTCGGAATAGTGGGGATGG
1 ACGAAAGAAAATTTGAATTTTTATTAGAACAGGGTTGGAGTATCCCCTCAGAATAGTGGGGATGG
19329 AATTTCCCCAAAGAAAACATTTC
66 AATTTCCCCAAAGAAAACATTTC
* * * *
19352 ACGAAAGAAGATTTGAATTTTTATTAGAACGGGGTTGGATTATTCCCTCAGAATAGTGGGGATGG
1 ACGAAAGAAAATTTGAATTTTTATTAGAACAGGGTTGGAGTATCCCCTCAGAATAGTGGGGATGG
*
19417 AGTTTCCC
66 AATTTCCC
19425 AAAAATTATA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 65 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (88 bp):
ACGAAAGAAAATTTGAATTTTTATTAGAACAGGGTTGGAGTATCCCCTCAGAATAGTGGGGATGG
AATTTCCCCAAAGAAAACATTTC
Found at i:19683 original size:84 final size:85
Alignment explanation
Indices: 19502--19732 Score: 268
Period size: 84 Copynumber: 2.7 Consensus size: 85
19492 GAGGATAGAA
* * * * * * *
19502 TTTCTCCAAAGGTAAAATTCTAAGAAGGAAGATTTAAATTTTTTTAGAGCGGGGTTAGAGTGTTT
1 TTTCCCCAAAGGTAAAATTCCAAGAAGTAA-ATTTGAATTTTTTTAGAAC-GGGTTAGAGTGATC
* *
19567 CTTCGAAGGAGTAGGGATGGAG
64 CCTCGAAGAAGTAGGGATGGAG
* *
19589 TTTCCCCAAAGGTAAAATTCCACGAAGTAAATTTGAATTCTTTTAGAACGGGTTAGAGT-ATCCC
1 TTTCCCCAAAGGTAAAATTCCAAGAAGTAAATTTGAATTTTTTTAGAACGGGTTAGAGTGATCCC
*
19653 TC-AGAGAAGTGGGGATGGAG
66 TCGA-AGAAGTAGGGATGGAG
* * *
19673 TTTCCGCAAAGGTAAAATTCCATGAAGTAAATTTGAATTTTTTTTAGAATGAGGTTAGAG
1 TTTCCCCAAAGGTAAAATTCCAAGAAGTAAATTTGAA-TTTTTTTAGAACG-GGTTAGAG
19733 AATGGAGTTT
Statistics
Matches: 125, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
83 1 0.01
84 53 0.42
85 21 0.17
86 24 0.19
87 26 0.21
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (85 bp):
TTTCCCCAAAGGTAAAATTCCAAGAAGTAAATTTGAATTTTTTTAGAACGGGTTAGAGTGATCCC
TCGAAGAAGTAGGGATGGAG
Found at i:19860 original size:154 final size:151
Alignment explanation
Indices: 19583--19875 Score: 408
Period size: 154 Copynumber: 1.9 Consensus size: 151
19573 AGGAGTAGGG
* * * *
19583 ATGGAGTTTCCCCAAAGGTAAAATTCCACGAAGTAAATTTGAATTCTTTTAGAACGGGTTAGAGT
1 ATGGAGTTTCCCCAAAGGTAAAATTCCACAAAGTAAATTTAAATTCTTTTAAAACGAGTTAGAGT
* * * * *
19648 ATCCCTCAGAGAAGTGGGGATGGAGTTTCCGCAAAGGTAAAATTCCATGAAGTAAATTTGAATTT
66 ATCCCTCAGAGAAATGGAGATAGAGTTTCCCCAAAGGTAAAATTCCATAAAGTAAATTTGAATTT
*
19713 TTTTTAGAATGAGGTTAGAGA
131 TTGTTAGAATGAGGTTAGAGA
* * *
19734 ATGGAGTTTCCCCAAAGGTAAAATTTCACAAAGTAAATTTAAATTTTTATTAAAACAGAGTTGGA
1 ATGGAGTTTCCCCAAAGGTAAAATTCCACAAAGTAAATTTAAATTCTT-TTAAAAC-GAGTTAGA
* *
19799 GTATTCCTTTAGA-ATAATGGAGATAGAGTTTCCCCAAAGGTAAAATTCCATAAAGTAAATTTGA
64 GTA-TCCCTCAGAGA-AATGGAGATAGAGTTTCCCCAAAGGTAAAATTCCATAAAGTAAATTTGA
19863 ATTTTTGTTAGAA
127 ATTTTTGTTAGAA
19876 CATGGTTAGA
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
151 44 0.36
152 6 0.05
153 10 0.08
154 63 0.51
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (151 bp):
ATGGAGTTTCCCCAAAGGTAAAATTCCACAAAGTAAATTTAAATTCTTTTAAAACGAGTTAGAGT
ATCCCTCAGAGAAATGGAGATAGAGTTTCCCCAAAGGTAAAATTCCATAAAGTAAATTTGAATTT
TTGTTAGAATGAGGTTAGAGA
Found at i:19916 original size:87 final size:87
Alignment explanation
Indices: 19738--19923 Score: 232
Period size: 87 Copynumber: 2.1 Consensus size: 87
19728 TAGAGAATGG
* *
19738 AGTTTCCCCAAAGGTAAAATTTCACAAAGTAAATTTAAATTTTTATTAAAACAGAGTTGGAGTAT
1 AGTTTCCCCAAAGGTAAAATTCCACAAAGTAAATTTAAATTTTTATTAAAACAGAGTTAGAGTAT
* * *
19803 TCCTTTAGAATAATGGAGATAG
66 TCCTTCAAAATAATGGAGATAA
* * * *
19825 AGTTTCCCCAAAGGTAAAATTCCATAAAGTAAATTTGAATTTTTGTTAGAACATG-GTTAGAGTA
1 AGTTTCCCCAAAGGTAAAATTCCACAAAGTAAATTTAAATTTTTATTAAAACA-GAGTTAGAGTA
* *
19889 -TCTCTTCAAAATAGTGGGGATAA
65 TTC-CTTCAAAATAATGGAGATAA
*
19912 AGTTTCTCCAAA
1 AGTTTCCCCAAA
19924 AATTATATGA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
86 2 0.02
87 82 0.96
88 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (87 bp):
AGTTTCCCCAAAGGTAAAATTCCACAAAGTAAATTTAAATTTTTATTAAAACAGAGTTAGAGTAT
TCCTTCAAAATAATGGAGATAA
Found at i:19972 original size:84 final size:84
Alignment explanation
Indices: 19884--20042 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 84
19874 AACATGGTTA
* * *
19884 GAGTAT-CTCTTCAAAATAGTGGGGATAAAGTTT-CTCCAAAAATTATATGAAGGAGAAATTTGA
1 GAGTATCCT-TTCAAAATAGTGAGGATAAAGTTTCCT-CAAAAATTATATAAAGGAAAAATTTGA
19947 GTTTTTTGAAGACCGAGATTG
64 GTTTTTTGAAGACCGAGATTG
* * *
19968 GAGTATCCTTTCAGAATAGTGAGGATAGAGTTTCCTTAAAAATTATATAAAGGAAAAATTTGAGT
1 GAGTATCCTTTCAAAATAGTGAGGATAAAGTTTCCTCAAAAATTATATAAAGGAAAAATTTGAGT
20033 TTTTTGAAGA
66 TTTTTGAAGA
20043 TTGGGGTTAG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
84 63 0.94
85 4 0.06
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.33
Consensus pattern (84 bp):
GAGTATCCTTTCAAAATAGTGAGGATAAAGTTTCCTCAAAAATTATATAAAGGAAAAATTTGAGT
TTTTTGAAGACCGAGATTG
Found at i:25709 original size:86 final size:88
Alignment explanation
Indices: 25611--25798 Score: 218
Period size: 86 Copynumber: 2.2 Consensus size: 88
25601 TCTTCTCATA
* * * ***
25611 TTAGGGAAACTCCACCCCCATTATTTCGAGAGGATACTCCA-ACCTGTTCTAACAAAAATTCAAA
1 TTAGGGAAACTCCACCCCCACTACTTCGAGAGGACACTCCAGACCCACTCTAACAAAAATTCAAA
25675 T-TTACTTCATGGAATTTCACCT
66 TCTTACTTCATGGAATTTCACCT
* * * * *
25697 TTAGGGAAACTCCATCCCCACTCCTTCGAGGGGACACTCTAGCCCCACTCTAACAAAAATTCAAA
1 TTAGGGAAACTCCACCCCCACTACTTCGAGAGGACACTCCAGACCCACTCTAACAAAAATTCAAA
* * * *
25762 TCTTCCTTCGTGGAATTTTATCT
66 TCTTACTTCATGGAATTTCACCT
*
25785 TTGGGGAAACTCCA
1 TTAGGGAAACTCCA
25799 TCCTTACTAT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
86 34 0.40
87 20 0.24
88 30 0.36
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (88 bp):
TTAGGGAAACTCCACCCCCACTACTTCGAGAGGACACTCCAGACCCACTCTAACAAAAATTCAAA
TCTTACTTCATGGAATTTCACCT
Found at i:25839 original size:88 final size:87
Alignment explanation
Indices: 25658--25848 Score: 222
Period size: 88 Copynumber: 2.2 Consensus size: 87
25648 TCCAACCTGT
*
25658 TCTAACAAAAATTCAAATTTACTTCATGGAATTTCACCTTTAGGGAAACTCCATCCCCACTCCTT
1 TCTAACAAAAATTCAAATTTACTTCATGGAATTTCACCTTTAGGGAAACTCCATCCCCACTCATT
*
25723 CGAGGGGACACTCTAGCCCCAC
66 CGAGGGGACACTCTAACCCCAC
* * * * * **
25745 TCTAACAAAAATTCAAATCTTCCTTCGTGGAATTTTATCTTTGGGGAAACTCCATCCTTACT-AT
1 TCTAACAAAAATTCAAAT-TTACTTCATGGAATTTCACCTTTAGGGAAACTCCATCCCCACTCAT
** * * *
25809 TCTGAGGGGGTACTTTAACCTCGC
65 TC-GAGGGGACACTCTAACCCCAC
*
25833 TTTAACAAAAATTCAA
1 TCTAACAAAAATTCAA
25849 TGTTTCCATC
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
87 21 0.24
88 66 0.76
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (87 bp):
TCTAACAAAAATTCAAATTTACTTCATGGAATTTCACCTTTAGGGAAACTCCATCCCCACTCATT
CGAGGGGACACTCTAACCCCAC
Found at i:33362 original size:96 final size:95
Alignment explanation
Indices: 33149--33388 Score: 250
Period size: 96 Copynumber: 2.5 Consensus size: 95
33139 CAATTTTTTG
* * * * * * * *
33149 GTTGAAAAACGAGGCTAGAATAT-CCTTCGGAGGAATGGAATTGGAGTGTCCCCGATGATGACAA
1 GTTGAAAAACGAGGTTAGAGTATCCCCTCAGAAGAATGG-GTTGGAGTAT-CTCGATGATGACAA
**
33213 TTTAAGTGAAAATAAGATTTAAATCTTAACAA
64 TTTAAGCAAAAATAAGATTTAAATCTTAACAA
* * *
33245 GTTGAAAGACGAGGTTAGAGTATCCCCT-TGAAAGAATGGGGTTGGAGTATCTCGATGATGGCAA
1 GTTGAAAAACGAGGTTAGAGTATCCCCTCAG-AAGAAT-GGGTTGGAGTATCTCGATGATGACAA
* *
33309 TTTAAGCAAAAATAAGATTTAAATCTTGACGA
64 TTTAAGCAAAAATAAGATTTAAATCTTAACAA
* * * * *
33341 GTTTAAAAATGGGGTTGGAGTATCCTCTCAGAAGAATGGGTTGGAGTA
1 GTTGAAAAACGAGGTTAGAGTATCCCCTCAGAAGAATGGGTTGGAGTA
33389 CCCCTGATAA
Statistics
Matches: 119, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
95 11 0.09
96 89 0.75
97 17 0.14
98 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.27
Consensus pattern (95 bp):
GTTGAAAAACGAGGTTAGAGTATCCCCTCAGAAGAATGGGTTGGAGTATCTCGATGATGACAATT
TAAGCAAAAATAAGATTTAAATCTTAACAA
Found at i:39173 original size:51 final size:50
Alignment explanation
Indices: 39102--39261 Score: 200
Period size: 51 Copynumber: 3.1 Consensus size: 50
39092 AGAATATATC
*
39102 GATACATTTAGG-TCAGAACCCAAAATGTATCGATACAATGAATAATGTATT
1 GATACATTT-GGATCA-AACCCAAAATGTATCGATACAATGAAAAATGTATT
* *
39153 GATATA-TTGGGTCAAAAACCCAAAATGTATCGATACAATGAAAAATGTATT
1 GATACATTTGGATC--AAACCCAAAATGTATCGATACAATGAAAAATGTATT
* *
39204 GATACATTTGGATCAAACCCAGAATGTATCGATACAAAT-AAAATATGTATA
1 GATACATTTGGATCAAACCCAAAATGTATCGATAC-AATGAAAA-ATGTATT
39255 GATACAT
1 GATACAT
39262 GAAAGCTTAT
Statistics
Matches: 97, Mismatches: 6, Indels: 12
0.84 0.05 0.10
Matches are distributed among these distances:
49 2 0.02
50 28 0.29
51 60 0.62
52 7 0.07
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (50 bp):
GATACATTTGGATCAAACCCAAAATGTATCGATACAATGAAAAATGTATT
Found at i:40031 original size:13 final size:13
Alignment explanation
Indices: 40013--40038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40003 CAATTTTTTG
40013 TGTATCGATACAT
1 TGTATCGATACAT
40026 TGTATCGATACAT
1 TGTATCGATACAT
40039 ACTTGTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:40777 original size:21 final size:21
Alignment explanation
Indices: 40736--40779 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40726 CTCTCTTTTA
* *
40736 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
40757 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
40778 TC
1 TC
40780 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:42604 original size:13 final size:13
Alignment explanation
Indices: 42586--42624 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
42576 ATAATCACCC
*
42586 TGTATCGATACAG
1 TGTATCGATACAA
42599 TGTATCGATACAA
1 TGTATCGATACAA
42612 TGTATCGATACAA
1 TGTATCGATACAA
42625 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:42635 original size:20 final size:20
Alignment explanation
Indices: 42610--42688 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
42600 GTATCGATAC
42610 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
42630 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
42655 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
42675 CATGTATCGATACA
1 AATGTATCGATACA
42689 TTTTGGATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:44723 original size:15 final size:15
Alignment explanation
Indices: 44703--44733 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44693 ATTTCGTTTG
*
44703 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
44718 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
44733 G
1 G
44734 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:46566 original size:21 final size:21
Alignment explanation
Indices: 46537--46581 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
46527 AAGTTTTCAT
*
46537 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
46557 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
46579 TTT
1 TTT
46582 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:48817 original size:13 final size:13
Alignment explanation
Indices: 48799--48824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48789 CAATTTTTTG
48799 TGTATCGATACAT
1 TGTATCGATACAT
48812 TGTATCGATACAT
1 TGTATCGATACAT
48825 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:51147 original size:33 final size:32
Alignment explanation
Indices: 51087--51151 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
51077 ACTTTTCAAG
*
51087 GTGTATCGATATTATGAACATGTATCGATATA
1 GTGTATCGATATTAAGAACATGTATCGATATA
* *
51119 GTGTGTCGATATTAAGCAATATGTATCGATATA
1 GTGTATCGATATTAAG-AACATGTATCGATATA
51152 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (32 bp):
GTGTATCGATATTAAGAACATGTATCGATATA
Found at i:53993 original size:20 final size:19
Alignment explanation
Indices: 53931--54002 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
53921 CATGTCCAGA
* **
53931 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-AAT
* *
53951 TGTATCGATACATGTTCAT
1 TGTATCGATACATGATAAT
*
53970 TGTATCCATACATGCATAAT
1 TGTATCGATACATG-ATAAT
53990 TGTATCGATACAT
1 TGTATCGATACAT
54003 TAAATTGGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.34
20 29 0.66
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATGATAAT
Found at i:62862 original size:33 final size:33
Alignment explanation
Indices: 62839--62915 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
62829 ACATTATGCT
62839 TTGTATCGATATATTGTATCGATACATGCACAA
1 TTGTATCGATATATTGTATCGATACATGCACAA
*
62872 TTGTATTGATATATTGTATCGATACATGCACAA
1 TTGTATCGATATATTGTATCGATACATGCACAA
62905 TTGTATCGATA
1 TTGTATCGATA
62916 CATGAAATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (33 bp):
TTGTATCGATATATTGTATCGATACATGCACAA
Found at i:62876 original size:20 final size:20
Alignment explanation
Indices: 62851--62919 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
62841 GTATCGATAT
62851 ATTGTATCGATACATGCACA
1 ATTGTATCGATACATGCACA
*
62871 ATTGTATTGAT--AT-----
1 ATTGTATCGATACATGCACA
62884 ATTGTATCGATACATGCACA
1 ATTGTATCGATACATGCACA
62904 ATTGTATCGATACATG
1 ATTGTATCGATACATG
62920 AAATTGGCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
13 10 0.25
15 2 0.05
18 2 0.05
20 26 0.65
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGCACA
Found at i:72825 original size:15 final size:15
Alignment explanation
Indices: 72805--72838 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
72795 TAGCAAGAAT
72805 GAAAGAAAAAAAAAA
1 GAAAGAAAAAAAAAA
* *
72820 GAAAGAGAGAAAAAA
1 GAAAGAAAAAAAAAA
72835 GAAA
1 GAAA
72839 TTCTAGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAAAAAAA
Found at i:74717 original size:16 final size:16
Alignment explanation
Indices: 74696--74729 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
74686 AGAATGATGA
*
74696 ATGACAAATGGAAGAT
1 ATGACAAATGAAAGAT
74712 ATGACAAATGAAAGAT
1 ATGACAAATGAAAGAT
74728 AT
1 AT
74730 AACATGCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.21
Consensus pattern (16 bp):
ATGACAAATGAAAGAT
Found at i:74757 original size:2 final size:2
Alignment explanation
Indices: 74750--74782 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
74740 GATGTTTACC
*
74750 TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
74783 GTGAGGCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79255 original size:20 final size:20
Alignment explanation
Indices: 79209--79247 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
79199 ACATGTATAG
*
79209 AATTAAGAATCATGAAATTA
1 AATTAAAAATCATGAAATTA
*
79229 AACTAAAAATCATGCAAAT
1 AATTAAAAATCATG-AAAT
79248 CAATTAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (20 bp):
AATTAAAAATCATGAAATTA
Found at i:80080 original size:59 final size:59
Alignment explanation
Indices: 80008--80119 Score: 179
Period size: 59 Copynumber: 1.9 Consensus size: 59
79998 TTTCTCTTAT
**
80008 GAGGAATAAACTAGCCCACTTTCATCAACTCGAATTTTCAAGACCCAAGTCTCGGTTAC
1 GAGGAATAAACTAGCCCACTTTCATCAACTAAAATTTTCAAGACCCAAGTCTCGGTTAC
* * *
80067 GAGGCATAAACTAGCCCACTTTCATCAACTAAAATTTTCAGGACCTAAGTCTC
1 GAGGAATAAACTAGCCCACTTTCATCAACTAAAATTTTCAAGACCCAAGTCTC
80120 AGTTTTCTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (59 bp):
GAGGAATAAACTAGCCCACTTTCATCAACTAAAATTTTCAAGACCCAAGTCTCGGTTAC
Found at i:85676 original size:20 final size:20
Alignment explanation
Indices: 85639--85693 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
85629 CTCTACAATT
* **
85639 TGTATTGATACTATAAGTTTA
1 TGTATCGATAC-ATAAGTAAA
85660 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAAGTAAA
85680 TGTATCGATACATA
1 TGTATCGATACATA
85694 CTTGTAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 21 0.68
21 10 0.32
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATAAGTAAA
Found at i:88316 original size:29 final size:26
Alignment explanation
Indices: 88273--88325 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
88263 CAAATTTTTC
*
88273 ATCTCTAGAGATACTCTAACTCCCACT
1 ATCTCTAGAGATACTCCAAC-CCCACT
88300 ATCTCTGAGAGGATACTCCAACCCCA
1 ATCTCT-AGA-GATACTCCAACCCCA
88326 TTTTTACTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 7 0.30
29 10 0.43
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (26 bp):
ATCTCTAGAGATACTCCAACCCCACT
Found at i:88341 original size:81 final size:80
Alignment explanation
Indices: 88186--88555 Score: 375
Period size: 79 Copynumber: 4.6 Consensus size: 80
88176 TAAAATACCG
* * **
88186 ATTTCTTCATCTCTAGGGATACTCCAA-CCCA-TCATCTCTAAAAAGG-TACTCCAACCTTATTT
1 ATTT-TTCATCTCTAGGGATACTCCAACCCCACT-ATCTCT-GAGAGGATACTCCAACCCCATTT
*
88248 TTACTTCTAAAACATCAA
63 TTACTTCCAAAACATCAA
* *
88266 ATTTTTCATCTCTAGAGATACTCTAACTCCCACTATCTCTGAGAGGATACTCCAACCCCATTTTT
1 ATTTTTCATCTCTAGGGATACTCCAAC-CCCACTATCTCTGAGAGGATACTCCAACCCCATTTTT
*
88331 ACTTCCAAAACGTCAA
65 ACTTCCAAAACATCAA
* *
88347 ATTTTTCATCTCT--GGATACTCCAACCCCACTATTTCTGATGA-GATACTCAAAACCCCATTTT
1 ATTTTTCATCTCTAGGGATACTCCAACCCCACTATCTCTGA-GAGGATACTC-CAACCCCATTTT
* *
88409 TACTTCTAAAA-AGCTAA
64 TACTTCCAAAACATC-AA
* * * * *
88426 ATTTTT-ATCTCTAGGGTTACTCCAACCTCGCCATCTCTGA-AGGGATACTCCAACCTCATTTTT
1 ATTTTTCATCTCTAGGGATACTCCAACCCCACTATCTCTGAGA-GGATACTCCAACCCCATTTTT
**
88489 ACTTCCAAAACATTGA
65 ACTTCCAAAACATCAA
* * *
88505 ATTCTTT-ATCTTTGGGGATACTCTAACCCCACTATCTCCT-AGAGGATACTC
1 ATT-TTTCATCTCTAGGGATACTCCAACCCCACTATCT-CTGAGAGGATACTC
88556 TAATCTCGGT
Statistics
Matches: 242, Mismatches: 33, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
78 28 0.12
79 85 0.35
80 72 0.30
81 56 0.23
82 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (80 bp):
ATTTTTCATCTCTAGGGATACTCCAACCCCACTATCTCTGAGAGGATACTCCAACCCCATTTTTA
CTTCCAAAACATCAA
Found at i:88527 original size:80 final size:80
Alignment explanation
Indices: 88146--88542 Score: 337
Period size: 79 Copynumber: 5.0 Consensus size: 80
88136 AAAACATAAA
* * * * **
88146 GAAGGG-TACTCCAATCCCTATTTTCACTTCTAAAATA-CCGATTTCTTCATCTCTAGGGATACT
1 GAAGGGATACTCCAA-CCCCATTTTTACTTCCAAAACATCAAATTT-TTCATCTCTAGGGATACT
*
88209 CCAACC-CATCATCTCT
64 CCAACCTCACCATCTCT
* * ** * *
88225 AAAAAGG-TACTCCAACCTTATTTTTACTTCTAAAACATCAAATTTTTCATCTCTAGAGATACTC
1 -GAAGGGATACTCCAACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCTCTAGGGATACTC
* * *
88289 TAACTCCCACTATCTCT
65 CAAC-CTCACCATCTCT
*
88306 G-AGAGGATACTCCAACCCCATTTTTACTTCCAAAACGTCAAATTTTTCATCTCT--GGATACTC
1 GAAG-GGATACTCCAACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCTCTAGGGATACTC
* * *
88368 CAACCCCACTATTTCT
65 CAACCTCACCATCTCT
* * * * * *
88384 GATGAGATACTCAAAACCCCATTTTTACTTCTAAAA-AGCTAAATTTTT-ATCTCTAGGGTTACT
1 GAAGGGATACTC-CAACCCCATTTTTACTTCCAAAACATC-AAATTTTTCATCTCTAGGGATACT
*
88447 CCAACCTCGCCATCTCT
64 CCAACCTCACCATCTCT
* ** * *
88464 GAAGGGATACTCCAACCTCATTTTTACTTCCAAAACATTGAATTCTTT-ATCTTTGGGGATACTC
1 GAAGGGATACTCCAACCCCATTTTTACTTCCAAAACATCAAATT-TTTCATCTCTAGGGATACTC
* * *
88528 TAACCCCACTATCTC
65 CAACCTCACCATCTC
88543 CTAGAGGATA
Statistics
Matches: 259, Mismatches: 46, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
78 26 0.10
79 105 0.41
80 77 0.30
81 51 0.20
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (80 bp):
GAAGGGATACTCCAACCCCATTTTTACTTCCAAAACATCAAATTTTTCATCTCTAGGGATACTCC
AACCTCACCATCTCT
Found at i:93062 original size:14 final size:14
Alignment explanation
Indices: 93043--93073 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
93033 TTTTATTTAT
*
93043 TATAATGTTTAAAA
1 TATAATGATTAAAA
93057 TATAATGATTAAAA
1 TATAATGATTAAAA
93071 TAT
1 TAT
93074 TAAATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
TATAATGATTAAAA
Found at i:100550 original size:107 final size:108
Alignment explanation
Indices: 100361--100577 Score: 339
Period size: 107 Copynumber: 2.0 Consensus size: 108
100351 TATTTATGTC
*
100361 CATGATATTCCTGTTTGAACATATATTACATCTTGTTTAACTTTCTCATAGTTTGTGTTTAAAAA
1 CATGATATTCCTGTTTGAACATATATTACATCTCGTTTAACTTTCTCATAGTTTGTGTTTAAAAA
*
100426 GAAAATAGTT-AAAAAAAAAAAGGGAAAAAGAAAGTCTATTAA
66 GAAAATAGTTAAAAAAAAAAAAAGGAAAAAGAAAGTCTATTAA
* *
100468 CATGATATTCCTGTTTGAACATATATTATATCTCGTTT-ACTTTTCTTATAGTTTGTGTTTAAAA
1 CATGATATTCCTGTTTGAACATATATTACATCTCGTTTAAC-TTTCTCATAGTTTGTGTTTAAAA
* *
100532 AGAAAATAGTAAATAAAAAAAAAAAAGGAAAAAGAAATTCTATTAA
65 AGAAAATAGT-TA-AAAAAAAAAAAAGGAAAAAGAAAGTCTATTAA
100578 GTTTTCTGCC
Statistics
Matches: 100, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
106 2 0.02
107 68 0.68
110 30 0.30
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (108 bp):
CATGATATTCCTGTTTGAACATATATTACATCTCGTTTAACTTTCTCATAGTTTGTGTTTAAAAA
GAAAATAGTTAAAAAAAAAAAAAGGAAAAAGAAAGTCTATTAA
Found at i:101606 original size:2 final size:2
Alignment explanation
Indices: 101599--101635 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
101589 TTAATAAGGT
101599 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
101636 ATATATATAT
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:101640 original size:2 final size:2
Alignment explanation
Indices: 101635--101663 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
101625 TCTCTCTCTC
101635 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 T
101664 GCTGTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104132 original size:37 final size:36
Alignment explanation
Indices: 104063--104142 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 36
104053 AAGAAATAAA
* *
104063 ATACATTGCTTTTTTTTTTTTTTTTGAAAAGTGTGC
1 ATACATTGCTTTTTGTTTTATTTTTGAAAAGTGTGC
*
104099 ATACATTGCTATTTTGTTTTATTTTTGAGAAGTGTGC
1 ATACATTGCT-TTTTGTTTTATTTTTGAAAAGTGTGC
*
104136 ATTCATT
1 ATACATT
104143 TTGACATAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 10 0.26
37 29 0.74
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.55
Consensus pattern (36 bp):
ATACATTGCTTTTTGTTTTATTTTTGAAAAGTGTGC
Found at i:112261 original size:26 final size:26
Alignment explanation
Indices: 112232--112314 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 26
112222 TTTGAAAAAC
112232 TCGACAAAATTACTCCACAAAAGAAT
1 TCGACAAAATTACTCCACAAAAGAAT
* *
112258 TCGAGATAAAGCATTA-T-CATCAAAAG--C
1 TC--GACAAA--ATTACTCCA-CAAAAGAAT
*
112285 TCGACAAAATTACTCCATAAAAGAAT
1 TCGACAAAATTACTCCACAAAAGAAT
112311 TCGA
1 TCGA
112315 GATAAAGCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
23 4 0.09
24 6 0.14
25 7 0.16
26 6 0.14
27 2 0.05
28 7 0.16
29 7 0.16
30 4 0.09
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (26 bp):
TCGACAAAATTACTCCACAAAAGAAT
Found at i:112294 original size:53 final size:53
Alignment explanation
Indices: 112226--112332 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
112216 AATATGTTTG
112226 AAAAACTCGACAAAATTACTCCACAAAAGAATTCGAGATAAAGCATTATCATC
1 AAAAACTCGACAAAATTACTCCACAAAAGAATTCGAGATAAAGCATTATCATC
* * * *
112279 AAAAGCTCGACAAAATTACTCCATAAAAGAATTCGAGATAAAGCCTTCTCATC
1 AAAAACTCGACAAAATTACTCCACAAAAGAATTCGAGATAAAGCATTATCATC
112332 A
1 A
112333 TTCCTAGGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.21
Consensus pattern (53 bp):
AAAAACTCGACAAAATTACTCCACAAAAGAATTCGAGATAAAGCATTATCATC
Found at i:119533 original size:13 final size:13
Alignment explanation
Indices: 119515--119539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119505 CATTTTATGG
119515 TGTATCGATACAA
1 TGTATCGATACAA
119528 TGTATCGATACA
1 TGTATCGATACA
119540 TACTGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:119555 original size:32 final size:33
Alignment explanation
Indices: 119492--119559 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
119482 CGTTACAAGC
**
119492 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
119525 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
119557 CAA
1 CAA
119560 ATTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:119638 original size:20 final size:21
Alignment explanation
Indices: 119591--119639 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
119581 GCCAATGACC
**
119591 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
119612 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
119632 TGTATCGA
1 TGTATCGA
119640 CACAATGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:121659 original size:20 final size:22
Alignment explanation
Indices: 121620--121664 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
121610 GCTGCTAGTG
*
121620 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
121642 TGGGGG-TG-CCGGTCGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
121662 TGG
1 TGG
121665 TGGATGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.04, C:0.29, G:0.49, T:0.18
Consensus pattern (22 bp):
TGGGGGCTGCCCGGTCGCGACC
Found at i:121963 original size:20 final size:21
Alignment explanation
Indices: 121934--121974 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
121924 TATTTTTGAT
121934 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
121953 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
121975 AAGAGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:122553 original size:32 final size:30
Alignment explanation
Indices: 122517--122575 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
122507 GAAATCAAAT
122517 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
122549 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
122576 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:122873 original size:12 final size:12
Alignment explanation
Indices: 122856--122880 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122846 CATATTTATG
122856 TGTATCGATACA
1 TGTATCGATACA
122868 TGTATCGATACA
1 TGTATCGATACA
122880 T
1 T
122881 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:122892 original size:31 final size:32
Alignment explanation
Indices: 122835--122898 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
122825 TTACAAGCCA
122835 ATGTATCGATACATATTTATGTGTATCGATAC
1 ATGTATCGATACATATTTATGTGTATCGATAC
122867 ATGTATCGATACATATTT-TGTGTATCGATAC
1 ATGTATCGATACATATTTATGTGTATCGATAC
122898 A
1 A
122899 AGTTTGGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (32 bp):
ATGTATCGATACATATTTATGTGTATCGATAC
Found at i:127581 original size:15 final size:15
Alignment explanation
Indices: 127545--127582 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
127535 TTCATCAATT
* *
127545 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
127560 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
127575 TCATTTTG
1 TCATTTTG
127583 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:129415 original size:21 final size:21
Alignment explanation
Indices: 129386--129430 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
129376 AAGTTTTTAT
*
129386 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
129406 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
129428 TTT
1 TTT
129431 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:130999 original size:13 final size:13
Alignment explanation
Indices: 130981--131019 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
130971 CAAAACCCCT
130981 TGTATCGATACAG
1 TGTATCGATACAG
*
130994 TGTATCGATACAA
1 TGTATCGATACAG
131007 TGTATCGATACAG
1 TGTATCGATACAG
131020 AGAATGCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:137049 original size:13 final size:13
Alignment explanation
Indices: 137031--137055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
137021 CATAAAGTGT
137031 TGTATCGATACAA
1 TGTATCGATACAA
137044 TGTATCGATACA
1 TGTATCGATACA
137056 TATTTTTTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:137137 original size:13 final size:13
Alignment explanation
Indices: 137119--137143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
137109 ATCACTTAAA
137119 TGTATCGATACAT
1 TGTATCGATACAT
137132 TGTATCGATACA
1 TGTATCGATACA
137144 CGAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:137208 original size:52 final size:52
Alignment explanation
Indices: 137152--137280 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
137142 CACGAATCTT
*
137152 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
137204 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
137256 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
137281 TCATATTTTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:151079 original size:1 final size:1
Alignment explanation
Indices: 151059--151138 Score: 61
Period size: 1 Copynumber: 80.0 Consensus size: 1
151049 GGCGTCCTCC
* * * * ** * * *
151059 AAAAAACAAACAAAACAAAAAAAAAAACAAAAAAAAAAAACCAAAAACAAAAACAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
151124 ACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAA
151139 GGGGGTCCGG
Statistics
Matches: 59, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:151083 original size:19 final size:18
Alignment explanation
Indices: 151059--151138 Score: 99
Period size: 19 Copynumber: 4.3 Consensus size: 18
151049 GGCGTCCTCC
*
151059 AAAAAACAAACAAAACAA
1 AAAAAACAAACAAAAAAA
151077 AAAAAA-AAACAAAAAAA
1 AAAAAACAAACAAAAAAA
*
151094 AAAAACCAAAAACAAAAACAA
1 AAAAA--ACAAACAAAAA-AA
151115 AAAAAACAAACAAAAACAA
1 AAAAAACAAACAAAAA-AA
151134 AAAAA
1 AAAAA
151139 GGGGGTCCGG
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
17 15 0.27
18 6 0.11
19 19 0.34
20 9 0.16
21 7 0.12
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAACAAACAAAAAAA
Found at i:151090 original size:26 final size:25
Alignment explanation
Indices: 151061--151137 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
151051 CGTCCTCCAA
151061 AAAACAAACAAAACAAAAAAAAAAAC
1 AAAA-AAACAAAACAAAAAAAAAAAC
* *
151087 AAAAAAAAAAAACCAAAAACAAAAAC
1 AAAAAAACAAAA-CAAAAAAAAAAAC
151113 AAAAAAA-ACAAACAAAAACAAAAAA
1 AAAAAAACA-AAACAAAAA-AAAAAA
151138 AGGGGGTCCG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.31
26 31 0.69
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAAAAACAAAACAAAAAAAAAAAC
Found at i:152568 original size:30 final size:30
Alignment explanation
Indices: 152524--152811 Score: 166
Period size: 30 Copynumber: 9.7 Consensus size: 30
152514 TTTATCACCC
* *
152524 TTCAAAAGTCCACAAGTTAGTGGCATTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TTTTT
152555 TTC-AAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATTTTT
***
152584 TTCAAAAGCCCACAAGTCAGTGGCA--ACC
1 TTCAAAAGCCCACAAGTCAGTGGCATTTTT
* **
152612 TTC-AAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TTTTT
* * * *
152642 TTC-GAAGCCCACAAGTCGGTGGC-CTCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATTTTT
* * * *
152670 TTCCAAAGCTCACAACTCTA-TAGCACTCTTTTT
1 TTCAAAAGCCCACAAGTC-AGTGGCA---TTTTT
*** * ***
152703 CTTTTTAAGCCCACAAGTTAGTGGCACCCTT
1 -TTCAAAAGCCCACAAGTCAGTGGCATTTTT
* ***
152734 TTCAAAAGCCCATAAGTCAGTGGCA-ACCT
1 TTCAAAAGCCCACAAGTCAGTGGCATTTTT
***
152763 TT-AAAAGCCCACAAGTCAGTGGCA-ACCT
1 TTCAAAAGCCCACAAGTCAGTGGCATTTTT
152791 TT-AAAAGCCCACAAGTCAGTG
1 TTCAAAAGCCCACAAGTCAGTG
152812 ATGCAAACCT
Statistics
Matches: 206, Mismatches: 39, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
27 20 0.10
28 55 0.27
29 26 0.13
30 80 0.39
31 5 0.02
33 4 0.02
34 16 0.08
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCATTTTT
Found at i:152778 original size:28 final size:28
Alignment explanation
Indices: 152558--152835 Score: 173
Period size: 30 Copynumber: 9.4 Consensus size: 28
152548 ATTTTTTTTC
***
152558 AAAGCCCACAAGTCAGTGGCATTTTTTTCA
1 AAAGCCCACAAGTCAGTGGCA-ACCTTT-A
*
152588 AAAGCCCACAAGTCAGTGGCAACC-TTC
1 AAAGCCCACAAGTCAGTGGCAACCTTTA
* * *
152615 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAACC--TTTA
* * ** * *
152645 GAAGCCCACAAGTCGGTGGCCTCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACCTTT-A
* * * * *
152674 AAAGCTCACAACTCTA-TAGCACTCTTTTTCTTTT
1 AAAGCCCACAAGTC-AGTGGCA-AC-----CTTTA
* * *
152708 TAAGCCCACAAGTTAGTGGCACCCTTTTCA
1 AAAGCCCACAAGTCAGTGGCAACC-TTT-A
*
152738 AAAGCCCATAAGTCAGTGGCAACCTTTA
1 AAAGCCCACAAGTCAGTGGCAACCTTTA
152766 AAAGCCCACAAGTCAGTGGCAACCTTTA
1 AAAGCCCACAAGTCAGTGGCAACCTTTA
*
152794 AAAGCCCACAAGTCAGTGATGCAAACCTCTCA
1 AAAGCCCACAAGTCAGTG--GC-AACCT-TTA
152826 AAAGCCCACA
1 AAAGCCCACA
152836 CAAGTTGGTG
Statistics
Matches: 197, Mismatches: 33, Indels: 34
0.75 0.12 0.13
Matches are distributed among these distances:
27 22 0.11
28 52 0.26
29 21 0.11
30 66 0.34
31 5 0.03
32 12 0.06
33 2 0.01
34 14 0.07
35 3 0.02
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTTA
Found at i:152784 original size:58 final size:59
Alignment explanation
Indices: 152709--152835 Score: 170
Period size: 58 Copynumber: 2.2 Consensus size: 59
152699 TTTTCTTTTT
* * * *
152709 AAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCATAAGTCAGTG-GC-AACCT-TTAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGAGCAAACCTCTCAA
152767 AAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGATGCAAACCTCTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGA-GCAAACCTCTCAA
152827 AAGCCCACA
1 AAGCCCACA
152836 CAAGTTGGTG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
56 18 0.30
57 3 0.05
58 23 0.38
59 5 0.08
60 12 0.20
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (59 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGAGCAAACCTCTCAA
Found at i:152924 original size:48 final size:48
Alignment explanation
Indices: 152855--153083 Score: 256
Period size: 48 Copynumber: 4.8 Consensus size: 48
152845 GGCGTCTCCT
* *
152855 TTTAAGCCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTGC-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-CAC
* * *
152903 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA-C
* * *
152952 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA----C-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAC
152995 -TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CA-C
* * *
153046 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
153084 ACATCCTTTT
Statistics
Matches: 152, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
42 37 0.24
45 1 0.01
47 1 0.01
48 41 0.27
49 37 0.24
51 1 0.01
52 34 0.22
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (48 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAC
Found at i:153012 original size:42 final size:42
Alignment explanation
Indices: 152953--153038 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
152943 ACCTTCATAT
*
152953 TTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACC
1 TTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
* *
152995 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 TTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
153037 TT
1 TT
153039 TTCCATCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (42 bp):
TTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
Found at i:153031 original size:91 final size:93
Alignment explanation
Indices: 152904--153083 Score: 292
Period size: 91 Copynumber: 1.9 Consensus size: 93
152894 CACCTTGCCT
*
152904 TTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACC-TT-CATATTTAAGTCCAATGTA
1 TTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACCTTTCCATATTTAAGTCCAATGTA
152967 GCTGACCTTGAATCAGCACATTGGCACC
66 GCTGACCTTGAATCAGCACATTGGCACC
* * *
152995 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGT
1 TTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACC-TTTCCATATTTAAGTCCAATGT
*
153060 AGCTGGCCTTGAATCAGCACATTG
65 AGCTGACCTTGAATCAGCACATTG
153084 ACATCCTTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
91 40 0.49
93 2 0.02
94 39 0.48
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (93 bp):
TTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACCTTTCCATATTTAAGTCCAATGTA
GCTGACCTTGAATCAGCACATTGGCACC
Found at i:153038 original size:21 final size:21
Alignment explanation
Indices: 152971--153038 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
152961 AATGTAGCTG
*
152971 ACCTTGAATCAGCACATTGGC
1 ACCTTGAATCAGCATATTGGC
** *
152992 ACCTT-AAGTCCAATATAGCTGG-
1 ACCTTGAA-T-CAGCATA-TTGGC
153014 -CCTTGAATCAGCATATTGGC
1 ACCTTGAATCAGCATATTGGC
153034 ACCTT
1 ACCTT
153039 TTCCATCTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
19 3 0.09
20 7 0.21
21 15 0.44
22 6 0.18
23 3 0.09
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
ACCTTGAATCAGCATATTGGC
Found at i:153073 original size:52 final size:53
Alignment explanation
Indices: 152995--153146 Score: 180
Period size: 52 Copynumber: 2.8 Consensus size: 53
152985 CATTGGCACC
*
152995 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAGCT
* * * *
153047 TTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAGCT
* * * * * *
153102 TTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
153147 ATCACTTTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
52 36 0.44
53 5 0.06
54 6 0.07
55 35 0.43
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.35
Consensus pattern (53 bp):
TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAGCT
Found at i:156760 original size:13 final size:13
Alignment explanation
Indices: 156742--156766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
156732 CATTTTATGG
156742 TGTATCGATACAA
1 TGTATCGATACAA
156755 TGTATCGATACA
1 TGTATCGATACA
156767 TACTGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:156782 original size:32 final size:33
Alignment explanation
Indices: 156719--156786 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
156709 CGTTACAAGC
**
156719 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
156752 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
156784 CAA
1 CAA
156787 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:156886 original size:20 final size:21
Alignment explanation
Indices: 156819--156891 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
156809 CCAATGACCT
156819 GTATCGATACATCTTTTTCAA
1 GTATCGATACATCTTTTTCAA
156840 GTATCGATACATCTTTTTCAA
1 GTATCGATACATCTTTTTCAA
** *
156861 GTATCGATACAT-TTGGTCAT
1 GTATCGATACATCTTTTTCAA
156881 GTATCGATACA
1 GTATCGATACA
156892 ATGTATCGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 16 0.33
21 33 0.67
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (21 bp):
GTATCGATACATCTTTTTCAA
Found at i:156897 original size:13 final size:13
Alignment explanation
Indices: 156879--156903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
156869 ACATTTGGTC
156879 ATGTATCGATACA
1 ATGTATCGATACA
156892 ATGTATCGATAC
1 ATGTATCGATAC
156904 TGTGCAACAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:157630 original size:14 final size:15
Alignment explanation
Indices: 157611--157641 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
157601 ACGCATTAGA
157611 AAAGTTCAAAT-ATT
1 AAAGTTCAAATAATT
157625 AAAGTTCAAATAATT
1 AAAGTTCAAATAATT
157640 AA
1 AA
157642 GGCTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (15 bp):
AAAGTTCAAATAATT
Found at i:160065 original size:21 final size:20
Alignment explanation
Indices: 160020--160072 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
160010 ATCGATACAT
**
160020 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
160040 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAA-A
*
160061 TGTATCAATACA
1 TGTATCGATACA
160073 GGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:160142 original size:13 final size:13
Alignment explanation
Indices: 160124--160148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
160114 ACACACAGTA
160124 TGTATCGATACAT
1 TGTATCGATACAT
160137 TGTATCGATACA
1 TGTATCGATACA
160149 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:160145 original size:32 final size:33
Alignment explanation
Indices: 160104--160171 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
160094 GTAGCCAAAC
**
160104 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
160136 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
160169 TTG
1 TTG
160172 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:166048 original size:13 final size:13
Alignment explanation
Indices: 166030--166067 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
166020 CAGCATTCTC
*
166030 TGTATCGATACAT
1 TGTATCGATACAG
166043 TGTATCGATACAG
1 TGTATCGATACAG
*
166056 TGTATCAATACA
1 TGTATCGATACA
166068 AGGGGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:166545 original size:21 final size:21
Alignment explanation
Indices: 166501--166542 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
166491 CCCCTAGGCA
*
166501 GCACCCACCAGGTCGCGACCG
1 GCACCCACCAGGTCGCAACCG
166522 GCACCC-CCAGGTCGCAACCG
1 GCACCCACCAGGTCGCAACCG
166542 G
1 G
166543 GCAGTCCCCA
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:0.19, C:0.48, G:0.29, T:0.05
Consensus pattern (21 bp):
GCACCCACCAGGTCGCAACCG
Found at i:168588 original size:21 final size:20
Alignment explanation
Indices: 168540--168591 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
168530 ATCGATACAT
**
168540 TGTATCGATACGTGACCAAA
1 TGTATCGATACGTGAAAAAA
* *
168560 TATATCGATACTTGAAAAGAA
1 TGTATCGATACGTGAAAA-AA
168581 TGTATCGATAC
1 TGTATCGATAC
168592 AGGTCATTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (20 bp):
TGTATCGATACGTGAAAAAA
Found at i:168663 original size:13 final size:13
Alignment explanation
Indices: 168645--168670 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
168635 ACACACATTA
168645 TGTATCGATACAT
1 TGTATCGATACAT
168658 TGTATCGATACAT
1 TGTATCGATACAT
168671 CCCTAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:176970 original size:20 final size:20
Alignment explanation
Indices: 176945--176996 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
176935 TACAAGCCAA
** *
176945 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
176965 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
176984 TGTATCGATACAA
1 TGTATCGATACAA
176997 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:177002 original size:19 final size:18
Alignment explanation
Indices: 176945--177002 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
176935 TACAAGCCAA
*
176945 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
176965 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
176984 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
177003 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:177702 original size:21 final size:21
Alignment explanation
Indices: 177659--177704 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
177649 TAATTCACGC
* *
177659 ATTCTCCCCCGTTTATTAATA
1 ATTCTCCCCCGTTAATCAATA
177680 ATTCTCCCCC-TTAATCAAGTA
1 ATTCTCCCCCGTTAATCAA-TA
177701 ATTC
1 ATTC
177705 ATATCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCTCCCCCGTTAATCAATA
Found at i:179527 original size:13 final size:13
Alignment explanation
Indices: 179509--179547 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
179499 ATAATCACCC
179509 TGTATCGATACAA
1 TGTATCGATACAA
179522 TGTATCGATACAA
1 TGTATCGATACAA
179535 TGTATCGATACAA
1 TGTATCGATACAA
179548 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:183464 original size:21 final size:21
Alignment explanation
Indices: 183435--183479 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
183425 AAGTTTTTAT
*
183435 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
183455 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
183477 TTT
1 TTT
183480 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:185702 original size:13 final size:13
Alignment explanation
Indices: 185684--185709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
185674 CAATTTTTTG
185684 TGTATCGATACAT
1 TGTATCGATACAT
185697 TGTATCGATACAT
1 TGTATCGATACAT
185710 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:185724 original size:32 final size:33
Alignment explanation
Indices: 185664--185728 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
185654 TACAAGCCAA
** *
185664 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
185697 TGTATCGATAC-ATACTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
185729 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:186992 original size:15 final size:15
Alignment explanation
Indices: 186972--187002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
186962 TAAAAATGTC
*
186972 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
186987 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
187002 C
1 C
187003 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:189099 original size:13 final size:13
Alignment explanation
Indices: 189081--189119 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
189071 ACATTTTTCT
189081 TTGTATCGATACA
1 TTGTATCGATACA
189094 TTGTATCGATACA
1 TTGTATCGATACA
189107 TTGTATCGATACA
1 TTGTATCGATACA
189120 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:189285 original size:21 final size:21
Alignment explanation
Indices: 189240--189286 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
189230 AAATCTTTTG
189240 CAAAA-TACTTGTTTTTCACT
1 CAAAATTACTTGTTTTTCACT
*
189260 TAAAATTACTTTGTTTTTCA-T
1 CAAAATTAC-TTGTTTTTCACT
189281 CAAAAT
1 CAAAAT
189287 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 9 0.39
22 10 0.43
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (21 bp):
CAAAATTACTTGTTTTTCACT
Found at i:191233 original size:34 final size:35
Alignment explanation
Indices: 191195--191261 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
191185 CCTTACAACA
191195 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
191229 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
191262 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:191737 original size:13 final size:13
Alignment explanation
Indices: 191719--191744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
191709 CAATTTTTTG
191719 TGTATCGATACAT
1 TGTATCGATACAT
191732 TGTATCGATACAT
1 TGTATCGATACAT
191745 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:191809 original size:21 final size:21
Alignment explanation
Indices: 191783--191858 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
191773 CTGCCAAGAA
191783 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
191804 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
191824 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
191845 ATGTATCGATACAT
1 ATGTATCGATACAT
191859 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:191828 original size:20 final size:20
Alignment explanation
Indices: 191803--191876 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
191793 ACATCTTTTT
191803 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
191823 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
191844 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
191864 CATGTATCGATAC
1 CATGTATCGATAC
191877 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:191840 original size:41 final size:41
Alignment explanation
Indices: 191783--191876 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
191773 CTGCCAAGAA
191783 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
191824 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
191865 ATGTATCGATAC
1 ATGTATCGATAC
191877 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:192534 original size:21 final size:21
Alignment explanation
Indices: 192493--192536 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
192483 CTCCCCTTTA
* *
192493 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
192514 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
192535 TC
1 TC
192537 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:193546 original size:13 final size:13
Alignment explanation
Indices: 193528--193552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193518 ACTGAAGCAA
193528 TGTATCGATACAT
1 TGTATCGATACAT
193541 TGTATCGATACA
1 TGTATCGATACA
193553 ATCTGGAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:194152 original size:23 final size:24
Alignment explanation
Indices: 194107--194153 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
194097 CAAAGAATTG
*
194107 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
194131 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
194154 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:196749 original size:34 final size:35
Alignment explanation
Indices: 196711--196777 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
196701 CCTTACAACA
196711 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
196745 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
196778 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:197253 original size:13 final size:13
Alignment explanation
Indices: 197235--197260 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
197225 CAATTTTTTG
197235 TGTATCGATACAT
1 TGTATCGATACAT
197248 TGTATCGATACAT
1 TGTATCGATACAT
197261 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:197325 original size:21 final size:21
Alignment explanation
Indices: 197299--197374 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
197289 CTGCCAAGAA
197299 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
197320 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
197340 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
197361 ATGTATCGATACAT
1 ATGTATCGATACAT
197375 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:197344 original size:20 final size:20
Alignment explanation
Indices: 197319--197392 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
197309 ACATCTTTTT
197319 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
197339 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
197360 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
197380 CATGTATCGATAC
1 CATGTATCGATAC
197393 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:197356 original size:41 final size:41
Alignment explanation
Indices: 197299--197392 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
197289 CTGCCAAGAA
197299 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
197340 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
197381 ATGTATCGATAC
1 ATGTATCGATAC
197393 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:198415 original size:13 final size:13
Alignment explanation
Indices: 198397--198422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
198387 TACAGCAAGT
198397 ATGTATCGATACA
1 ATGTATCGATACA
198410 ATGTATCGATACA
1 ATGTATCGATACA
198423 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:206795 original size:24 final size:26
Alignment explanation
Indices: 206768--206817 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
206758 ATCAAAATTT
206768 TATTCAT-C-GGGGACACTCCAACCC
1 TATTCATCCAGGGGACACTCCAACCC
*
206792 TATTCCTCCGAGGGGACACTCCAACC
1 TATTCATCC-AGGGGACACTCCAACC
206818 TTGTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 1 0.05
27 15 0.68
ACGTcount: A:0.24, C:0.38, G:0.18, T:0.20
Consensus pattern (26 bp):
TATTCATCCAGGGGACACTCCAACCC
Found at i:208851 original size:20 final size:20
Alignment explanation
Indices: 208828--208901 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
208818 ACAATTCAAA
208828 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
208848 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
208869 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
208889 GTATCGATACATG
1 GTATCGATACATG
208902 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:208872 original size:21 final size:21
Alignment explanation
Indices: 208846--208921 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
208836 ACATGTTGCA
208846 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
208867 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
208887 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
208908 ATGTATCGATACAT
1 ATGTATCGATACAT
208922 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:208879 original size:41 final size:41
Alignment explanation
Indices: 208828--208921 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
208818 ACAATTCAAA
208828 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
208869 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
208910 GTATCGATACAT
1 GTATCGATACAT
208922 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:208978 original size:13 final size:13
Alignment explanation
Indices: 208960--208985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208950 TACAGCAAGT
208960 ATGTATCGATACA
1 ATGTATCGATACA
208973 ATGTATCGATACA
1 ATGTATCGATACA
208986 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:209506 original size:34 final size:35
Alignment explanation
Indices: 209443--209509 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
209433 CTAAGTGATT
209443 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
209479 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
209510 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:214076 original size:30 final size:30
Alignment explanation
Indices: 214017--214378 Score: 386
Period size: 31 Copynumber: 11.8 Consensus size: 30
214007 TCTCTTTTCT
*
214017 TCAAAATCCACGACTCAGTGGCAATCTCTTC
1 TCAAAGTCCACGACTCAGTGGC-ATCTCTTC
*
214048 TCAAAGTCTACGACTCAGTGGCATCTCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTCTTC
* * *
214078 -CTAAAGTCCATGACTTAGTGGCATCTTTTC
1 TC-AAAGTCCACGACTCAGTGGCATCTCTTC
* * * *
214108 TTCAAAATCCACGACTCAGTGACGTCTCTTT
1 -TCAAAGTCCACGACTCAGTGGCATCTCTTC
* *
214139 TCTAAGTCCACGACTCAGTGGCATCTTTTTTC
1 TCAAAGTCCACGACTCAGTGGCATC--TCTTC
* * *
214171 TTCAAATTCCATGACTTAGTGGCAATCTCTTC
1 -TCAAAGTCCACGACTCAGTGGC-ATCTCTTC
*
214203 TTAAAGTCCACGACTCAGTGGCATCTCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTCTTC
* *
214233 TCAAAGTCCACAACTCAGTGGCATCTTTTC
1 TCAAAGTCCACGACTCAGTGGCATCTCTTC
* * *
214263 TTCAAAGTCCACTACTTAGTAGCAATCTCTTC
1 -TCAAAGTCCACGACTCAGTGGC-ATCTCTTC
*
214295 TCAATGTCCACGACTCAGTGGCATCT-TGTC
1 TCAAAGTCCACGACTCAGTGGCATCTCT-TC
* *
214325 CCAAAGTCCACGACTCAGTGGCAATCTCTTT
1 TCAAAGTCCACGACTCAGTGGC-ATCTCTTC
* *
214356 TCAAAGTCCACAACTCTGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
214379 CCCTTTTAAG
Statistics
Matches: 274, Mismatches: 45, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.01
30 115 0.42
31 120 0.44
32 16 0.06
33 18 0.07
34 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (30 bp):
TCAAAGTCCACGACTCAGTGGCATCTCTTC
Found at i:214113 original size:61 final size:61
Alignment explanation
Indices: 214023--214378 Score: 389
Period size: 61 Copynumber: 5.8 Consensus size: 61
214013 TTCTTCAAAA
*
214023 TCCACGACTCAGTGGCAATCTCTTCTCAAAGTCTACGACTCAGTGGCATCTCTTCCTAAAG
1 TCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCCTAAAG
* * * * * * *
214084 TCCATGACTTAGTGGC-ATCTTTTCTTCAAAATCCACGACTCAGTGACGTCTCTTTTCT-AAG
1 TCCACGACTCAGTGGCAATCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTC-TTCCTAAAG
* * * * *
214145 TCCACGACTCAGTGGC-ATCTTTTTTCTTCAAATTCCATGACTTAGTGGCAATCTCTTCTTAAAG
1 TCCACGACTCAGTGGCAATC--TCTTC-TCAAAGTCCACGACTCAGTGGC-ATCTCTTCCTAAAG
* * *
214209 TCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAG
1 TCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCCT-AAAG
* * * * *
214270 TCCACTACTTAGTAGCAATCTCTTCTCAATGTCCACGACTCAGTGGCATCT-TGTCCCAAAG
1 TCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCT-TCCTAAAG
* * *
214331 TCCACGACTCAGTGGCAATCTCTTTTCAAAGTCCACAACTCTGTGGCA
1 TCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCA
214379 CCCTTTTAAG
Statistics
Matches: 249, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
60 16 0.06
61 138 0.55
62 42 0.17
63 27 0.11
64 26 0.10
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (61 bp):
TCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCCTAAAG
Found at i:214366 original size:92 final size:92
Alignment explanation
Indices: 214017--214365 Score: 447
Period size: 92 Copynumber: 3.8 Consensus size: 92
214007 TCTCTTTTCT
* * *
214017 TCAAAATCCACGACTCAGTGGCAATCTCTTCTCAAAGTCTACGACTCAGTGGCATCTCTTCCT-A
1 TCAAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTTCA
*
214081 AAGTCCATGACTTAGTGGC-ATCTTTTC
65 AAGTCCATGACTTAGTGGCAATCTCTTC
* * * * * *
214108 TTCAAAATCCACGACTCAGTGACGTCTCTTTTCTAAGTCCACGACTCAGTGGCATCTTTTTTCTT
1 -TCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATC--TCTTCTT
*
214173 CAAATTCCATGACTTAGTGGCAATCTCTTC
63 CAAAGTCCATGACTTAGTGGCAATCTCTTC
* * *
214203 TTAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAA
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAA
*
214268 AGTCCACT-ACTTAGTAGCAATCTCTTC
66 AGTCCA-TGACTTAGTGGCAATCTCTTC
* *
214295 TCAATGTCCACGACTCAGTGGCATCT-TGTCCCAAAGTCCACGACTCAGTGGCAATCTCTT-TTC
1 TCAAAGTCCACGACTCAGTGGCATCTCT-TCTCAAAGTCCACGACTCAGTGGC-ATCTCTTCTTC
214358 AAAGTCCA
64 AAAGTCCA
214366 CAACTCTGTG
Statistics
Matches: 227, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
91 30 0.13
92 111 0.49
93 12 0.05
94 67 0.30
95 7 0.03
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.32
Consensus pattern (92 bp):
TCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAA
AGTCCATGACTTAGTGGCAATCTCTTC
Found at i:214644 original size:13 final size:13
Alignment explanation
Indices: 214626--214655 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
214616 CATAAAATGT
214626 TGTATCGATACAA
1 TGTATCGATACAA
214639 TGTATCGATACAA
1 TGTATCGATACAA
214652 TGTA
1 TGTA
214656 AGCTACTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:214714 original size:13 final size:13
Alignment explanation
Indices: 214696--214720 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
214686 ATTACTCACA
214696 TGTATCGATACAT
1 TGTATCGATACAT
214709 TGTATCGATACA
1 TGTATCGATACA
214721 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.