Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013066.1 Corchorus capsularis cultivar CVL-1 contig13087, 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: 122420
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7621 original size:45 final size:45
Alignment explanation
Indices: 7570--7660 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
7560 ACCTATTTTG
7570 AGTACTAATTTTTTTTATCCCGGTATCCAGGGCTTTGTCTTGACT
1 AGTACTAATTTTTTTTATCCCGGTATCCAGGGCTTTGTCTTGACT
*
7615 AGTACTAATTTTTTTTATCCTGGTATCCAGGGCTTTGTCTTGACT
1 AGTACTAATTTTTTTTATCCCGGTATCCAGGGCTTTGTCTTGACT
7660 A
1 A
7661 ATCCGGATCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.45
Consensus pattern (45 bp):
AGTACTAATTTTTTTTATCCCGGTATCCAGGGCTTTGTCTTGACT
Found at i:9921 original size:30 final size:30
Alignment explanation
Indices: 9879--9939 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
9869 TCCCCCACAA
*
9879 TTTTTTGTCAAAAAAAAAG-CCCCTTTATT
1 TTTTTTGGCAAAAAAAAAGTCCCCTTTATT
*
9908 TTTTTTGAGCAAAAAAAAAGTTCCCTTTATT
1 TTTTTTG-GCAAAAAAAAAGTCCCCTTTATT
9939 T
1 T
9940 GTTAACGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.25
30 11 0.39
31 10 0.36
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (30 bp):
TTTTTTGGCAAAAAAAAAGTCCCCTTTATT
Found at i:10509 original size:113 final size:112
Alignment explanation
Indices: 10163--10500 Score: 586
Period size: 113 Copynumber: 3.0 Consensus size: 112
10153 AATGTGAGTT
* * *
10163 TAATTTGTAATTTGTTTGTTTATTTGATTTGTAGGTAGTTATAGTTTCTAGTTTCTAGATTCAAA
1 TAATTTGTAATTTGTTTGTTTATTTGGTTTGTAGGTAGTTATAGTTTCTAGTTTCTAGGTTCAAG
* *
10228 AGCATGTATTATAAGATTTCAATTATAATTGTTGGGGAAAGGATTTG
66 AGCATGTATTATGAGATTTCAATTGTAATTGTTGGGGAAAGGATTTG
*
10275 TAATTTGTAATTTGTTTGTTTATTTAGTTTGTAGGTAGTTATAGTTTCTAGTTTCTAGGTTCAAG
1 TAATTTGTAATTTGTTTGTTTATTTGGTTTGTAGGTAGTTATAGTTTCTAGTTTCTAGGTTCAAG
*
10340 AGCATGTATTATGAGATGATCAATTGTAATTGTTGGGGAAAGGATTTG
66 AGCATGTATTATGAGAT-TTCAATTGTAATTGTTGGGGAAAGGATTTG
10388 TAATTTGTAATTTGTTTGTTTATTTGGTTTGTAGGTAGTTATAGTTTCTAGTTTCTAGGTTCAAG
1 TAATTTGTAATTTGTTTGTTTATTTGGTTTGTAGGTAGTTATAGTTTCTAGTTTCTAGGTTCAAG
* *
10453 AGCATGTATTATGAGATTTCAATTGTAATTGTTAGGGAAAGAATTTG
66 AGCATGTATTATGAGATTTCAATTGTAATTGTTGGGGAAAGGATTTG
10500 T
1 T
10501 TGGCTTGTAG
Statistics
Matches: 214, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
112 105 0.49
113 109 0.51
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (112 bp):
TAATTTGTAATTTGTTTGTTTATTTGGTTTGTAGGTAGTTATAGTTTCTAGTTTCTAGGTTCAAG
AGCATGTATTATGAGATTTCAATTGTAATTGTTGGGGAAAGGATTTG
Found at i:15780 original size:20 final size:19
Alignment explanation
Indices: 15741--15791 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
15731 AAAAATGGCT
* *
15741 ACAGACATATATCGTTTTGCC
1 ACAGACAT-TACCATTTTG-C
15762 ACAGACATTACCATTTTGC
1 ACAGACATTACCATTTTGC
15781 ATCAGACATTA
1 A-CAGACATTA
15792 TGTTATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 8 0.30
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (19 bp):
ACAGACATTACCATTTTGC
Found at i:16900 original size:26 final size:26
Alignment explanation
Indices: 16864--16917 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
16854 AAGTAGATTT
16864 ATTGTTGAAGATTATCATTCCTTGCA
1 ATTGTTGAAGATTATCATTCCTTGCA
16890 ATTGTTGAAGATTATCATTCCTTGCA
1 ATTGTTGAAGATTATCATTCCTTGCA
16916 AT
1 AT
16918 CCAGATTGAC
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:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (26 bp):
ATTGTTGAAGATTATCATTCCTTGCA
Found at i:19983 original size:19 final size:20
Alignment explanation
Indices: 19961--19998 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19951 ACCTTAAATG
19961 ATGAAAAA-AAAAATCTTAA
1 ATGAAAAACAAAAATCTTAA
*
19980 ATGAAAAACAAAATTCTTA
1 ATGAAAAACAAAAATCTTA
19999 CTCTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (20 bp):
ATGAAAAACAAAAATCTTAA
Found at i:19987 original size:20 final size:21
Alignment explanation
Indices: 19944--19998 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
19934 ATTAATTTCT
* *
19944 AAAAAGAACCTTAAATGATGAA
1 AAAAAAAATCTTAAATGA-GAA
19966 AAAAAAAATCTTAAATGA-AA
1 AAAAAAAATCTTAAATGAGAA
* *
19986 AACAAAATTCTTA
1 AAAAAAAATCTTA
19999 CTCTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (21 bp):
AAAAAAAATCTTAAATGAGAA
Found at i:26526 original size:18 final size:18
Alignment explanation
Indices: 26500--26534 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26490 TCTGCCACTA
*
26500 CCAATTTTAGTCAATTCC
1 CCAAGTTTAGTCAATTCC
*
26518 CCAAGTTTATTCAATTC
1 CCAAGTTTAGTCAATTC
26535 GCATAGTAAC
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:0.29, C:0.26, G:0.06, T:0.40
Consensus pattern (18 bp):
CCAAGTTTAGTCAATTCC
Found at i:28196 original size:159 final size:159
Alignment explanation
Indices: 27907--28232 Score: 598
Period size: 159 Copynumber: 2.0 Consensus size: 159
27897 ATTCATTACA
*
27907 TGAAATTACAACGACCATACTATCAATTACAATATATTGAAATTAGCTTTCCTTCTCCATTTCTA
1 TGAAATTACAACGACCATACTATCAATTACAATATATCGAAATTAGCTTTCCTTCTCCATTTCTA
27972 TATTGGAATCTCGAGCTTTATAATGTGAATCATCTGATTTATTTAGAGTCTCAATTTTTCTAATT
66 TATTGGAATCTCGAGCTTTATAATGTGAATCATCTGATTTATTTAGAGTCTCAATTTTTCTAATT
*
28037 CATAAATTTTTGACATGTACAATAACTAC
131 CATAAATTTTTGACACGTACAATAACTAC
*
28066 TGAAATTACAACGACCATACTATCAATTACAATATATCGAAATTAGTTTTCCTTCTCCATTTCTA
1 TGAAATTACAACGACCATACTATCAATTACAATATATCGAAATTAGCTTTCCTTCTCCATTTCTA
* *
28131 TATTGGAATCTCGAGCTTTATAGTGTGAATCATCTGATTTATTTAGAGTCTCGATTTTTCTAATT
66 TATTGGAATCTCGAGCTTTATAATGTGAATCATCTGATTTATTTAGAGTCTCAATTTTTCTAATT
28196 CATAAATTTTTGACACGTACAATAACTAC
131 CATAAATTTTTGACACGTACAATAACTAC
28225 TGATAATT
1 TGA-AATT
28233 TTCGCTTATG
Statistics
Matches: 161, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
159 157 0.98
160 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (159 bp):
TGAAATTACAACGACCATACTATCAATTACAATATATCGAAATTAGCTTTCCTTCTCCATTTCTA
TATTGGAATCTCGAGCTTTATAATGTGAATCATCTGATTTATTTAGAGTCTCAATTTTTCTAATT
CATAAATTTTTGACACGTACAATAACTAC
Found at i:30433 original size:13 final size:13
Alignment explanation
Indices: 30415--30439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30405 TTTAATGTTC
30415 TAAATATTATTTA
1 TAAATATTATTTA
30428 TAAATATTATTT
1 TAAATATTATTT
30440 GGAATTCCAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:32620 original size:22 final size:23
Alignment explanation
Indices: 32594--32636 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
32584 GGTTTCATGG
32594 TTTGTG-TTTGCCCATAATTAGT
1 TTTGTGTTTTGCCCATAATTAGT
*
32616 TTTGTGTTTTGTCCATAATTA
1 TTTGTGTTTTGCCCATAATTA
32637 ATCAATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.53
Consensus pattern (23 bp):
TTTGTGTTTTGCCCATAATTAGT
Found at i:40177 original size:17 final size:17
Alignment explanation
Indices: 40155--40188 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40145 CACCGGCTCT
40155 CTGCTATATAATTCATA
1 CTGCTATATAATTCATA
40172 CTGCTATATAATTCATA
1 CTGCTATATAATTCATA
40189 TTGAAAATAA
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:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (17 bp):
CTGCTATATAATTCATA
Found at i:44776 original size:152 final size:152
Alignment explanation
Indices: 44500--44808 Score: 618
Period size: 152 Copynumber: 2.0 Consensus size: 152
44490 TCATGGATAT
44500 GACCAGTCTTTTAGCTTACTTTTTCTTAAATATGAGCCAAGGTTACTAAATGAGCAGCAGGGCAA
1 GACCAGTCTTTTAGCTTACTTTTTCTTAAATATGAGCCAAGGTTACTAAATGAGCAGCAGGGCAA
44565 CCATCACAATTCACTGGAAATATTTCCCCACTACAGGAATGAATTAAACAATTTGAAAAACTATT
66 CCATCACAATTCACTGGAAATATTTCCCCACTACAGGAATGAATTAAACAATTTGAAAAACTATT
44630 TCTGTTTATAATTCACCTATAA
131 TCTGTTTATAATTCACCTATAA
44652 GACCAGTCTTTTAGCTTACTTTTTCTTAAATATGAGCCAAGGTTACTAAATGAGCAGCAGGGCAA
1 GACCAGTCTTTTAGCTTACTTTTTCTTAAATATGAGCCAAGGTTACTAAATGAGCAGCAGGGCAA
44717 CCATCACAATTCACTGGAAATATTTCCCCACTACAGGAATGAATTAAACAATTTGAAAAACTATT
66 CCATCACAATTCACTGGAAATATTTCCCCACTACAGGAATGAATTAAACAATTTGAAAAACTATT
44782 TCTGTTTATAATTCACCTATAA
131 TCTGTTTATAATTCACCTATAA
44804 GACCA
1 GACCA
44809 TAGAAGCATG
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 157 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (152 bp):
GACCAGTCTTTTAGCTTACTTTTTCTTAAATATGAGCCAAGGTTACTAAATGAGCAGCAGGGCAA
CCATCACAATTCACTGGAAATATTTCCCCACTACAGGAATGAATTAAACAATTTGAAAAACTATT
TCTGTTTATAATTCACCTATAA
Found at i:48356 original size:21 final size:21
Alignment explanation
Indices: 48330--48372 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
48320 CCTCTTTAAC
*
48330 TAACACTTGCCACATGGCTCA
1 TAACACCTGCCACATGGCTCA
*
48351 TAACACCTGCCACATGGTTCA
1 TAACACCTGCCACATGGCTCA
48372 T
1 T
48373 CTCATTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.26
Consensus pattern (21 bp):
TAACACCTGCCACATGGCTCA
Found at i:59302 original size:30 final size:30
Alignment explanation
Indices: 59266--59326 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
59256 ACTTTGCTTC
*
59266 TATTTTGTGTTAGAGAAGTGGGGTTTAAGT
1 TATTTTGTGTTAGAGAAGTGAGGTTTAAGT
59296 TATTTTGTGTTAGAGAAGTGAGGTTTAAGT
1 TATTTTGTGTTAGAGAAGTGAGGTTTAAGT
59326 T
1 T
59327 CAATTTCCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (30 bp):
TATTTTGTGTTAGAGAAGTGAGGTTTAAGT
Found at i:61359 original size:21 final size:21
Alignment explanation
Indices: 61321--61360 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61311 ATTATAGTGG
*
61321 TTTCTAAATTATCACAAGAAA
1 TTTCTAAATTATAACAAGAAA
61342 TTTCT-AATTATAATCAAGA
1 TTTCTAAATTATAA-CAAGA
61361 TTCAAGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
TTTCTAAATTATAACAAGAAA
Found at i:61505 original size:16 final size:16
Alignment explanation
Indices: 61475--61507 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61465 CGAAATGTGA
61475 GTTTACTTTATAATTT
1 GTTTACTTTATAATTT
61491 GTTTA-TTTATGAATTT
1 GTTTACTTTAT-AATTT
61507 G
1 G
61508 GTAGGTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.61
Consensus pattern (16 bp):
GTTTACTTTATAATTT
Found at i:61737 original size:13 final size:13
Alignment explanation
Indices: 61719--61743 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61709 CATAACTTAT
61719 TCAAAATTAATGA
1 TCAAAATTAATGA
61732 TCAAAATTAATG
1 TCAAAATTAATG
61744 GGGAGATGTT
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
TCAAAATTAATGA
Found at i:67239 original size:13 final size:14
Alignment explanation
Indices: 67221--67254 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
67211 GAAATAAATT
*
67221 AAAAGAGAA-AAAA
1 AAAAGAAAAGAAAA
67234 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
67248 AAAAGAA
1 AAAAGAA
67255 GAGATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAA
Found at i:67250 original size:17 final size:18
Alignment explanation
Indices: 67221--67256 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
67211 GAAATAAATT
67221 AAAAGAGAAAAAAAAAAG
1 AAAAGAGAAAAAAAAAAG
*
67239 AAAAGA-AAAAAAAGAAG
1 AAAAGAGAAAAAAAAAAG
67256 A
1 A
67257 GATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAGAAAAAAAAAAG
Found at i:71442 original size:259 final size:257
Alignment explanation
Indices: 70966--71459 Score: 873
Period size: 259 Copynumber: 1.9 Consensus size: 257
70956 ACATGCAACA
* * * * *
70966 CTTAATTTATCAGTATCTATAACTACATATGAAAGCAAGGTATAAGGGCCCCTTCTCACCAAGTG
1 CTTAATTTACCAGTATCTATAACTACATATAAAAGCAAGATACAAGGGCCCCTTCTCACCAAATG
*
71031 CTGACAAGTGGCGCACTGTGGAGGAGATATTCTATTTGGGTTTTGTTCTTATTGGGCCTTAGAGG
66 CTGACAAGTGGCGCACTGTGGAGGAGATATTCTATTTGGGTTTTGTTCTTATTGGGCATTAGAGG
71096 ATTAGGGTTTAGCTTCATTTTAAAGGTGCACGGGTCCCACACGGTTTAGAGTTTAGCTTCATTTA
131 ATTAGGGTTTAGCTTCATTTTAAAGGTGCACGGGTCCCACACGGTTTAGAGTTTAGCTTCATTTA
71161 GAGATATATAGATTCCAGTCAGTCTTAAATTTGATTGGTGCATGGGTCCCACACGGTTTAGT
196 GAGATATATAGATTCCAGTCAGTCTTAAATTTGATTGGTGCATGGGTCCCACACGGTTTAGT
*
71223 CTTAATTTACCAGTATCTATATAACTACATATAAAAGCAAGATACAAGGGTCCCTTCTCACCAAA
1 CTTAATTTACCAGTATC--TATAACTACATATAAAAGCAAGATACAAGGGCCCCTTCTCACCAAA
*
71288 TGCTGACAAGTGGCGCACTGTGGAGGAGATATTCTATTTGGGTTTTGTTCTTATTGGGCATTGGA
64 TGCTGACAAGTGGCGCACTGTGGAGGAGATATTCTATTTGGGTTTTGTTCTTATTGGGCATTAGA
*
71353 GGCTTAGGGTTTAGCTTCATTTTAAAGGTGCACGGGTCCCACACGGTTTAG-GATTTAGCTTCAT
129 GGATTAGGGTTTAGCTTCATTTTAAAGGTGCACGGGTCCCACACGGTTTAGAG-TTTAGCTTCAT
71417 TTAGAGATATATAGATTCCAGTCAGTCTTAAATTTGATTGGTG
193 TTAGAGATATATAGATTCCAGTCAGTCTTAAATTTGATTGGTG
71460 ACAATATGGG
Statistics
Matches: 225, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
257 16 0.07
258 1 0.00
259 208 0.92
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (257 bp):
CTTAATTTACCAGTATCTATAACTACATATAAAAGCAAGATACAAGGGCCCCTTCTCACCAAATG
CTGACAAGTGGCGCACTGTGGAGGAGATATTCTATTTGGGTTTTGTTCTTATTGGGCATTAGAGG
ATTAGGGTTTAGCTTCATTTTAAAGGTGCACGGGTCCCACACGGTTTAGAGTTTAGCTTCATTTA
GAGATATATAGATTCCAGTCAGTCTTAAATTTGATTGGTGCATGGGTCCCACACGGTTTAGT
Found at i:72107 original size:19 final size:20
Alignment explanation
Indices: 72066--72114 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
72056 CTCTAATCTC
72066 TCTTTGATTGGTCTTTGTTTT
1 TCTTT-ATTGGTCTTTGTTTT
*
72087 TCTTTATTGGT-TTTTTTTT
1 TCTTTATTGGTCTTTGTTTT
72106 TCTTTATTG
1 TCTTTATTG
72115 CTTAGCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 16 0.59
20 6 0.22
21 5 0.19
ACGTcount: A:0.06, C:0.08, G:0.14, T:0.71
Consensus pattern (20 bp):
TCTTTATTGGTCTTTGTTTT
Found at i:80539 original size:3 final size:3
Alignment explanation
Indices: 80531--80556 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
80521 ACAATCCTTA
80531 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
80557 AATACTTATT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:80743 original size:40 final size:38
Alignment explanation
Indices: 80699--80795 Score: 122
Period size: 40 Copynumber: 2.5 Consensus size: 38
80689 TTTGAGCTCA
* * *
80699 CTTGAATCAAGCTTGTTAACTAATTCTAAAAAATTAAAAC
1 CTTGAATCAAGCTCGTTAACTAATACGAAAAAA--AAAAC
* * *
80739 CTTGAATCATGCTCATTAACTAATAGGAAAAAAAAAAC
1 CTTGAATCAAGCTCGTTAACTAATACGAAAAAAAAAAC
80777 CTTGAATCAAGCTCGTTAA
1 CTTGAATCAAGCTCGTTAA
80796 AAACTTTGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 22 0.45
40 27 0.55
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.29
Consensus pattern (38 bp):
CTTGAATCAAGCTCGTTAACTAATACGAAAAAAAAAAC
Found at i:80804 original size:23 final size:23
Alignment explanation
Indices: 80771--80814 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
80761 ATAGGAAAAA
*
80771 AAAAACCTTGAATCAAGCTCGTT
1 AAAAACCTTGAATCAAACTCGTT
*
80794 AAAAACTTTGAATCAAACTCG
1 AAAAACCTTGAATCAAACTCG
80815 ATATTTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (23 bp):
AAAAACCTTGAATCAAACTCGTT
Found at i:81307 original size:103 final size:103
Alignment explanation
Indices: 81123--81442 Score: 586
Period size: 103 Copynumber: 3.1 Consensus size: 103
81113 AACTATCTAT
81123 ACTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTAACTCGGATACAAACTCAGTTTTTA
1 ACTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTAACTCGGATACAAACTCAGTTTTTA
81188 AAAGATTAAAAACTACCCATTTCAAACTAAACCACCAA
66 AAAGATTAAAAACTACCCATTTCAAACTAAACCACCAA
*
81226 ACTAATTATAATGTGAAGTCCTGAATTTGTGTCACGAGTTAACTCGGATACAAACTCAGTTTTTA
1 ACTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTAACTCGGATACAAACTCAGTTTTTA
*
81291 AAAGATTAAAAGCTACCCATTTCAAACTAAACCACCAA
66 AAAGATTAAAAACTACCCATTTCAAACTAAACCACCAA
81329 ACTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTAACTCGGATACAAACTCAGTTTTTA
1 ACTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTAACTCGGATACAAACTCAGTTTTTA
* *
81394 AAAAATTAAAAATTACCCATTTCAAACTAAACCACCAA
66 AAAGATTAAAAACTACCCATTTCAAACTAAACCACCAA
*
81432 ACATATTTATA
1 AC-TAATTATA
81443 TCACTTAAAA
Statistics
Matches: 209, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
103 202 0.97
104 7 0.03
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (103 bp):
ACTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTAACTCGGATACAAACTCAGTTTTTA
AAAGATTAAAAACTACCCATTTCAAACTAAACCACCAA
Found at i:81922 original size:22 final size:22
Alignment explanation
Indices: 81881--81922 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
81871 AACAAACCCG
**
81881 TAACCCGAATAATCTGAGAAGT
1 TAACCCGAATAATCCAAGAAGT
*
81903 TAACCCGAATGATCCAAGAA
1 TAACCCGAATAATCCAAGAA
81923 TATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
TAACCCGAATAATCCAAGAAGT
Found at i:82453 original size:31 final size:31
Alignment explanation
Indices: 82415--82473 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
82405 TATGTTAGAC
* *
82415 AAATAAGGATATAATTGATGTTTCAAAAATT
1 AAATAAGGACATAATAGATGTTTCAAAAATT
*
82446 AAATAAGGACATAATAGGTGTTTCAAAA
1 AAATAAGGACATAATAGATGTTTCAAAA
82474 GTTTTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (31 bp):
AAATAAGGACATAATAGATGTTTCAAAAATT
Found at i:84197 original size:43 final size:41
Alignment explanation
Indices: 84133--84220 Score: 140
Period size: 43 Copynumber: 2.1 Consensus size: 41
84123 AAAGGTAGCC
84133 ATCCTACATTTGGGATGGCCTTGCACTATATTGGTACAGGACT
1 ATCCTACATTTGGGATGGCCTTGCAC-ATATT-GTACAGGACT
* *
84176 ATCCTACATTTGGGATTGCCTTGCACATATTGTGCAGGACT
1 ATCCTACATTTGGGATGGCCTTGCACATATTGTACAGGACT
84217 ATCC
1 ATCC
84221 ACAGTCTAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 13 0.30
42 5 0.12
43 25 0.58
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (41 bp):
ATCCTACATTTGGGATGGCCTTGCACATATTGTACAGGACT
Found at i:95716 original size:29 final size:29
Alignment explanation
Indices: 95683--95757 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
95673 ACGAGGGGAC
95683 AAAGATGGGGCACTCGTTACACCAAAAAA
1 AAAGATGGGGCACTCGTTACACCAAAAAA
95712 AAAGATGGGGCACTCGTTACACCAAAAAA
1 AAAGATGGGGCACTCGTTACACCAAAAAA
* *
95741 AAAAATTGGGCACTCGT
1 AAAGATGGGGCACTCGT
95758 ACAGAACTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (29 bp):
AAAGATGGGGCACTCGTTACACCAAAAAA
Found at i:103331 original size:19 final size:19
Alignment explanation
Indices: 103309--103355 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
103299 ACATTTTAAA
*
103309 TTATTTTTT-ATTCATATTT
1 TTATTTTTTAAAT-ATATTT
103328 TTATTTTTTAAATATATTT
1 TTATTTTTTAAATATATTT
103347 TCTATTTTT
1 T-TATTTTT
103356 ATTTTCTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTTTTAAATATATTT
Found at i:103346 original size:32 final size:29
Alignment explanation
Indices: 103283--103352 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
103273 TCTATGTGGC
103283 TTTTTTATTATTTTTTACATTTTAAATTA
1 TTTTTTATTATTTTTTACATTTTAAATTA
**
103312 TTTTTTATTCATATTTTTATTTTTTAAATATA
1 TTTTTTATT-AT-TTTTTACATTTTAAAT-TA
*
103344 TTTTCTATT
1 TTTTTTATT
103353 TTTATTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 9 0.26
30 2 0.06
31 14 0.40
32 10 0.29
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTTTTATTATTTTTTACATTTTAAATTA
Found at i:107269 original size:49 final size:49
Alignment explanation
Indices: 107191--107421 Score: 275
Period size: 49 Copynumber: 4.7 Consensus size: 49
107181 TTCAATTTTT
* * *
107191 CAAAACGCCCTTCCCAGACAGAAGGCATTTATTTTTACCCGCCATTTCC
1 CAAAACGCCCTGCCCAGACGGAAGACATTTATTTTTACCCGCCATTTCC
* *
107240 TAAAACGCCCTGCCCAGACGGAAGCCATTTATTTTTACCCGCCATTTCC
1 CAAAACGCCCTGCCCAGACGGAAGACATTTATTTTTACCCGCCATTTCC
* * ** *
107289 TAAAACGCCCTGCCCAGACGGAAGACATTCATTTTTACTTGTCATTTCC
1 CAAAACGCCCTGCCCAGACGGAAGACATTTATTTTTACCCGCCATTTCC
* * * ** **
107338 CAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGTTATTTCC
1 CAAAACGCCCTGCCCAGACGGAAGACATTTATTTTTACCCGCCATTTCC
* *
107387 CAAAGCGCCCCT-CCCAGACGGAAGACACTTATTTT
1 CAAAACG-CCCTGCCCAGACGGAAGACATTTATTTT
107422 ACTTGCTATT
Statistics
Matches: 164, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
49 160 0.98
50 4 0.02
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (49 bp):
CAAAACGCCCTGCCCAGACGGAAGACATTTATTTTTACCCGCCATTTCC
Found at i:107448 original size:98 final size:98
Alignment explanation
Indices: 107191--107507 Score: 295
Period size: 98 Copynumber: 3.2 Consensus size: 98
107181 TTCAATTTTT
* * * * ** * * * *
107191 CAAAACGCCCTTCCCAGACAGAAGGCATTTATTTTTACCCGCCATTTCCTAAAACGCCCTGCCCA
1 CAAAACGCCCTGCCCAGACGGAAGACATTCATTTTTACTTGTCATTTCCAAAAACGACCTTCCCA
* * **
107256 GACGGAAGCCATTTATTTTTACCCGCCATTTCC
66 GACGGAAGCCATTAATTTTTACCTGTTATTTCC
* * *
107289 TAAAACGCCCTGCCCAGACGGAAGACATTCATTTTTACTTGTCATTTCCCAAAACGCCCTTCCCA
1 CAAAACGCCCTGCCCAGACGGAAGACATTCATTTTTACTTGTCATTTCCAAAAACGACCTTCCCA
* *
107354 GACGGAAGCCATTCATTTTTACTTGTTATTTCC
66 GACGGAAGCCATTAATTTTTACCTGTTATTTCC
* *
107387 CAAAGCGCCCCT-CCCAGACGGAAGACACTT-A-TTTTACTTG-CTATTCTCCAAAAATGACCTT
1 CAAAACG-CCCTGCCCAGACGGAAGACA-TTCATTTTTACTTGTC-ATT-TCCAAAAACGACCTT
* * * * *
107448 CCCGGATGGAAGACACTAATCTTTACCTGTT-TTTCC
62 CCCAGACGGAAGCCATTAATTTTTACCTGTTATTTCC
* *
107484 CAAAATGCCCTTCCCCA-ACGGAAG
1 CAAAACGCCC-TGCCCAGACGGAAG
107508 GCACTAGGTT
Statistics
Matches: 184, Mismatches: 29, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
96 4 0.02
97 30 0.16
98 144 0.78
99 6 0.03
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (98 bp):
CAAAACGCCCTGCCCAGACGGAAGACATTCATTTTTACTTGTCATTTCCAAAAACGACCTTCCCA
GACGGAAGCCATTAATTTTTACCTGTTATTTCC
Found at i:107459 original size:147 final size:146
Alignment explanation
Indices: 107191--107507 Score: 343
Period size: 147 Copynumber: 2.2 Consensus size: 146
107181 TTCAATTTTT
* * * *
107191 CAAAACGCCCTTCCCAGACAGAAGGCATTTATTTTTACCCGCCATTTCCTAAAACGCCCTGCCCA
1 CAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACCCGCCATTTCCCAAAACGCCCTGCCCA
* * * * * *
107256 GACGGAAGCCATTTATTTTTACCCGCCATTTCCTAAAACGCCCTGCCCAGACGGAAGACATTCAT
66 GACGGAAGACACTTATTTTTACCCGCCATTTCCAAAAACGACCTGCCCAGACGGAAGACACTAAT
* *
107321 TTTTACTTGTCATTTCC
131 CTTTACCTGT-ATTTCC
** ** *
107338 CAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGTTATTTCCCAAAGCGCCCCT-CCC
1 CAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACCCGCCATTTCCCAAAACG-CCCTGCCC
** * * * * *
107402 AGACGGAAGACACTTA-TTTTACTTGCTATTCTCCAAAAATGACCTTCCCGGATGGAAGACACTA
65 AGACGGAAGACACTTATTTTTACCCGCCATT-TCCAAAAACGACCTGCCCAGACGGAAGACACTA
*
107466 ATCTTTACCTGTTTTTCC
129 ATCTTTACCTGTATTTCC
*
107484 CAAAATGCCCTTCCCCA-ACGGAAG
1 CAAAACGCCCTT-CCCAGACGGAAG
107508 GCACTAGGTT
Statistics
Matches: 141, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
146 34 0.24
147 103 0.73
148 4 0.03
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (146 bp):
CAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACCCGCCATTTCCCAAAACGCCCTGCCCA
GACGGAAGACACTTATTTTTACCCGCCATTTCCAAAAACGACCTGCCCAGACGGAAGACACTAAT
CTTTACCTGTATTTCC
Found at i:107463 original size:49 final size:48
Alignment explanation
Indices: 107406--107498 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
107396 CCTCCCAGAC
* *
107406 GGAAGACACTTAT-TTTACTTGCTATTCTCCAAAAATGACCTTCCCGGAT
1 GGAAGACACTAATCTTTACCTG-T-TTCTCCAAAAATGACCTTCCCGGAT
* * *
107455 GGAAGACACTAATCTTTACCTGTTTTTCCCAAAATGCCCTTCCC
1 GGAAGACACTAATCTTTACCTGTTTCTCCAAAAATGACCTTCCC
107499 CAACGGAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
48 18 0.47
49 13 0.34
50 7 0.18
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (48 bp):
GGAAGACACTAATCTTTACCTGTTTCTCCAAAAATGACCTTCCCGGAT
Found at i:107507 original size:48 final size:49
Alignment explanation
Indices: 107191--107556 Score: 235
Period size: 49 Copynumber: 7.5 Consensus size: 49
107181 TTCAATTTTT
* * * * ** *
107191 CAAAACGCCCTTCCCAGACAGAAGGCATTTATTTTTACCCGCCA-TTTCC
1 CAAAACGCCCTTCCCAGACGGAAGACACTAATTTTTACTTG-TATTTTCC
* * * * * ** *
107240 TAAAACGCCCTGCCCAGACGGAAGCCATTTATTTTTACCCGCCA-TTTCC
1 CAAAACGCCCTTCCCAGACGGAAGACACTAATTTTTACTTG-TATTTTCC
* * * *
107289 TAAAACGCCCTGCCCAGACGGAAGACATTCATTTTTACTTGTCA-TTTCC
1 CAAAACGCCCTTCCCAGACGGAAGACACTAATTTTTACTTGT-ATTTTCC
* * *
107338 CAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGT-TATTTCC
1 CAAAACGCCCTTCCCAGACGGAAGACACTAATTTTTACTTGTAT-TTTCC
* * * *
107387 CAAAGCGCCCCTCCCAGACGGAAGACACTTA-TTTTACTTGCTATTCTCC
1 CAAAACGCCCTTCCCAGACGGAAGACACTAATTTTTACTTG-TATTTTCC
* * * * * * *
107436 AAAAATGACCTTCCCGGATGGAAGACACTAATCTTTACCTGT-TTTTCC
1 CAAAACGCCCTTCCCAGACGGAAGACACTAATTTTTACTTGTATTTTCC
* * ** *
107484 CAAAATGCCCTTCCCCA-ACGGAAGGCACTAGGTTTTATTTGCT-TTTTCC
1 CAAAACGCCCTT-CCCAGACGGAAGACACTAATTTTTACTTG-TATTTTCC
* * * *
107533 TAAAACACCCTTCCCTGAAGGAAG
1 CAAAACGCCCTTCCCAGACGGAAG
107557 GCGCTAGTTT
Statistics
Matches: 264, Mismatches: 44, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
48 44 0.17
49 212 0.80
50 8 0.03
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (49 bp):
CAAAACGCCCTTCCCAGACGGAAGACACTAATTTTTACTTGTATTTTCC
Found at i:107592 original size:48 final size:49
Alignment explanation
Indices: 107477--107592 Score: 137
Period size: 49 Copynumber: 2.4 Consensus size: 49
107467 TCTTTACCTG
* * *
107477 TTTTTCCCAAAATGCCCTTCCCCAACGGAAGGCACTAGGTTTTATTTGC
1 TTTTTCCTAAAATGCCCTTCCCCAACGGAAGGCACTAGGTTTTACTCGC
** * *
107526 TTTTTCCTAAAACACCCTTCCCTGAA-GGAAGGCGCTA-GTTTTACTCGC
1 TTTTTCCTAAAATGCCCTTCCC-CAACGGAAGGCACTAGGTTTTACTCGC
*
107574 TTTTTCTTAAAATGCCCTT
1 TTTTTCCTAAAATGCCCTT
107593 TCCGGACGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
48 25 0.45
49 29 0.52
50 2 0.04
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (49 bp):
TTTTTCCTAAAATGCCCTTCCCCAACGGAAGGCACTAGGTTTTACTCGC
Found at i:107606 original size:48 final size:49
Alignment explanation
Indices: 107477--107607 Score: 138
Period size: 48 Copynumber: 2.7 Consensus size: 49
107467 TCTTTACCTG
* * * *
107477 TTTTTCCCAAAATGCCCTTCCCCAACGGAAGGCACTAGGTTTTATTTGC
1 TTTTTCCTAAAATGCCCTTCCCCGACGGAAGGCACTAGGTTTTACTCGC
** * * *
107526 TTTTTCCTAAAACACCCTTCCCTGAAGGAAGGCGCTA-GTTTTACTCGC
1 TTTTTCCTAAAATGCCCTTCCCCGACGGAAGGCACTAGGTTTTACTCGC
* * * *
107574 TTTTTCTTAAAATGCCCTTTCCGGACGAAAGGCA
1 TTTTTCCTAAAATGCCCTTCCCCGACGGAAGGCA
107608 AGTTCGTTTT
Statistics
Matches: 65, Mismatches: 17, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
48 35 0.54
49 30 0.46
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (49 bp):
TTTTTCCTAAAATGCCCTTCCCCGACGGAAGGCACTAGGTTTTACTCGC
Found at i:108723 original size:19 final size:19
Alignment explanation
Indices: 108701--108747 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
108691 ACATTTTAAA
*
108701 TTATTTTTT-ACTCATATTT
1 TTATTTTTTAAAT-ATATTT
108720 TTATTTTTTAAATATATTT
1 TTATTTTTTAAATATATTT
108739 TCTATTTTT
1 T-TATTTTT
108748 ATTTTTCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTTTTAAATATATTT
Found at i:112184 original size:24 final size:25
Alignment explanation
Indices: 112134--112184 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
112124 TTACTCAACT
**
112134 AAAAACTCTATTTTTATTTTCTGTA
1 AAAAACTCTATTTTTATTTAATGTA
*
112159 AAAAACTTTATTTTTATTTAAT-TA
1 AAAAACTCTATTTTTATTTAATGTA
112183 AA
1 AA
112185 TCTAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (25 bp):
AAAAACTCTATTTTTATTTAATGTA
Found at i:114464 original size:9 final size:9
Alignment explanation
Indices: 114450--114478 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
114440 ATATGTTAGT
114450 AATAAAGCC
1 AATAAAGCC
114459 AATAAAGCC
1 AATAAAGCC
114468 AATAAAGCC
1 AATAAAGCC
114477 AA
1 AA
114479 GCGTCTCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (9 bp):
AATAAAGCC
Found at i:122390 original size:22 final size:22
Alignment explanation
Indices: 122365--122420 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
122355 TACAGTTAGG
*
122365 GGGTCGCGACCCGGCCTAG-GCT
1 GGGTCGCGACCC-GCCCAGTGCT
*
122387 GGGTCGCGACCCGCCCAGTGGT
1 GGGTCGCGACCCGCCCAGTGCT
122409 GGGTCGCGACCC
1 GGGTCGCGACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.09, C:0.38, G:0.41, T:0.12
Consensus pattern (22 bp):
GGGTCGCGACCCGCCCAGTGCT
Done.