Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023837.1 Corchorus olitorius cultivar O-4 contig23870, 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: 156220
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:6153 original size:6 final size:6
Alignment explanation
Indices: 6132--6166 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
6122 GAGAAAGTGA
*
6132 TCTGCT T-TGAT TCTGCT TCTGCT TCTGCT TCTGCT
1 TCTGCT TCTGCT TCTGCT TCTGCT TCTGCT TCTGCT
6167 GCCTATGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.03, C:0.29, G:0.17, T:0.51
Consensus pattern (6 bp):
TCTGCT
Found at i:8845 original size:3 final size:3
Alignment explanation
Indices: 8839--8876 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
8829 TATAATAATA
* *
8839 ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT ATA ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8877 ATATAGTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:8877 original size:6 final size:6
Alignment explanation
Indices: 8819--8877 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
8809 TATATATATA
* * *
8819 TATAA- TATAA- TATAAT AATAAT TATTATTAT TATTAT TATTAT TATAAT
1 TATAAT TATAAT TATAAT TATAAT TA-TA--AT TATAAT TATAAT TATAAT
8868 TATAAT TATA
1 TATAAT TATA
8878 TATAGTAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
5 10 0.22
6 29 0.63
7 2 0.04
8 1 0.02
9 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TATAAT
Found at i:8893 original size:5 final size:5
Alignment explanation
Indices: 8883--8933 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
8873 TTATATATAG
*
8883 TAAGA TAAGA TAAGA TAAGA TAAAA TAAGA TAAGA T-AG- TAAGA T-AGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
8930 TAAG
1 TAAG
8934 GTATTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 32 0.78
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:11172 original size:15 final size:15
Alignment explanation
Indices: 11152--11191 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
11142 TTTTTTTGAC
11152 AAAACCCCTGCCGCT
1 AAAACCCCTGCCGCT
11167 AAAACCCCTGCCGCT
1 AAAACCCCTGCCGCT
11182 AAAACCCCTG
1 AAAACCCCTG
11192 ACTCGCCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.45, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAACCCCTGCCGCT
Found at i:19898 original size:30 final size:30
Alignment explanation
Indices: 19846--19928 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
19836 TCATATAGTC
* * *
19846 TTAGGTCTATTGTTACTGCATATAGTTTGC-T
1 TTAGGTCTA-TCTTATTGCATATAG-TTCCTT
19877 TTAGGTCTATCTTATTGCATATAGTTCCTT
1 TTAGGTCTATCTTATTGCATATAGTTCCTT
* *
19907 TTAGGTGTATCGTTATAGCATA
1 TTAGGTCTATC-TTATTGCATA
19929 ACGATGTCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
29 3 0.07
30 24 0.53
31 18 0.40
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (30 bp):
TTAGGTCTATCTTATTGCATATAGTTCCTT
Found at i:20048 original size:27 final size:27
Alignment explanation
Indices: 19982--20148 Score: 133
Period size: 27 Copynumber: 5.9 Consensus size: 27
19972 AACTATATGC
*
19982 ATTTAGGTCTATCGTTATTGCATATAG
1 ATTTAGGTCTATCGTTATAGCATATAG
*
20009 CATTTAGGTCTATCGTTATAGCGTATAG
1 -ATTTAGGTCTATCGTTATAGCATATAG
**
20037 ATTTAGGTCTATCGTTACGGCATATAG
1 ATTTAGGTCTATCGTTATAGCATATAG
*
20064 -TCTTAGGTCTATTGTTACT-GCATATAGTTTG
1 AT-TTAGGTCTATCGTTA-TAGCATATA----G
* *
20095 TTTTAGGTCTATC-TTATTGCATATAG
1 ATTTAGGTCTATCGTTATAGCATATAG
* *
20121 TTCCTCTTAGATCTATCGTTATAGCATA
1 ---AT-TTAGGTCTATCGTTATAGCATA
20149 ACGATAATCC
Statistics
Matches: 115, Mismatches: 11, Indels: 23
0.77 0.07 0.15
Matches are distributed among these distances:
26 2 0.02
27 45 0.39
28 25 0.22
29 2 0.02
30 20 0.17
31 20 0.17
32 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (27 bp):
ATTTAGGTCTATCGTTATAGCATATAG
Found at i:20309 original size:27 final size:27
Alignment explanation
Indices: 20204--20360 Score: 131
Period size: 27 Copynumber: 5.6 Consensus size: 27
20194 ACTATATGCA
* * **
20204 TTTAAGTCTATCGTTATTGCATATAAC
1 TTTAGGTCTATCGTTACTGCATATAGT
* * *
20231 ATTAGGTCTATCGTTA-TAGCGTATAGA
1 TTTAGGTCTATCGTTACT-GCATATAGT
*
20258 TTTAGGTCTATC-TTACGGCATATAGT
1 TTTAGGTCTATCGTTACTGCATATAGT
20284 TTTAGGTCTATCGTTACTGCATATAGTTTGT
1 TTTAGGTCTATCGTTACTGCATATA----GT
*
20315 TTTAGGTCTATC-TTATTGCATATAGTTCCT
1 TTTAGGTCTATCGTTACTGCATATAG----T
20345 TTTAGGTCTATCGTTA
1 TTTAGGTCTATCGTTA
20361 TAGCATAACG
Statistics
Matches: 107, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
26 24 0.22
27 42 0.39
30 24 0.22
31 17 0.16
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (27 bp):
TTTAGGTCTATCGTTACTGCATATAGT
Found at i:20337 original size:30 final size:30
Alignment explanation
Indices: 20258--20360 Score: 126
Period size: 30 Copynumber: 3.5 Consensus size: 30
20248 AGCGTATAGA
*
20258 TTTAGGTCTATC-TTACGGCATATA---GT
1 TTTAGGTCTATCGTTACTGCATATAGTTGT
20284 TTTAGGTCTATCGTTACTGCATATAGTTTGT
1 TTTAGGTCTATCGTTACTGCATATAG-TTGT
* *
20315 TTTAGGTCTATC-TTATTGCATATAGTTCCT
1 TTTAGGTCTATCGTTACTGCATATAGTT-GT
20345 TTTAGGTCTATCGTTA
1 TTTAGGTCTATCGTTA
20361 TAGCATAACG
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.18
27 11 0.16
29 2 0.03
30 25 0.37
31 17 0.25
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (30 bp):
TTTAGGTCTATCGTTACTGCATATAGTTGT
Found at i:20357 original size:219 final size:221
Alignment explanation
Indices: 19837--20419 Score: 1055
Period size: 219 Copynumber: 2.7 Consensus size: 221
19827 CCAAAGGAAT
*
19837 CATATAGTCTTAGGTCTATTGTTACTGCATATAGTTTGCTTTAGGTCTATCTTATTGCATATAGT
1 CATATAGTCTTAGGTCTATTGTTACTGCATATAGTTTGTTTTAGGTCTATCTTATTGCATATAGT
* * *
19902 TCCTTTTAGGTGTATCGTTATAGCATAACGAT-GTCCTAAAACTATATGCTATAACGATAGACCT
66 TCCTTTTAGGTCTATCGTTATAGCATAACGATAATCCTAAAACTATATGCAATAACGATAGACCT
* *
19966 AAAAGGAACTATATGCATTTAGGTCTATCGTTATTGCATATAGCATTTAGGTCTATCGTTATAGC
131 AAAAGGAACTATATGCATTTAAGTCTATCGTTATTGCATATAACATTTAGGTCTATCGTTATAGC
20031 GTATAGATTTAGGTCTATCGTTACGG
196 GTATAGATTTAGGTCTATCGTTACGG
20057 CATATAGTCTTAGGTCTATTGTTACTGCATATAGTTTGTTTTAGGTCTATCTTATTGCATATAGT
1 CATATAGTCTTAGGTCTATTGTTACTGCATATAGTTTGTTTTAGGTCTATCTTATTGCATATAGT
* *
20122 TCCTCTTAGATCTATCGTTATAGCATAACGATAATCCTAAAACTATATGCAATAACGATAGACCT
66 TCCTTTTAGGTCTATCGTTATAGCATAACGATAATCCTAAAACTATATGCAATAACGATAGACCT
20187 AAAAGGAACTATATGCATTTAAGTCTATCGTTATTGCATATAACA-TTAGGTCTATCGTTATAGC
131 AAAAGGAACTATATGCATTTAAGTCTATCGTTATTGCATATAACATTTAGGTCTATCGTTATAGC
20251 GTATAGATTTAGGTCTATC-TTACGG
196 GTATAGATTTAGGTCTATCGTTACGG
* *
20276 CATATAGTTTTAGGTCTATCGTTACTGCATATAGTTTGTTTTAGGTCTATCTTATTGCATATAGT
1 CATATAGTCTTAGGTCTATTGTTACTGCATATAGTTTGTTTTAGGTCTATCTTATTGCATATAGT
20341 TCCTTTTAGGTCTATCGTTATAGCATAACGATAATCCTAAAACTATATGCAATAACGATAGACCT
66 TCCTTTTAGGTCTATCGTTATAGCATAACGATAATCCTAAAACTATATGCAATAACGATAGACCT
20406 AAAAGGAACTATAT
131 AAAAGGAACTATAT
20420 TCAATAAGAT
Statistics
Matches: 350, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
219 146 0.42
220 131 0.37
221 73 0.21
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (221 bp):
CATATAGTCTTAGGTCTATTGTTACTGCATATAGTTTGTTTTAGGTCTATCTTATTGCATATAGT
TCCTTTTAGGTCTATCGTTATAGCATAACGATAATCCTAAAACTATATGCAATAACGATAGACCT
AAAAGGAACTATATGCATTTAAGTCTATCGTTATTGCATATAACATTTAGGTCTATCGTTATAGC
GTATAGATTTAGGTCTATCGTTACGG
Found at i:20433 original size:30 final size:31
Alignment explanation
Indices: 20381--20439 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
20371 ATAATCCTAA
20381 AACTATATGCAATAACGATAGACCTAAAAGG
1 AACTATATGCAATAACGATAGACCTAAAAGG
*
20412 AACTATATTCAATAA-GATAGACCTAAAA
1 AACTATATGCAATAACGATAGACCTAAAA
20440 CAAATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (31 bp):
AACTATATGCAATAACGATAGACCTAAAAGG
Found at i:20449 original size:30 final size:31
Alignment explanation
Indices: 20380--20450 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
20370 GATAATCCTA
* *
20380 AAACTATATGCAATAACGATAGACCTAAAAG
1 AAACTATATTCAATAACGATAGACCTAAAAC
*
20411 GAACTATATTCAATAA-GATAGACCTAAAAC
1 AAACTATATTCAATAACGATAGACCTAAAAC
*
20441 AAATTATATT
1 AAACTATATT
20451 GTTATTCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.25
Consensus pattern (31 bp):
AAACTATATTCAATAACGATAGACCTAAAAC
Found at i:20718 original size:13 final size:13
Alignment explanation
Indices: 20700--20725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20690 ATGTATTTAC
20700 TGCATTTTTATAA
1 TGCATTTTTATAA
20713 TGCATTTTTATAA
1 TGCATTTTTATAA
20726 ATCAAAACCA
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:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TGCATTTTTATAA
Found at i:27774 original size:39 final size:40
Alignment explanation
Indices: 27731--27808 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
27721 ATTCAAGTAT
27731 GAATTTATGTTACACTTTTCTTTC-TTTCTTTTTTTTTTC
1 GAATTTATGTTACACTTTTCTTTCTTTTCTTTTTTTTTTC
*
27770 GAATTTATGTTACGCTTTTCTTTCTTTTCTTTTTTTTTT
1 GAATTTATGTTACACTTTTCTTTCTTTTCTTTTTTTTTT
27809 GTACTTACAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 23 0.62
40 14 0.38
ACGTcount: A:0.12, C:0.14, G:0.06, T:0.68
Consensus pattern (40 bp):
GAATTTATGTTACACTTTTCTTTCTTTTCTTTTTTTTTTC
Found at i:28906 original size:21 final size:21
Alignment explanation
Indices: 28881--28923 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28871 GCTATCTTAA
28881 AAATAAT-ATATATTATTAAAT
1 AAATAATAATATATT-TTAAAT
28902 AAATAATAAATATATTTTAAAT
1 AAATAAT-AATATATTTTAAAT
28924 GATAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 6 0.30
23 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAATAATATATTTTAAAT
Found at i:28928 original size:21 final size:24
Alignment explanation
Indices: 28878--28923 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
28868 TTTGCTATCT
28878 TAAA-AATAATATATATTATTAAA
1 TAAATAATAATATATATTATTAAA
28901 TAAATAATAA-ATATATT-TTAAA
1 TAAATAATAATATATATTATTAAA
28923 T
1 T
28924 GATAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAATAATAATATATATTATTAAA
Found at i:29612 original size:2 final size:2
Alignment explanation
Indices: 29605--29630 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29595 CAAAATGGGA
29605 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29631 GTTAGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31948 original size:6 final size:6
Alignment explanation
Indices: 31937--31962 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31927 TGAACAGAGG
31937 AGTTCT AGTTCT AGTTCT AGTTCT AG
1 AGTTCT AGTTCT AGTTCT AGTTCT AG
31963 AATAGCAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.46
Consensus pattern (6 bp):
AGTTCT
Found at i:44772 original size:27 final size:27
Alignment explanation
Indices: 44734--44788 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
44724 GTTCATGTTG
44734 GGAGACTCACCCACCATTACCAGGTGC
1 GGAGACTCACCCACCATTACCAGGTGC
*
44761 GGAGGCTCACCCACCATTACCAGGTGC
1 GGAGACTCACCCACCATTACCAGGTGC
44788 G
1 G
44789 CAACGCAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.36, G:0.25, T:0.15
Consensus pattern (27 bp):
GGAGACTCACCCACCATTACCAGGTGC
Found at i:44918 original size:3 final size:3
Alignment explanation
Indices: 44910--44965 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
44900 AAAATATATA
*
44910 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44958 TAT TAT TA
1 TAT TAT TA
44966 AAATTGCATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:53484 original size:19 final size:18
Alignment explanation
Indices: 53447--53481 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53437 GGATATTCCA
*
53447 TTTCTTTTGAACTTCAAT
1 TTTCTTTTGAACTCCAAT
*
53465 TTTCTTTTTAACTCCAA
1 TTTCTTTTGAACTCCAA
53482 ATTCACACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTCTTTTGAACTCCAAT
Found at i:67757 original size:30 final size:30
Alignment explanation
Indices: 67721--67780 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
67711 AAAAAAAATT
67721 GGGTGTTTTTTGATTTTGCGCTCAATCAGC
1 GGGTGTTTTTTGATTTTGCGCTCAATCAGC
67751 GGGTGTTTTTTGATTTTGCGCTCAATCAGC
1 GGGTGTTTTTTGATTTTGCGCTCAATCAGC
67781 CCTAAACCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.17, G:0.27, T:0.43
Consensus pattern (30 bp):
GGGTGTTTTTTGATTTTGCGCTCAATCAGC
Found at i:74093 original size:19 final size:19
Alignment explanation
Indices: 74069--74126 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
74059 CTGTTTGACA
*
74069 ACTGTATAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
74088 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
74109 ACTGTACAAATGAGATTA
1 ACTGTACAGATGAGATTA
74127 TTAAAACATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:74792 original size:18 final size:18
Alignment explanation
Indices: 74751--74796 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
74741 TAAGGTAATG
* *
74751 TATTTCTTCTGTTCTTTTC
1 TATTTC-TCTTTTATTTTC
74770 T-TTTCTCTTTTATTTTC
1 TATTTCTCTTTTATTTTC
74787 TATTTCTCTT
1 TATTTCTCTT
74797 CCCTTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.46
18 12 0.50
19 1 0.04
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.72
Consensus pattern (18 bp):
TATTTCTCTTTTATTTTC
Found at i:87329 original size:27 final size:26
Alignment explanation
Indices: 87294--87345 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
87284 CCAGTTTTTA
87294 CAAAGAAAAAAAGGGATAATTAGGCT
1 CAAAGAAAAAAAGGGATAATTAGGCT
87320 CAAAGAAAAAAAGGGATAATTAGGCT
1 CAAAGAAAAAAAGGGATAATTAGGCT
87346 TGAAAATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (26 bp):
CAAAGAAAAAAAGGGATAATTAGGCT
Found at i:87516 original size:32 final size:32
Alignment explanation
Indices: 87410--87530 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 32
87400 TATTAAATTG
* * *
87410 AATGAGGACAAATTTCCAATGCATTAATTGCA
1 AATGGGGACAAATTTGCAATGCATTAATTTCA
* *
87442 CATGGGGACAAATTTACAATGCATTAATTGT-A
1 AATGGGGACAAATTTGCAATGCATTAATT-TCA
87474 AATGGGGACAAATTTGCAATGCATTAATTTCA
1 AATGGGGACAAATTTGCAATGCATTAATTTCA
* * * *
87506 AATAGAGACAATTTTGCAATTCATT
1 AATGGGGACAAATTTGCAATGCATT
87531 TAAGTATATG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
31 1 0.01
32 76 0.99
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (32 bp):
AATGGGGACAAATTTGCAATGCATTAATTTCA
Found at i:87516 original size:64 final size:64
Alignment explanation
Indices: 87410--87551 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 64
87400 TATTAAATTG
* * *
87410 AATGAGGACAAATTTCCAATGCATTAATTGCACATGGGGACAAATTTACAATGCATTAATTGTA
1 AATGAGGACAAATTTCCAATGCATTAATTGCAAATAGAGACAAATTTACAATGCATTAATTGTA
* * * * * *
87474 AATGGGGACAAATTTGCAATGCATTAATTTCAAATAGAGACAATTTTGCAATTCATTTAA--GTA
1 AATGAGGACAAATTTCCAATGCATTAATTGCAAATAGAGACAAATTTACAATGCA-TTAATTGTA
* *
87537 TATGAAGACAAATTT
1 AATGAGGACAAATTT
87552 ACAAATTAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
63 15 0.23
64 46 0.71
65 4 0.06
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (64 bp):
AATGAGGACAAATTTCCAATGCATTAATTGCAAATAGAGACAAATTTACAATGCATTAATTGTA
Found at i:88532 original size:30 final size:30
Alignment explanation
Indices: 88498--88561 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
88488 TTAGTGAAAT
*
88498 TAGTTCTGGCAATAAAAAAACGTAATAGAG
1 TAGTTCTGGCAAAAAAAAAACGTAATAGAG
* *
88528 TAGTTCTGGTAAAAAAAAAACGTAATATAG
1 TAGTTCTGGCAAAAAAAAAACGTAATAGAG
88558 TAGT
1 TAGT
88562 CTGTTCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.27
Consensus pattern (30 bp):
TAGTTCTGGCAAAAAAAAAACGTAATAGAG
Found at i:90132 original size:29 final size:31
Alignment explanation
Indices: 90073--90131 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
90063 TGAGTGGGAC
* *
90073 TAAAATGTCCTCATATTACAAGTTTAAGGGG
1 TAAAAAGTCCTCAAATTACAAGTTTAAGGGG
90104 TAAAAAGT-CTCAAATTA-AAG-TTAAGGGG
1 TAAAAAGTCCTCAAATTACAAGTTTAAGGGG
90132 GCAAAAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
29 3 0.12
30 8 0.31
31 7 0.27
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (31 bp):
TAAAAAGTCCTCAAATTACAAGTTTAAGGGG
Found at i:90137 original size:28 final size:30
Alignment explanation
Indices: 90082--90138 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
90072 CTAAAATGTC
* *
90082 CTCATATTACAAGTTTAAGGGGTAAAAAGT
1 CTCAAATTACAAGTTTAAGGGGGAAAAAGT
90112 CTCAAATTA-AAG-TTAAGGGGGCAAAAA
1 CTCAAATTACAAGTTTAAGGGGG-AAAAA
90139 AGGGACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.33
29 8 0.33
30 8 0.33
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.25
Consensus pattern (30 bp):
CTCAAATTACAAGTTTAAGGGGGAAAAAGT
Found at i:90137 original size:29 final size:30
Alignment explanation
Indices: 90082--90138 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
90072 CTAAAATGTC
* *
90082 CTCATATTACAAGTTTAAGGGGTAAAAAGT
1 CTCAAATTACAAGTTTAAGGGGCAAAAAGT
90112 CTCAAATTA-AAG-TTAAGGGGGCAAAAA
1 CTCAAATTACAAGTTTAA-GGGGCAAAAA
90139 AGGGACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 12 0.50
30 8 0.33
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.25
Consensus pattern (30 bp):
CTCAAATTACAAGTTTAAGGGGCAAAAAGT
Found at i:103031 original size:14 final size:14
Alignment explanation
Indices: 103012--103045 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
103002 TTTTATAATT
103012 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
103026 ATTTTATTTTTACT
1 ATTTTATTTTTACC
103040 ATTTTA
1 ATTTTA
103046 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:103093 original size:15 final size:15
Alignment explanation
Indices: 103073--103103 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
103063 GATTAACATG
103073 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
103088 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
103103 T
1 T
103104 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:110901 original size:26 final size:28
Alignment explanation
Indices: 110843--110909 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
110833 TATCGACTTC
* *
110843 ATGAAAGGAA-TTTTTTTTTTTGCCAGA
1 ATGAAAGGAAGGTTTTTTTTTGGCCAGA
110870 ATGAAAGGAAGGTTTTTTTTTGGCCAG-
1 ATGAAAGGAAGGTTTTTTTTTGGCCAGA
110897 A-GAAAGGAAGGTT
1 ATGAAAGGAAGGTT
110910 AAAATTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 12 0.32
27 11 0.30
28 14 0.38
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (28 bp):
ATGAAAGGAAGGTTTTTTTTTGGCCAGA
Found at i:111317 original size:36 final size:36
Alignment explanation
Indices: 111275--111354 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
111265 CTCTCTCCCC
111275 CTCTCCCTCTGAATCTGAGCAGCAGCAGCAACCTCT
1 CTCTCCCTCTGAATCTGAGCAGCAGCAGCAACCTCT
* * * *
111311 GTCTCCCTCTGACTCTGAGCAGCAGCAGTAGCCTCT
1 CTCTCCCTCTGAATCTGAGCAGCAGCAGCAACCTCT
111347 CTCTCCCT
1 CTCTCCCT
111355 ATAATTCCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.17, C:0.40, G:0.17, T:0.25
Consensus pattern (36 bp):
CTCTCCCTCTGAATCTGAGCAGCAGCAGCAACCTCT
Found at i:111367 original size:36 final size:36
Alignment explanation
Indices: 111291--111369 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
111281 CTCTGAATCT
* * * *
111291 GAGCAGCAGCAGCAACCTCTGTCTCCCTCTGACTCT
1 GAGCAGCAGCAGCAACCTCTCTCTCCCTATAACTCC
* * *
111327 GAGCAGCAGCAGTAGCCTCTCTCTCCCTATAATTCC
1 GAGCAGCAGCAGCAACCTCTCTCTCCCTATAACTCC
111363 GAGCAGC
1 GAGCAGC
111370 CTCTCTCTCC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.22
Consensus pattern (36 bp):
GAGCAGCAGCAGCAACCTCTCTCTCCCTATAACTCC
Found at i:111942 original size:24 final size:23
Alignment explanation
Indices: 111865--111948 Score: 69
Period size: 29 Copynumber: 3.3 Consensus size: 23
111855 TGAGGATTTG
* *
111865 TTGAAGAATATGAAGGTTGAAGG
1 TTGAAGAAAATGAAGGTTGAAGT
*
111888 TTGAAGAAAATGAAGTGAAGATTAATAGT
1 TTGAAGAAAATGAA--G--G-TTGA-AGT
111917 TTGAAGAAAATGAAGGTTGAGAGT
1 TTGAAGAAAATGAAGGTTGA-AGT
*
111941 TTTAAGAA
1 TTGAAGAA
111949 GTTGTAAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
23 13 0.27
24 13 0.27
25 2 0.04
27 2 0.04
28 3 0.06
29 16 0.33
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (23 bp):
TTGAAGAAAATGAAGGTTGAAGT
Found at i:116337 original size:14 final size:14
Alignment explanation
Indices: 116318--116347 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
116308 ATCACCTAAC
116318 TGCATATAATGAAA
1 TGCATATAATGAAA
116332 TGCATATAATGAAA
1 TGCATATAATGAAA
116346 TG
1 TG
116348 AAATGGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (14 bp):
TGCATATAATGAAA
Found at i:131912 original size:12 final size:12
Alignment explanation
Indices: 131895--131919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
131885 GCGAAGGAGG
131895 AGCAGTTGGCAA
1 AGCAGTTGGCAA
131907 AGCAGTTGGCAA
1 AGCAGTTGGCAA
131919 A
1 A
131920 ATTTAACCGA
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (12 bp):
AGCAGTTGGCAA
Found at i:139605 original size:13 final size:13
Alignment explanation
Indices: 139587--139615 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
139577 TGAGAAAAAC
139587 TAAGCTCAACAAG
1 TAAGCTCAACAAG
139600 TAAGCTCAACAAG
1 TAAGCTCAACAAG
139613 TAA
1 TAA
139616 AAATAGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (13 bp):
TAAGCTCAACAAG
Found at i:140176 original size:26 final size:27
Alignment explanation
Indices: 140139--140190 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
140129 CCTAGGAATG
140139 TTATTTTAGTGGGAA-AGTATACTTTT
1 TTATTTTAGTGGGAATAGTATACTTTT
*
140165 TTATTTTTGTGGGAATAGTATACTTT
1 TTATTTTAGTGGGAATAGTATACTTT
140191 CCACGAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.52
Consensus pattern (27 bp):
TTATTTTAGTGGGAATAGTATACTTTT
Found at i:142640 original size:190 final size:189
Alignment explanation
Indices: 142295--142677 Score: 721
Period size: 190 Copynumber: 2.0 Consensus size: 189
142285 CTTGTCTTGG
*
142295 TCTTTCTAATCTTAATTATCAGCTGATTGGCTGTTGTCTTTTCAAAACAATTTGATAGGTACAGA
1 TCTTTCCAATCTTAATTATCAGCTGATTGGCTGTTGTCTTTTCAAAACAATTTGATAGGTACAGA
142360 TTTTACATTTGCTGCCTTGAATGTGATGAGACTTTGCATGTTTGACACATGTCTTTATGTGTTTG
66 TTTTACATTTGCTGCCTTGAATGTGATGAGACTTTGCATGTTTGACACATGTCTTTATGTGTTTG
*
142425 AATATTGTGATTATATTAATGAATTAGAGAGAGCTAAGGAGAATAGCTTCATCTCCTCC
131 AATATTGTGACTATATTAATGAATTAGAGAGAGCTAAGGAGAATAGCTTCATCTCCTCC
142484 TCTTTCCAATCTTAATTATCAGCCTGATTGGCTGTTGTCTTTTCAAAACAATTTGATAGGTACAG
1 TCTTTCCAATCTTAATTATCAG-CTGATTGGCTGTTGTCTTTTCAAAACAATTTGATAGGTACAG
* *
142549 ATTTTACATTTGCTGCCTTGCATGTGATGAGACTTTGCATGTTTGACACCTGTCTTTATGTGTTT
65 ATTTTACATTTGCTGCCTTGAATGTGATGAGACTTTGCATGTTTGACACATGTCTTTATGTGTTT
142614 GAATATTGTGACTATATTAATGAATTAGAGAGAGCTAAGGAGAATAGCTTCATCTCCTCC
130 GAATATTGTGACTATATTAATGAATTAGAGAGAGCTAAGGAGAATAGCTTCATCTCCTCC
142674 TCTT
1 TCTT
142678 CCTTTCCTCC
Statistics
Matches: 189, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
189 21 0.11
190 168 0.89
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (189 bp):
TCTTTCCAATCTTAATTATCAGCTGATTGGCTGTTGTCTTTTCAAAACAATTTGATAGGTACAGA
TTTTACATTTGCTGCCTTGAATGTGATGAGACTTTGCATGTTTGACACATGTCTTTATGTGTTTG
AATATTGTGACTATATTAATGAATTAGAGAGAGCTAAGGAGAATAGCTTCATCTCCTCC
Found at i:142999 original size:26 final size:26
Alignment explanation
Indices: 142970--143023 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
142960 GCCTAACTTG
142970 GCTATTTCTTCATCAATCTAAAATTA
1 GCTATTTCTTCATCAATCTAAAATTA
142996 GCTATTTCTTCATCAATCTAAAATTA
1 GCTATTTCTTCATCAATCTAAAATTA
143022 GC
1 GC
143024 AGCGTTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (26 bp):
GCTATTTCTTCATCAATCTAAAATTA
Found at i:155037 original size:311 final size:310
Alignment explanation
Indices: 154019--155170 Score: 906
Period size: 311 Copynumber: 3.6 Consensus size: 310
154009 TTTTTTGTAG
* * * * * * *
154019 AAAGTCTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCTACAATGGATTTAAGGATTTG
1 AAAGACTCCTTGAAAAATCTAAATTCATCTAACCAAAACTTAGCCACATTGGATTTAAGGATTTG
* * *
154084 TTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAAATTCGGGGAAAAAATGAAAAA
66 -GTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC--GG-AAAAATGGAAAA
* *
154149 ACGATATTAGAAACGTGAAAAACCCTTCAA-TTTTTTGGCGTTGAATGAAATATTTTTTGAGTAT
127 ACGATATTAG-AACGTGAAAAACCCTTCAATTTTTTTGGCGTTGAAT--TATA-TATTT-AG--T
* * * * * * * *
154213 TGTGGCAAAGAATTAAGGAAAA-ATTTTTCGGGTCAGTTTTT-G-C-AAAATTTTAGTCGAAATC
185 TG-AGCAAAAAAATGA-GAAAATACTTTTCAGGACAGTTTTTAGCCGAAAA---TCGT-G-AA-C
** * * *** * * *
154274 GTTTATTCATCACGGGTTTTGGATAAAATCGTATTCCGGGGTCC-CGAC-CTAGTTTTGCAT-GA
242 ---TAACCATCACGGTTTTTGGATAAAAACACGTTACAGGG-CCTCGACTC-AATTTTGCATGGA
154336 GTTTTGGC-T
302 -TTTTGGCAT
* * * * * * ** * * *
154345 GAAATACTCCTTTAAATATCTAAATTCATCGAATCAAATCCCAACCACAACACAATGGATTTAAC
1 -AAAGACTCCTTGAAAAATCTAAATTCATCTAACCAAA-ACTTA--GC--CACATTGGATTTAAG
* * *
154410 GATTTGGTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGG
60 GATTTGG-TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAATGG
* *
154475 AAAAACCATATTAGAAGGATGAAAAACCCTTCAATATTTTTT-GCGTTGAATTATATACATTTTA
123 AAAAACGATATTAGAACG-TGAAAAACCCTTCAAT-TTTTTTGGCGTTGAATTATAT--A--TT-
* *
154539 TGAGTATTGTAGCAAAAAAATGAGAAAATTCTTTTCAGGTCAGTTTTTAGCCGAAAATCGTGAAC
181 T-AG--TTG-AGCAAAAAAATGAGAAAATACTTTTCAGGACAGTTTTTAGCCGAAAATCGTGAAC
* * * * * * *
154604 TAACCATCATGGTTTTTGGATGAAAACGCGTTTCGGGGCCTCGACTTAGTTTTGCATGGATTTTG
242 TAACCATCACGGTTTTTGGATAAAAACACGTTACAGGGCCTCGACTCAATTTTGCATGGATTTTG
154669 GCAT
307 GCAT
* * *
154673 AAAGACTCTTTGAAATATCTAAATTCATCTAACCAAAACTTAGCCACATTGGATTTAAGGATTTT
1 AAAGACTCCTTGAAAAATCTAAATTCATCTAACCAAAACTTAGCCACATTGGATTTAAGGATTTG
* *
154738 GTTTCATGAGCATCTGAATCTTGTTTCTATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACG
66 GTTT-ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACG
*
154803 ATATTAGAATCGTG-AAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTT-G-TG-GCAAAA
130 ATATTAGAA-CGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTAGTTGAGCAAAA
* * * *
154864 AATTGAGAAAA-ACTTTCTC-GGACGGTTTTTAGCTG-AAATCGTGTACTAACCATCACGGTTTT
194 AAATGAGAAAATACTTT-TCAGGACAGTTTTTAGCCGAAAATCGTGAACTAACCATCACGG----
* *
154926 TCTTTTGGCA-AAAAACACGTTACAGGGCCTCGACTCAATTTTGCATGGTTTTTGGTAT
254 T-TTTTGG-ATAAAAACACGTTACAGGGCCTCGACTCAATTTTGCATGGATTTTGGCAT
** * ** *
154984 AAAGACTCCTTGAAAAATCTCTATTCATCTAACTAATTCTCT-GCCACATTGGATTTAAGGAGTT
1 AAAGACTCCTTGAAAAATCTAAATTCATCTAACCAAAACT-TAGCCACATTGGATTTAAGGATTT
*
155048 GGCTTTACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT-GTCGAAACAATAAAGG
65 GG-TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCG--GAAA-AAT---GG
* * *
155112 AAAAACGATATTATAAGCGTGAAAAACCCTTCAA-TTTTTTGGCCTGGAATTATATATTT
123 AAAAACGATATTAGAA-CGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTT
155171 TTTCTGAGTA
Statistics
Matches: 692, Mismatches: 92, Indels: 93
0.79 0.10 0.11
Matches are distributed among these distances:
306 21 0.03
307 17 0.02
308 18 0.03
310 4 0.01
311 140 0.20
312 9 0.01
313 4 0.01
315 1 0.00
316 46 0.07
317 11 0.02
318 1 0.00
319 6 0.01
320 26 0.04
321 27 0.04
322 61 0.09
324 1 0.00
326 4 0.01
327 113 0.16
328 6 0.01
329 6 0.01
330 39 0.06
331 11 0.02
332 76 0.11
333 38 0.05
334 1 0.00
335 1 0.00
336 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (310 bp):
AAAGACTCCTTGAAAAATCTAAATTCATCTAACCAAAACTTAGCCACATTGGATTTAAGGATTTG
GTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACGA
TATTAGAACGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTAGTTGAGCAAAAAA
ATGAGAAAATACTTTTCAGGACAGTTTTTAGCCGAAAATCGTGAACTAACCATCACGGTTTTTGG
ATAAAAACACGTTACAGGGCCTCGACTCAATTTTGCATGGATTTTGGCAT
Found at i:155433 original size:197 final size:200
Alignment explanation
Indices: 155054--155456 Score: 550
Period size: 197 Copynumber: 2.0 Consensus size: 200
155044 AGTTGGCTTT
155054 ACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTGTCGAAACAATAAAGGAAAAACG
1 ACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTG-CGAAACAAT--AGGAAAAACG
* * * *
155119 ATATTATAAGCGTGAAAAACCCTTCAATTTTTTGGCCTGGAATTATATATTTTTTCTGAGTATTG
63 ATATAAGAAACGTGAAAAACCCTTCAATTTTTTGGCCTGAAATTATATATTTTTTCTGAGTATTG
* * *
155184 TGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTTCAAAATTTTAGCCGAAATCGTATAG
128 TGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTATAC
155249 TAACCATC
193 TAACCATC
** *
155257 ACGAGAATCTGAATCTT-TTTTTATTTAATTAGAAATTAATT-CGGAAA-AAT-GGAAAAACGAT
1 ACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTGC-GAAACAATAGGAAAAACGAT
*
155318 ATAAGAAACGTGAAAAACCCTTC-ATTTTTTTGCCGGTGAAATATATATATTTTTT-TGAGTATT
65 ATAAGAAACGTGAAAAACCCTTCAATTTTTTGGCC--TGAAAT-TATATATTTTTTCTGAGTATT
* * * * *
155381 GTGGCAAAAAATTGAGGGAAAACTTTTTGGGTCAATTTTTGCAAAA-TTTAGCCGATATCGTGTT
127 GTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTATA
155445 CTAACCATC
192 CTAACCATC
155454 ACG
1 ACG
155457 GTTTTTGGCT
Statistics
Matches: 180, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
196 10 0.06
197 57 0.32
198 55 0.31
199 12 0.07
200 4 0.02
201 4 0.02
202 21 0.12
203 17 0.09
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (200 bp):
ACGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTGCGAAACAATAGGAAAAACGATA
TAAGAAACGTGAAAAACCCTTCAATTTTTTGGCCTGAAATTATATATTTTTTCTGAGTATTGTGG
CAAAAAATTGAGGAAAAACTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTAA
CCATC
Done.