Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009604.1 Corchorus capsularis cultivar CVL-1 contig09625, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 109465
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:59 original size:30 final size:30
Alignment explanation
Indices: 25--98 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 30
15 CGTTAGGTTG
25 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
* *
55 AGGGGGCAAAATGT-CCAAGATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
*
84 GGGGGGCAAAACGTC
1 AGGGGGCAAAACGTC
99 TAAACGCTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAGTTC
Found at i:77 original size:29 final size:29
Alignment explanation
Indices: 25--125 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
15 CGTTAGGTTG
*
25 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGT-CCAAGATTGAAGTTC
*
55 AGGGGGCAAAATGTCCAAGATTGAAGTTC
1 AGGGGGCAAAACGTCCAAGATTGAAGTTC
* * * **
84 GGGGGGCAAAACGTCTAAACGCTACAAGTTC
1 AGGGGGCAAAACGTC-CAA-GATTGAAGTTC
115 AGGGGGCAAAA
1 AGGGGGCAAAA
126 TGATAAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
29 27 0.45
30 15 0.25
31 18 0.30
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.16
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAGATTGAAGTTC
Found at i:12010 original size:16 final size:16
Alignment explanation
Indices: 11989--12019 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11979 TTGAAAAATA
11989 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
12005 TTACTAAATTTTTAT
1 TTACTAAATATTTAT
12020 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:12830 original size:204 final size:199
Alignment explanation
Indices: 12362--14010 Score: 1787
Period size: 204 Copynumber: 8.3 Consensus size: 199
12352 ATAATAAGTT
* * * **
12362 TTATTGTACGAATACAATCTGTCAATGTAAATTTTGGACTTCATAAGTAGGTTAAGAAGTTGACA
1 TTATTATAC-AATAC-A-CTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACA
* * * *
12427 CATACCCCATTTTATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGGATACATG
63 CATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA-GAGGACACATG
** * * * ** *
12492 TCAACCCTTAAACCATGCATGTACAGTCTGCTAAACTCTACTGACGGTGTATTGTA-AATTTTTT
127 TCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGATAGTGTATTGTATAATTTTTC
*
12556 TTGTAGGA
192 TTATAGGA
* * * * *
12564 TTATTATACAAAACATTGTCAGTGTAAATTTTGAACTCCACAACCGGGTTAAGAAGTTGACACAT
1 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
** * *
12629 ACCTTATTTCATAATTAATTAGATA-TAAATTATTAATACATATTCCCTAAGAGGACACATGTCA
66 ACCCCATTTCATAATTAATTAAATATTTAA-TATTAATACATATTCCCTAAGAGGACACATGTCA
* * * *
12693 ACCCTTAAACCCCGCGCATCCAATCTGCTAAACTCCACTGATAGTGTAATACTGTATAATTTTTG
130 ACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGATAGTGT-AT--TGTATAA-TTTT-
* *
12758 TTTTATATGA
190 TCTTATAGGA
* *
12768 TTATTATACAATATACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAC
1 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
* * * * * *
12833 ACCCCATTTCATAATTAATAAAATATGTAATATTAATAAATATTCCATAAGGGGATACATGTCAA
66 ACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGAGGACACATGTCAA
*
12898 CCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTAACT-GTGTATT-TGATAATTTTTCTT
131 CCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGA-TAGTGTATTGT-ATAATTTTTCTT
*
12961 AGAGG-
194 ATAGGA
* * * * * **
12966 --ATTAT-CAATACACTGCCAGTATAAAATTTTGAACTACATAAGCGAGTTAAGAAGTTGACAGG
1 TTATTATACAATACACTGTCAGTGT-AAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
* * * * *
13028 TATCTCATTTCTTAATAAATTAAATATTTAACATTAATACATATTCCCTAA-AGGGACACATGTC
65 TACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGA-GGACACATGTC
* * *
13092 AACCCTTAAATCCTGCACGTGCAGTCTGCTAAAATCCACT--TACG-GTATTGTATAATTTTTCT
129 AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGATA-GTGTATTGTATAATTTTTCT
13154 TATAGGA
193 TATAGGA
* * * *
13161 TTATTATACAATACA---T---TGTAAAATTTGAACTCTATAAGCAGGTTAAGAAGTTGACACAT
1 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
* * ** *
13220 ACCCTATTTCATAATTAATTAGATATAAAATATTAATACATATTCCCTAAGAGGACATATGTCAA
66 ACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGAGGACACATGTCAA
* * *
13285 CCCTTAAACCCCGCGCGTGCAGTCTGCTAAACTCCACTGACAGTGTATTGTATAATTTTCGTTTT
131 CCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGATAGTGTATTGTATAATTTT--TCTT
*
13350 ATATGA
194 ATAGGA
* * *
13356 TTATTATACAATACACTGTTAGTGTAAA-TTTGGACTCCATAAGCAGATTAAGAAGTTGACACAT
1 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
* * * *
13420 ACCCGACCCATTTCATAACTAATTAAATATTTAATATTGATACATATTCCCTAAGGGGATACATG
66 A--C--CCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGAGGACACATG
* * * **
13485 TCAACCCTTGAACCCCGCACGTGCAGTATGCTAAACTCCACTAACT-GTGTATTGCGTAATTTTT
127 TCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGA-TAGTGTATTGTATAATTTTT
*
13549 CTTATAGAA
191 CTTATAGGA
* * * *
13558 TTATTATACAATACACTGTCAATATAAATTTTGGACTCCATAAGCGAGTTAAGAAGTTGACAGAT
1 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
* * *
13623 ACCTCATTTCATAATAAATTAAATATTTAATA-TAATACATA-TCCTTAA-AGGGACACATGTCA
66 ACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGA-GGACACATGTCA
* * * * * *
13685 ACCCTTAAATCCTGCACGTGCAGTCTGCTAAAATCCA-T-TTACG-ATATTGTATAATTTTTCTC
130 ACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGATA-GTGTATTGTATAATTTTTCTT
13747 ATAGGA
194 ATAGGA
* * *
13753 TTATTATACAATACATTGTCAAGTGTAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACAAA
1 TTATTATACAATACACTGTC-AGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
* * * * *
13818 TACCCTA-TT-A-CA-TAATTAAATAATTAATATTAATACATATTCCCTAAGCGTACACATGTC-
65 TACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGAGGACACATGTCA
* * * *
13878 ACCCTTAAAGTTAAACCCCGCATGTGCAATCTGCTAAACTCCACTGATGGTGTATTGTATAAATT
130 ACCC------TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGATAGTGTATTGTATAATTT
13943 TTCTTATAGGA
189 TTCTTATAGGA
* * *
13954 TTATTATATAATACACTGTCAATGTAAATTTTGTACTCCATAAGC-GGTTAAGAAGTT
1 TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTT
14011 TTTGTGCCAA
Statistics
Matches: 1213, Mismatches: 181, Indels: 109
0.81 0.12 0.07
Matches are distributed among these distances:
191 120 0.10
192 19 0.02
193 31 0.03
194 39 0.03
195 80 0.07
196 173 0.14
197 54 0.04
198 67 0.06
199 158 0.13
200 64 0.05
201 61 0.05
202 43 0.04
203 39 0.03
204 262 0.22
205 3 0.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (199 bp):
TTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT
ACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGAGGACACATGTCAA
CCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGATAGTGTATTGTATAATTTTTCTTAT
AGGA
Found at i:17938 original size:37 final size:37
Alignment explanation
Indices: 17865--17938 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
17855 GTAATTTGTG
* *
17865 TTATGAGCAATTTATTCCAACAATTAAGGTAGAGTAA
1 TTATGAGCAATTTATTCCAAAAATTAAGGCAGAGTAA
* **
17902 TTATGAGTAATTTATTGTAAAACATTAAGGCA-AGTAA
1 TTATGAGCAATTTATTCCAAAA-ATTAAGGCAGAGTAA
17939 ACGGATAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 23 0.74
38 8 0.26
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (37 bp):
TTATGAGCAATTTATTCCAAAAATTAAGGCAGAGTAA
Found at i:20412 original size:2 final size:2
Alignment explanation
Indices: 20407--20439 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20397 GAGGTGATCA
20407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20440 AAAGTATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20503 original size:31 final size:31
Alignment explanation
Indices: 20475--20533 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
20465 TGTTTTCCGA
*
20475 TTATACCCTTATT-TTTAAAATATATTTCCAG
1 TTATACCCTT-TTCTTTAAAACATATTTCCAG
* *
20506 TTGTATCCTTTTCTTTAAAACATATTTC
1 TTATACCCTTTTCTTTAAAACATATTTC
20534 TAAATTGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (31 bp):
TTATACCCTTTTCTTTAAAACATATTTCCAG
Found at i:20871 original size:19 final size:20
Alignment explanation
Indices: 20844--20881 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
20834 TACTATTATT
20844 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
20864 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
20882 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:21073 original size:22 final size:22
Alignment explanation
Indices: 21045--21110 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
21035 CTTGTCTCTA
*
21045 TGTGGTTATCAAAATTTCATAG
1 TGTGGTTACCAAAATTTCATAG
21067 TGTGGTTACCAAAATTTCATAG
1 TGTGGTTACCAAAATTTCATAG
*
21089 TGTGGTTACCATAATTTCATAG
1 TGTGGTTACCAAAATTTCATAG
21111 GATCAGGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (22 bp):
TGTGGTTACCAAAATTTCATAG
Found at i:21225 original size:22 final size:22
Alignment explanation
Indices: 21200--21258 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
21190 ATCAAAAAGA
*
21200 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
21222 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
21244 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
21259 TAAATATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:21404 original size:22 final size:22
Alignment explanation
Indices: 21335--21605 Score: 143
Period size: 22 Copynumber: 12.4 Consensus size: 22
21325 TAAAAGTCTC
* *
21335 AATTTCAT-AAG-GAGTACCAA
1 AATTTCATAAAGTGATTATCAA
*
21355 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATA-AAGTGATTATCAA
* *
21375 AATCTCATAAAGTGATTATCGA
1 AATTTCATAAAGTGATTATCAA
*
21397 AATTTCATAGAGATCTGATTATCAA
1 AATTTCATA-A-A-GTGATTATCAA
**
21422 AATTT-ATAGAA-AAATTATCAA
1 AATTTCATA-AAGTGATTATCAA
**
21443 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAAAG-TGATTATCAA
21465 AATTTC--AAAGTGAGGTTATCAA
1 AATTTCATAAAGTGA--TTATCAA
** *
21487 AATTAAATAATGTGATTATCAA
1 AATTTCATAAAGTGATTATCAA
* * * * *
21509 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGTGATTATCAA
* * *
21531 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAAAGTGATTATCAA
* * *
21553 AATTTCATAAAGAGGTTATTAA
1 AATTTCATAAAGTGATTATCAA
*
21575 ATTTTCA-AAATGTGATTA-CAA
1 AATTTCATAAA-GTGATTATCAA
21596 GAATTTCATA
1 -AATTTCATA
21606 GTGGTATTTC
Statistics
Matches: 193, Mismatches: 39, Indels: 35
0.72 0.15 0.13
Matches are distributed among these distances:
19 5 0.03
20 18 0.09
21 26 0.13
22 115 0.60
23 3 0.02
24 12 0.06
25 14 0.07
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
AATTTCATAAAGTGATTATCAA
Found at i:21717 original size:19 final size:19
Alignment explanation
Indices: 21687--21734 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
21677 TTATGGAGTA
21687 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
21707 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
21726 ATCAAAATT
1 ATCAAAATT
21735 TCATATCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:21833 original size:22 final size:22
Alignment explanation
Indices: 21687--22239 Score: 228
Period size: 22 Copynumber: 25.6 Consensus size: 22
21677 TTATGGAGTA
*
21687 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
*
21707 ATCAAAA-TTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
***
21726 ATCAAAATTTCATATCAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
21748 ATCAAAATTTCACA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
**
21770 ATCAAAATTTCATAGGGAGAAT
1 ATCAAAATTTCATAGGGAGGTT
* **
21792 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
21814 ATCAAAAAATCATAGGGAGG-T
1 ATCAAAATTTCATAGGGAGGTT
* *
21835 AACAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
21851 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
21873 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
21896 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
21919 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
21941 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* ** * *
21963 ATCAAAATTTCAGATTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* *
21985 A-CTAACAA-TTCATATGGAGATT
1 ATC-AA-AATTTCATAGGGAGGTT
* ** *
22007 -TTAAAATTTTCATAACGCGGTT
1 ATCAAAA-TTTCATAGGGAGGTT
* * *
22029 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
22051 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
22074 ATCAAAA-TTCATTGGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
22095 ATCAAAGTTTCATATTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* * *
22118 -TCAAAATTCCTTAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
22139 AACCAAATTTCATAAGAAGATT
1 ATCAAAATTTCATAGGGAGGTT
** *** *
22161 AAAAAAATTT-ATAAAAAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
22182 CTCGAAAGTTCATA-GTATCGTT
1 ATCAAAATTTCATAGGGA-GGTT
* *
22204 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
22226 ATCAAAATTTCATA
1 ATCAAAATTTCATA
22240 ATGGGATCAT
Statistics
Matches: 401, Mismatches: 105, Indels: 52
0.72 0.19 0.09
Matches are distributed among these distances:
15 1 0.00
16 8 0.02
17 2 0.00
18 2 0.00
19 18 0.04
20 13 0.03
21 40 0.10
22 254 0.63
23 63 0.16
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:22385 original size:3 final size:3
Alignment explanation
Indices: 22377--22408 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
22367 ATATATATAT
22377 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22409 GCAGATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:22397 original size:14 final size:14
Alignment explanation
Indices: 22380--22408 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22370 TATATATATA
22380 ATAATAATAATAAT
1 ATAATAATAATAAT
22394 ATAATAATAATAAT
1 ATAATAATAATAAT
22408 A
1 A
22409 GCAGATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:22397 original size:17 final size:17
Alignment explanation
Indices: 22375--22408 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22365 ATATATATAT
22375 ATATAATAATAATAATA
1 ATATAATAATAATAATA
22392 ATATAATAATAATAATA
1 ATATAATAATAATAATA
22409 GCAGATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATAATAATAATAATA
Found at i:27054 original size:22 final size:23
Alignment explanation
Indices: 27029--27071 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27019 CGGATATTAG
*
27029 AGGATTAGA-AAAAAAATTACGA
1 AGGATTACAGAAAAAAATTACGA
*
27051 AGGATTACAGAAAAGAATTAC
1 AGGATTACAGAAAAAAATTAC
27072 ATTAAAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (23 bp):
AGGATTACAGAAAAAAATTACGA
Found at i:33190 original size:2 final size:2
Alignment explanation
Indices: 33183--33211 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33173 AAATATAGAA
33183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33212 AACGAATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35790 original size:1 final size:1
Alignment explanation
Indices: 35784--35813 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
35774 GTTTCATAGG
35784 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35814 CCTGTTATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39296 original size:2 final size:2
Alignment explanation
Indices: 39289--39362 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
39279 ACCCCCGGCA
39289 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39331 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39363 ACACACACAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:54642 original size:74 final size:72
Alignment explanation
Indices: 54513--54659 Score: 224
Period size: 74 Copynumber: 2.0 Consensus size: 72
54503 ATTATGGGTA
* *
54513 ATTGTCCAATATCATGTAATCACATTAGACTACGATTAATTTGAAATCAAATCATAAAGAACCCC
1 ATTGCCCAATATCATGTAATCACATTAGACTACGATTAATCTGAAATCAAATCATAAAGAACCCC
54578 AAATGAG
66 AAATGAG
* *
54585 ATTGCCCAATATCATGTAAT-ATCATATCAGACTGCGATTAATCTGAAATCAAGTCATAAAGAAC
1 ATTGCCCAATATCATGTAATCA-CAT-T-AGACTACGATTAATCTGAAATCAAATCATAAAGAAC
54649 CCCAAATGAG
63 CCCAAATGAG
54659 A
1 A
54660 GTAAATCTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
71 1 0.01
72 22 0.32
73 1 0.01
74 44 0.65
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (72 bp):
ATTGCCCAATATCATGTAATCACATTAGACTACGATTAATCTGAAATCAAATCATAAAGAACCCC
AAATGAG
Found at i:56493 original size:31 final size:31
Alignment explanation
Indices: 56458--56617 Score: 149
Period size: 31 Copynumber: 5.5 Consensus size: 31
56448 TTTTGTGCAC
* * **
56458 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
56489 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* *
56520 GTGGCATGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
56551 GT-G---G-CAC--G--ACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * *
56573 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* *
56604 GTGGCGTGTCACGT
1 GTGGCATGCCACGT
56618 CGGACACCGT
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
22 16 0.15
23 1 0.01
24 1 0.01
26 3 0.03
27 4 0.04
29 1 0.01
30 1 0.01
31 81 0.75
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGGTACAT
Found at i:56568 original size:53 final size:53
Alignment explanation
Indices: 56506--56608 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
56496 GCCACGTGTC
** *
56506 ACTTTTTGGTACACGTGGCATGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGCACG
* * *
56559 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGC
56609 GTGTCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:58610 original size:2 final size:2
Alignment explanation
Indices: 58603--58635 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
58593 ATAGTACTCC
58603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58636 CGTAGCTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62695 original size:17 final size:16
Alignment explanation
Indices: 62673--62713 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
62663 ATTACTTATT
*
62673 AAAAAGAAAGAAGAAGG
1 AAAAAGAAA-AAAAAGG
62690 AAAAAGAAAAAAAAGG
1 AAAAAGAAAAAAAAGG
62706 AGAAAAGA
1 A-AAAAGA
62714 TTCTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGG
Found at i:64087 original size:7 final size:7
Alignment explanation
Indices: 64075--64102 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
64065 AATTGAAGAA
64075 CAGAAGC
1 CAGAAGC
64082 CAGAAGC
1 CAGAAGC
64089 CAGAAGC
1 CAGAAGC
64096 CAGAAGC
1 CAGAAGC
64103 TCAATCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.29, T:0.00
Consensus pattern (7 bp):
CAGAAGC
Found at i:74688 original size:33 final size:32
Alignment explanation
Indices: 74613--74690 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
74603 CCCCTATGTC
*
74613 AGGGTAAAATGTCTTGAATTTGAAAAGTATAG
1 AGGGCAAAATGTCTTGAATTTGAAAAGTATAG
*
74645 AGGGCAAAATGTCTTGAATTTTG-GAAGT-TCAG
1 AGGGCAAAATGTCTTGAA-TTTGAAAAGTAT-AG
74677 AGGGGCAAAATGTC
1 A-GGGCAAAATGTC
74691 CTGATTTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
31 1 0.02
32 24 0.59
33 16 0.39
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (32 bp):
AGGGCAAAATGTCTTGAATTTGAAAAGTATAG
Found at i:78502 original size:59 final size:57
Alignment explanation
Indices: 78409--78534 Score: 173
Period size: 59 Copynumber: 2.2 Consensus size: 57
78399 GCAATGGAGT
* * *
78409 AAAAT-TGAAATATGTTAAAGACGAGAATAGAGAGACAATAGAATATGGAGAAGAAG
1 AAAATATGAAGTATGTAAAAGACGAGAATAGAGAGACAATAAAATATGGAGAAGAAG
* * *
78465 AAAATATGAAGTATGTAAAAGACAAGAGAATATAGAGATAATAAAATATGGATAAGAAG
1 AAAATATGAAGTATGTAAAAGAC--GAGAATAGAGAGACAATAAAATATGGAGAAGAAG
78524 AAAATATGAAG
1 AAAATATGAAG
78535 AATTGGAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
56 5 0.08
57 15 0.25
59 41 0.67
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.19
Consensus pattern (57 bp):
AAAATATGAAGTATGTAAAAGACGAGAATAGAGAGACAATAAAATATGGAGAAGAAG
Found at i:79888 original size:11 final size:11
Alignment explanation
Indices: 79845--79882 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
79835 TTCCTATATA
*
79845 AAATAAATTAT
1 AAATTAATTAT
79856 CAAA-TAATTAT
1 -AAATTAATTAT
79867 AAATTAATTAT
1 AAATTAATTAT
79878 AAATT
1 AAATT
79883 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:85884 original size:15 final size:15
Alignment explanation
Indices: 85840--85886 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
85830 GGCAGCTTCA
85840 ATCAGCAGTCAGCAGC
1 ATCAGCA-TCAGCAGC
* *
85856 AT-TGCTATCTGCAGC
1 ATCAGC-ATCAGCAGC
85871 ATCAGCATCAGCAGC
1 ATCAGCATCAGCAGC
85886 A
1 A
85887 GAAGCAAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (15 bp):
ATCAGCATCAGCAGC
Found at i:88412 original size:11 final size:11
Alignment explanation
Indices: 88396--88427 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
88386 ATTTTCTAAA
88396 ACCCGACCGAG
1 ACCCGACCGAG
*
88407 ACCCGATCGAG
1 ACCCGACCGAG
88418 ACCCGACCGA
1 ACCCGACCGA
88428 CAGCCCAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.44, G:0.25, T:0.03
Consensus pattern (11 bp):
ACCCGACCGAG
Found at i:88767 original size:18 final size:18
Alignment explanation
Indices: 88744--88781 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
88734 AGCCCCTTTT
88744 AAAAATAAACAATACATA
1 AAAAATAAACAATACATA
88762 AAAAATAAACAATACATA
1 AAAAATAAACAATACATA
88780 AA
1 AA
88782 GGGTAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATAAACAATACATA
Found at i:94143 original size:3 final size:3
Alignment explanation
Indices: 94135--94160 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
94125 CCCTTTGTAA
94135 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
94161 CTAGAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:94700 original size:80 final size:81
Alignment explanation
Indices: 94566--94728 Score: 310
Period size: 80 Copynumber: 2.0 Consensus size: 81
94556 ATTTATAATT
*
94566 AATTTATAATTATTTGATTAATTTATTTTATATAGGAAAAGGGGATGAATGTCTTTTGATTTTTC
1 AATTTATAATTATTTGATTAATTTATTTTATATAGGAAAAGGGGATGAATGTCTTTTAATTTTTC
94631 CAAACTAAATGAATAC
66 CAAACTAAATGAATAC
94647 AATTTATAATTATTTGATTAATTTA-TTTATATAGGAAAAGGGGATGAATGTCTTTTAATTTTTC
1 AATTTATAATTATTTGATTAATTTATTTTATATAGGAAAAGGGGATGAATGTCTTTTAATTTTTC
94711 CAAACTAAATGAATAC
66 CAAACTAAATGAATAC
94727 AA
1 AA
94729 ATATAATAAA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 56 0.69
81 25 0.31
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (81 bp):
AATTTATAATTATTTGATTAATTTATTTTATATAGGAAAAGGGGATGAATGTCTTTTAATTTTTC
CAAACTAAATGAATAC
Found at i:95711 original size:2 final size:2
Alignment explanation
Indices: 95693--95736 Score: 52
Period size: 2 Copynumber: 21.0 Consensus size: 2
95683 CGTCATAATC
* *
95693 TA TA TC TA TA CTA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
95737 AAAGTACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 32 0.89
3 4 0.11
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:95819 original size:30 final size:32
Alignment explanation
Indices: 95765--95830 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
95755 AATTTTATGT
* * *
95765 TTTCCGATTATACCCTTATTTTT-AAAATATA
1 TTTCCAATTATACCCATATTTTTAAAAACATA
*
95796 TTTCCAATTGTACCCAT-TTTTTAAAAACATA
1 TTTCCAATTATACCCATATTTTTAAAAACATA
95827 TTTC
1 TTTC
95831 TAAATTGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTCCAATTATACCCATATTTTTAAAAACATA
Found at i:97229 original size:45 final size:44
Alignment explanation
Indices: 97094--97383 Score: 187
Period size: 44 Copynumber: 6.7 Consensus size: 44
97084 TTATGGAGTA
* * *
97094 ATCAAAATTTC--AGGGAGGA-TATTAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTTATAG-TGAGGTT
* * * *
97136 TTCAAAATTTCATAAGAGG-G-TTATCAAAATTTCATAGT-ACGTAG
1 ATCAAAATTTCAT-AG-GGAGATTATCAAAATTTTATAGTGAGGT-T
* *
97180 ATCAAAATTTCATAGGGAGATTAACAAAATTTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTT-ATAGTGAGGTT
** *
97225 ATCAAAAAATCATAGGGAGGTTATCAAAA--TT-T-GT-A-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTTATAGTGAGGTT
* * * * *
97263 ATCAAGATTTCATA-AGAAAGTTATCAAAATTTTATAGGGAGTTT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTTATAGTGAGGTT
* * * *
97307 ATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGTAAGGTT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTTATAGTGAGGTT
* *
97352 ATCACAAA-TTCATAGTGTGATTATCAAAATTT
1 ATCA-AAATTTCATAGGGAGATTATCAAAATTT
97384 CAGAGTGCGA
Statistics
Matches: 192, Mismatches: 36, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
37 2 0.01
38 23 0.12
39 1 0.01
40 3 0.02
41 2 0.01
42 14 0.07
43 9 0.05
44 65 0.34
45 65 0.34
46 8 0.04
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTTATAGTGAGGTT
Found at i:97277 original size:127 final size:127
Alignment explanation
Indices: 97131--97383 Score: 312
Period size: 127 Copynumber: 2.0 Consensus size: 127
97121 TTTCATAGTT
* ** *
97131 TAGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTACGTAGATCAAAATTTCATAG
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGA-GTAGATCAAAATTTCATAG
* * *
97195 GGAGA-TTAACAAAATTTTCATAATGAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTTG
65 GAAGATTTAACAAAA-TTTCATAATAAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTG
* * ** *
97258 TAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGTTTATCAAAATTTTATAGG
1 TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGAGTAGATCAAAATTTCATAGG
* * * * * *
97323 AAGATTTATCAAAATTTCATAGTAAGGTTATCACAAATTCATAGTGTGATTATCAAAATTT
66 AAGATTTAACAAAATTTCATAATAAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTT
97384 CAGAGTGCGA
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
127 96 0.91
128 10 0.09
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (127 bp):
TAGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGAGTAGATCAAAATTTCATAGG
AAGATTTAACAAAATTTCATAATAAGGTTATCAAAAAATCATAGGGAGATTATCAAAATTTG
Found at i:97334 original size:23 final size:22
Alignment explanation
Indices: 97094--97652 Score: 165
Period size: 22 Copynumber: 25.6 Consensus size: 22
97084 TTATGGAGTA
* *
97094 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGAAGGTT
* **
97114 ATTAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GAAGGTT
* * *
97136 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATAGGAAGGTT
* * *
97158 ATCAAAATTTCATA-GTACGTAG
1 ATCAAAATTTCATAGGAAGGT-T
* *
97180 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGAAGGTT
* *
97202 AACAAAATTTTCATAATG-AGGTT
1 ATCAAAA-TTTCAT-AGGAAGGTT
** *
97225 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGAAGGTT
*
97247 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGAAGGTT
* * *
97263 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGAAGGTT
* * *
97285 ATCAAAATTTTATAGGGAGTTT
1 ATCAAAATTTCATAGGAAGGTT
* *
97307 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGAAG-GTT
*
97330 ATCAAAATTTCATAGTAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
* *
97352 ATCACAAA-TTCATAGTG-TGATT
1 ATCA-AAATTTCATAG-GAAGGTT
* * *
97374 ATCAAAATTTCAGAGTG-CGATT
1 ATCAAAATTTCATAG-GAAGGTT
* *
97396 A-CTAACAA-TTCATA-TAGAGATT
1 ATC-AA-AATTTCATAGGA-AGGTT
* * * ** *
97418 TTTAAATTTTCATAACAATGTT
1 ATCAAAATTTCATAGGAAGGTT
* *
97440 ATCAATATATT-ATATGAAGGTT
1 ATCAAAAT-TTCATAGGAAGGTT
* * * **
97462 ATCAACATCTAATAGTGTTGGTT
1 ATCAAAATTTCATAG-GAAGGTT
* *
97485 ATCAAAATTTAATTGGGAA-GTT
1 ATCAAAATTTCA-TAGGAAGGTT
*
97507 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-GGAAGGT-T
* *
97530 -TCAAAATTCCTTA-GAGAGGTT
1 ATCAAAATTTCATAGGA-AGGTT
* *
97551 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
** **
97573 AAAAAAAATTT-ATAAAAAGGTT
1 -ATCAAAATTTCATAGGAAGGTT
* * * * ***
97595 CTCGAAATTCCATAGTATCATT
1 ATCAAAATTTCATAGGAAGGTT
* *
97617 ATTAAAATTTCATAGAAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
**
97639 ATTGAAATTTCATA
1 ATCAAAATTTCATA
97653 ATGAGATCAT
Statistics
Matches: 400, Mismatches: 100, Indels: 76
0.69 0.17 0.13
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 2 0.00
20 11 0.03
21 22 0.05
22 272 0.68
23 76 0.19
24 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAAGGTT
Found at i:97757 original size:3 final size:3
Alignment explanation
Indices: 97749--97783 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
97739 CCCTTTGTAA
97749 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
97784 AATTGTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:98160 original size:20 final size:21
Alignment explanation
Indices: 98135--98175 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
98125 ATCGTGTCAC
98135 GACACGATTAACAC-GTTTAA
1 GACACGATTAACACGGTTTAA
*
98155 GACACGATTGACACGGTTTAA
1 GACACGATTAACACGGTTTAA
98176 TTACCGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
GACACGATTAACACGGTTTAA
Found at i:101972 original size:22 final size:23
Alignment explanation
Indices: 101941--102149 Score: 165
Period size: 23 Copynumber: 9.0 Consensus size: 23
101931 AGTTTCTGTT
*
101941 TTTTTATGTTGAAAATGTTGCTG
1 TTTTGATGTTGAAAATGTTGCTG
* *
101964 TTTTG-TGTTGAAAATTTTGTTG
1 TTTTGATGTTGAAAATGTTGCTG
101986 TTTTG-TGTT-AATAATGTTGCTG
1 TTTTGATGTTGAA-AATGTTGCTG
* * *
102008 TTTTGTGTTGTGTTGAAAATGCTACTG
1 -TTT-TG--ATGTTGAAAATGTTGCTG
* *
102035 TTTTGCTGTTGAAAATGCTGCTG
1 TTTTGATGTTGAAAATGTTGCTG
* * * * *
102058 GTTTGCTGTTGAAATTGCTGTTG
1 TTTTGATGTTGAAAATGTTGCTG
* * *
102081 TTTTGATATTCAAAATGTTTCTG
1 TTTTGATGTTGAAAATGTTGCTG
***
102104 TTTTGATGTT-CTCATGTTGCTG
1 TTTTGATGTTGAAAATGTTGCTG
*
102126 TTTTGATGTTCAAAATGTTGCTG
1 TTTTGATGTTGAAAATGTTGCTG
102149 T
1 T
102150 AAATACTAAT
Statistics
Matches: 150, Mismatches: 28, Indels: 16
0.77 0.14 0.08
Matches are distributed among these distances:
21 2 0.01
22 50 0.33
23 77 0.51
24 2 0.01
25 2 0.01
26 3 0.02
27 12 0.08
28 2 0.01
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.51
Consensus pattern (23 bp):
TTTTGATGTTGAAAATGTTGCTG
Found at i:102018 original size:27 final size:27
Alignment explanation
Indices: 101983--102045 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
101973 GAAAATTTTG
* * *
101983 TTGTTTTGTGTT-AATAATGTTGCTGTT
1 TTGTGTTGTGTTGAA-AATGCTACTGTT
102010 TTGTGTTGTGTTGAAAATGCTACTGTT
1 TTGTGTTGTGTTGAAAATGCTACTGTT
102037 TTGCTGTTG
1 TTG-TGTTG
102046 AAAATGCTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.14, C:0.06, G:0.25, T:0.54
Consensus pattern (27 bp):
TTGTGTTGTGTTGAAAATGCTACTGTT
Found at i:102038 original size:49 final size:51
Alignment explanation
Indices: 101966--102068 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 51
101956 TGTTGCTGTT
** ** * *
101966 TTGTGTTGAAAATTTTGTTGTTTTG-TGTT-AATAATGTTGCTGTTTTG-TG
1 TTGTGTTGAAAATGCTACTGTTTTGCTGTTGAA-AATGCTGCTGGTTTGCTG
102015 TTGTGTTGAAAATGCTACTGTTTTGCTGTTGAAAATGCTGCTGGTTTGCTG
1 TTGTGTTGAAAATGCTACTGTTTTGCTGTTGAAAATGCTGCTGGTTTGCTG
102066 TTG
1 TTG
102069 AAATTGCTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 21 0.47
50 17 0.38
51 7 0.16
ACGTcount: A:0.17, C:0.07, G:0.26, T:0.50
Consensus pattern (51 bp):
TTGTGTTGAAAATGCTACTGTTTTGCTGTTGAAAATGCTGCTGGTTTGCTG
Found at i:103045 original size:30 final size:30
Alignment explanation
Indices: 103011--103109 Score: 78
Period size: 30 Copynumber: 3.2 Consensus size: 30
103001 TAATCAAACT
103011 AAAAATAGAAGTTCCTCAATCTCAGAAAAA
1 AAAAATAGAAGTTCCTCAATCTCAGAAAAA
*** * *
103041 AAAAATA-AATGTT-GAAAATGT-ATAATCAAA
1 AAAAATAGAA-GTTCCTCAATCTCAGAA--AAA
*
103071 CTAAAAATAGAAGTTCCTCAATCTCAGGAAAA
1 --AAAAATAGAAGTTCCTCAATCTCAGAAAAA
103103 AAAAATA
1 AAAAATA
103110 AAAATAAATG
Statistics
Matches: 50, Mismatches: 11, Indels: 16
0.65 0.14 0.21
Matches are distributed among these distances:
28 3 0.06
29 6 0.12
30 20 0.40
32 13 0.26
33 6 0.12
34 2 0.04
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (30 bp):
AAAAATAGAAGTTCCTCAATCTCAGAAAAA
Found at i:103375 original size:37 final size:37
Alignment explanation
Indices: 103266--103379 Score: 131
Period size: 37 Copynumber: 3.1 Consensus size: 37
103256 ACAGAAATGA
*
103266 ATATAGGACAGAAATGAATAAGAAAACTGGATTGCAG
1 ATATAGGACAGAAATGAATAAGAAAACAGGATTGCAG
* * ** * * *
103303 AGATA-GAAATGAATAAAAAAAACAAAACAGTATTGCAG
1 ATATAGGACA-GAA-ATGAATAAGAAAACAGGATTGCAG
103341 ATATAGGACAGAAATGAATAAGAAAACAGGATTGCAG
1 ATATAGGACAGAAATGAATAAGAAAACAGGATTGCAG
103378 AT
1 AT
103380 TTATCATCCA
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
36 3 0.05
37 28 0.47
38 25 0.42
39 3 0.05
ACGTcount: A:0.54, C:0.08, G:0.21, T:0.18
Consensus pattern (37 bp):
ATATAGGACAGAAATGAATAAGAAAACAGGATTGCAG
Found at i:105786 original size:18 final size:18
Alignment explanation
Indices: 105758--105802 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 18
105748 TTTCAAGCGT
105758 ACTTACAAAAAATTAGAAC
1 ACTT-CAAAAAATTAGAAC
105777 ACTTCAAAAAATTAGAAC
1 ACTTCAAAAAATTAGAAC
105795 ACTTCAAA
1 ACTTCAAA
105803 GAATAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.56, C:0.18, G:0.04, T:0.22
Consensus pattern (18 bp):
ACTTCAAAAAATTAGAAC
Done.