Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013464.1 Corchorus olitorius cultivar O-4 contig13497, 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: 63248
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:464 original size:11 final size:11
Alignment explanation
Indices: 448--473 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
438 AGATAATTTC
448 TTTTCTTCTAG
1 TTTTCTTCTAG
459 TTTTCTTCTAG
1 TTTTCTTCTAG
470 TTTT
1 TTTT
474 TAGGCAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:1263 original size:15 final size:15
Alignment explanation
Indices: 1233--1274 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1223 TTACTTTGCT
1233 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
1249 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
1264 TTGCTTTCTGT
1 TTGTTTTCTGT
1275 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:1744 original size:23 final size:23
Alignment explanation
Indices: 1630--1745 Score: 112
Period size: 23 Copynumber: 4.9 Consensus size: 23
1620 TTATTTTGTG
*
1630 TTTTGCGTCGA-AAAAAAAATA-T
1 TTTTGCGTC-ATAAAAAAAAGAGT
**
1652 TTTTGCGTCATAAAAAAAATTGT
1 TTTTGCGTCATAAAAAAAAGAGT
*
1675 TTCTGCGTCATAAAAAAAA-AGT
1 TTTTGCGTCATAAAAAAAAGAGT
*
1697 TTTTGCGTTTTTCTAAAAAAAAAAGAGT
1 TTTTGCG----TC-ATAAAAAAAAGAGT
1725 TTTTGCGTCATAAAAAAAAGA
1 TTTTGCGTCATAAAAAAAAGA
1746 AAATTTTTTG
Statistics
Matches: 80, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.01
22 26 0.32
23 30 0.38
24 2 0.03
26 2 0.03
27 9 0.11
28 10 0.12
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (23 bp):
TTTTGCGTCATAAAAAAAAGAGT
Found at i:7427 original size:11 final size:11
Alignment explanation
Indices: 7411--7436 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7401 AGATAATTTC
7411 TTTTCTTCTAG
1 TTTTCTTCTAG
7422 TTTTCTTCTAG
1 TTTTCTTCTAG
7433 TTTT
1 TTTT
7437 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:8217 original size:16 final size:16
Alignment explanation
Indices: 8196--8234 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
8186 TCACTTTGCT
8196 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
8212 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
8228 TTGTTTT
1 TTGTTTT
8235 GTGTCAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.15, C:0.05, G:0.13, T:0.67
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:22444 original size:21 final size:20
Alignment explanation
Indices: 22415--22456 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
22405 TTTCAAGTTT
* *
22415 TTCTTAATTTTAGTGGGATCA
1 TTCTAAATTTTAATGGG-TCA
22436 TTCTAAATTTTAATGGGTCA
1 TTCTAAATTTTAATGGGTCA
22456 T
1 T
22457 ATTAAGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.48
Consensus pattern (20 bp):
TTCTAAATTTTAATGGGTCA
Found at i:24528 original size:34 final size:33
Alignment explanation
Indices: 24490--24556 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
24480 TCATTAATGA
*
24490 TGAAGATCACCAATTTTCTTTCTAATTTTTTTTG
1 TGAAGATCACCAATTTTCTATCT-ATTTTTTTTG
* *
24524 TGAAGATTACCAATTTTCTATCTTTTTTTTTTG
1 TGAAGATCACCAATTTTCTATCTATTTTTTTTG
24557 GAAAAAATCC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 9 0.30
34 21 0.70
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.55
Consensus pattern (33 bp):
TGAAGATCACCAATTTTCTATCTATTTTTTTTG
Found at i:24689 original size:380 final size:379
Alignment explanation
Indices: 23927--24690 Score: 1151
Period size: 380 Copynumber: 2.0 Consensus size: 379
23917 AAAAAAATAG
23927 TTTTACTTTATATTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGGTTAACCAAAATGTGACA
1 TTTTACTTTATATTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGGTTAACCAAAATGTGACA
** * * *
23992 AATAAATAGGAACGGAGGGAGCATCAATTGAAGGTTATTAAAACAATTATGATATATTATGAATA
66 AATAAATAGGAACAAAGGGAGCATCAATTAAAGGTTATTAAAACAATTATGA-ATACTATGAACA
* *
24057 AATTCAATAACCTTACAATCTTATTAGCTTTAGTAAACTTTCATTAATGTACCAAAAAGATTACC
130 AATTCAATAACCTTACAATCTTATTAACTTTAGTAAACTTTCATTAATG---CAAAAAGATCACC
*
24122 GATTTTCTATCTAATTTATTATGAAGATTACCAATTTTCTATCTATTTTTGTTTTAAAAAAACCT
192 AATTTTCTATCTAATTTATTATGAAGATTACCAATTTTCTATCTATTTTTGTTTTAAAAAAACCT
24187 ATAATAATTATAAAAAAAGAGTATAGTACTATCAACTAATCTAATAACCTTAAATTCTCAATATT
257 ATAATAATTATAAAAAAAGAGTATAGTACTATCAACTAATCTAATAACCTTAAATTCTCAATATT
** **
24252 TTTGGTTATCAAGTTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
322 TTTAATTATCAAACTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
24310 TTTTACTTTATATTTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGGTTAACCAAAATGTGAC
1 TTTTACTTTATA-TTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGGTTAACCAAAATGTGAC
* * *
24375 AAATAAATAGGAACAAAGGGAGTATCAATTAAATGTTATTAAAATAATTATG-ATACTATGAACA
65 AAATAAATAGGAACAAAGGGAGCATCAATTAAAGGTTATTAAAACAATTATGAATACTATGAACA
* * **
24439 AATTCAATAACCTTACATTCTTATATAACTTTATTAAACTTTCATTAATG-ATGAAGATCACCAA
130 AATTCAATAACCTTACAATCTTAT-TAACTTTAGTAAACTTTCATTAATGCAAAAAGATCACCAA
* * * *
24503 TTTTCTTTCTAATTTTTTTTGTGAAGATTACCAATTTTCTATCT-TTTTT-TTTTGGAAAAAATC
194 TTTTCTATCTAA--TTTATTATGAAGATTACCAATTTTCTATCTATTTTTGTTTT--AAAAAAAC
* * ** *
24566 CTATAATGATTATAAAAAAA-TGTATAGTACTATCAACTAATCTAATAATTTTACATTCTCAATA
255 CTATAATAATTATAAAAAAAGAGTATAGTACTATCAACTAATCTAATAACCTTAAATTCTCAATA
24630 TTTTTAATTATCAAACTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
320 TTTTTAATTATCAAACTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
24690 T
1 T
24691 ACCAATTTTT
Statistics
Matches: 347, Mismatches: 28, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
379 25 0.07
380 102 0.29
381 54 0.16
382 33 0.10
383 35 0.10
384 98 0.28
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (379 bp):
TTTTACTTTATATTTTTTGAGAAAAATATTGTCAAACTTGAAGATTGGTTAACCAAAATGTGACA
AATAAATAGGAACAAAGGGAGCATCAATTAAAGGTTATTAAAACAATTATGAATACTATGAACAA
ATTCAATAACCTTACAATCTTATTAACTTTAGTAAACTTTCATTAATGCAAAAAGATCACCAATT
TTCTATCTAATTTATTATGAAGATTACCAATTTTCTATCTATTTTTGTTTTAAAAAAACCTATAA
TAATTATAAAAAAAGAGTATAGTACTATCAACTAATCTAATAACCTTAAATTCTCAATATTTTTA
ATTATCAAACTTCTTATTTATATTTACTAAAATTGCTTTTGTAAACGAAGATTA
Found at i:26067 original size:66 final size:66
Alignment explanation
Indices: 25961--26197 Score: 203
Period size: 66 Copynumber: 3.6 Consensus size: 66
25951 TTCTTGTCTC
* ** * *
25961 TGTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCAAGAGG-AGGTTATCAAAATTGC
1 TGTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCAAG-GGAAGGTTATCAAAATTGC
26025 AT
65 AT
* * *
26027 TGTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGGGAAGGTTATCAAACTTTCA
1 TGTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCAAGGGAAGGTTATCAAAATTGCA
26092 T
66 T
* * * * * * * **
26093 AGTGTGTTTACCATAATTTCATAGGATCAGGTTATTAAAATTTCTTA-GGAAGGTTATTGAAATT
1 TGTGTGGTTACCAAAATTTCATAAGA--AAGTTATCAAAATTTC-AAGGGAAGGTTATCAAAATT
**
26157 TTAT
63 GCAT
* *
26161 AGTGTGGTTATCACAAATTT-AT-AGAAAGGTTATCAAA
1 TGTGTGGTTACCA-AAATTTCATAAGAAA-GTTATCAAA
26198 GAATTATCAA
Statistics
Matches: 139, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
65 3 0.02
66 85 0.61
67 2 0.01
68 44 0.32
69 5 0.04
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (66 bp):
TGTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCAAGGGAAGGTTATCAAAATTGCA
T
Found at i:26141 original size:24 final size:22
Alignment explanation
Indices: 25966--26193 Score: 106
Period size: 22 Copynumber: 10.3 Consensus size: 22
25956 GTCTCTGTGT
* * *
25966 GGTTATCAAAATTTCATAAGAT
1 GGTTATTAAAATTTCATAGGAA
* *
25988 GGTTATTATAATTTCA-AGAGGA
1 GGTTATTAAAATTTCATAG-GAA
* * * *
26010 GGTTATCAAAATTGCATTGTG-T
1 GGTTATTAAAATTTCATAG-GAA
** *
26032 GGTTACCAAAATTTCATAAGAA
1 GGTTATTAAAATTTCATAGGAA
* * *
26054 AGTTATCAAAATTTCATGGGAA
1 GGTTATTAAAATTTCATAGGAA
* * *
26076 GGTTATCAAACTTTCATAGTG-T
1 GGTTATTAAAATTTCATAG-GAA
* ** *
26098 GTTTACCATAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGGA--A
*
26122 GGTTATTAAAATTTCTTAGGAA
1 GGTTATTAAAATTTCATAGGAA
* * *
26144 GGTTATTGAAATTTTATAGTG-T
1 GGTTATTAAAATTTCATAG-GAA
* *
26166 GGTTATCACAAATTT-ATAGAAA
1 GGTTATTA-AAATTTCATAGGAA
26188 GGTTAT
1 GGTTAT
26194 CAAAGAATTA
Statistics
Matches: 154, Mismatches: 42, Indels: 20
0.71 0.19 0.09
Matches are distributed among these distances:
21 3 0.02
22 125 0.81
23 10 0.06
24 16 0.10
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGAA
Found at i:26247 original size:22 final size:22
Alignment explanation
Indices: 26201--26664 Score: 137
Period size: 22 Copynumber: 20.9 Consensus size: 22
26191 TATCAAAGAA
* *
26201 TTATCAAAATGTCATAGCGAT-G
1 TTATCAAAATTTCATAGTG-TGG
26223 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGTGG
* *
26245 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGTGG
* * * * **
26267 TTA-CTAATATTTTATGGGGAAG
1 TTATC-AAAATTTCATAGTGTGG
26289 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
** *
26311 TTATCAAAATTTTTTAGTCTGG
1 TTATCAAAATTTCATAGTGTGG
** *
26333 TTATCAAAATTTTTTAGTCTGG
1 TTATCAAAATTTCATAGTGTGG
*
26355 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-TGG
* * *
26377 TTATAAAAGCCTCAATTTCAT-GAAG-AG
1 TTAT-CAA-----AATTTCATAG-TGTGG
* * **
26404 -TACCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGTGTGG
* *
26424 TTATC--AGTTCTCATA-TAGTGA
1 TTATCAAAATT-TCATAGT-GTGG
*
26445 TTATCAAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTG-T-GG
* ***
26469 ATTACCAAAATTT-ATAG-GAAAAA
1 -TTATCAAAATTTCATAGTG--TGG
* * *
26492 TTACCAAAATTTCATATTGTTG
1 TTATCAAAATTTCATAGTGTGG
* ** *
26514 TTATCAAAATTTCAAAACGAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
26536 TTATCAAAATTACATACTGTGA
1 TTATCAAAATTTCATAGTGTGG
* *
26558 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGTGG
* * * * ** *
26580 TCAACGAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGTGG
** * *
26602 TTATCAAAATTTCATAAAGAGT
1 TTATCAAAATTTCATAGTGTGG
* * *
26624 TTATCAAAATTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGTGG
*
26646 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
26665 GTATTTCTGG
Statistics
Matches: 330, Mismatches: 81, Indels: 62
0.70 0.17 0.13
Matches are distributed among these distances:
19 3 0.01
20 12 0.04
21 16 0.05
22 252 0.76
23 15 0.05
24 7 0.02
25 13 0.04
26 2 0.01
27 1 0.00
28 8 0.02
29 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:26544 original size:44 final size:44
Alignment explanation
Indices: 26496--26661 Score: 165
Period size: 44 Copynumber: 3.8 Consensus size: 44
26486 GAAAAATTAC
*
26496 CAAAATTTCATATTGTTG-TTATCAAAATTTCA-AAACGAGGTTAT
1 CAAAATTTCATAATG-TGATTATCAAAATTTCATAAA-GAGGTTAT
* * * * * *
26540 CAAAATTACATACTGTGATTATCAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAATGTGATTATCAAAATTTCATAAAGAGGTTAT
* * * * * *
26584 CGAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGTTTAT
1 CAAAATTTCATAATGTGATTATCAAAATTTCATAAAGAGGTTAT
* *
26628 CAAAATTTCAAAATGTGATTACCAAAATTTCATA
1 CAAAATTTCATAATGTGATTATCAAAATTTCATA
26662 GTGGTATTTC
Statistics
Matches: 95, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
43 2 0.02
44 91 0.96
45 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (44 bp):
CAAAATTTCATAATGTGATTATCAAAATTTCATAAAGAGGTTAT
Found at i:26704 original size:22 final size:21
Alignment explanation
Indices: 26675--27014 Score: 173
Period size: 22 Copynumber: 15.9 Consensus size: 21
26665 GTATTTCTGG
26675 GGAGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* *
26696 GTATGGTTA-CCAAA--T--TA
1 GGA-GGTTATCAAAATTTCATA
* *
26713 GGAAGGTTATTAAACTTTCATA
1 GG-AGGTTATCAAAATTTCATA
* * *
26735 AGAGGGTTATCAATATTTCA-G
1 GGA-GGTTATCAAAATTTCATA
* *
26756 GGACGATATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* *
26777 GTTTA-GTTTTCAAAATTTCATA
1 G--GAGGTTATCAAAATTTCATA
*
26799 AGAGGGTTATCAAAATTTCATA
1 GGA-GGTTATCAAAATTTCATA
* * * *
26821 GTATGTAGATCAAAATATCATA
1 GGAGGT-TATCAAAATTTCATA
* *
26843 GGGAGATTAACAAAATTTCATAA
1 -GGAGGTTATCAAAATTTCAT-A
* * **
26866 CGAGGTTATAAAAAAATCATA
1 GGAGGTTATCAAAATTTCATA
26887 GGGAGGTTATCAAAA-TT--T-
1 -GGAGGTTATCAAAATTTCATA
* * *
26905 GTA-GTTATCAAGATTTCGTAA
1 GGAGGTTATCAAAATTTCAT-A
*
26926 GGAGGTTATCAAAATTTTATA
1 GGAGGTTATCAAAATTTCATA
*
26947 GGGATGTTTATCAAAAAATTTTCATA
1 -GGA-GGTTATC--AAAA-TTTCATA
26973 GCGAGGTTATCAAAATTTCATA
1 G-GAGGTTATCAAAATTTCATA
* *
26995 GTGTGATTATCAAAATTTCA
1 G-GAGGTTATCAAAATTTCA
27015 GGGTGTGATT
Statistics
Matches: 236, Mismatches: 54, Indels: 57
0.68 0.16 0.16
Matches are distributed among these distances:
16 9 0.04
17 12 0.05
18 3 0.01
19 3 0.01
20 15 0.06
21 17 0.07
22 143 0.61
23 15 0.06
25 11 0.05
26 8 0.03
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.34
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTCATA
Found at i:26982 original size:25 final size:24
Alignment explanation
Indices: 26927--26987 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
26917 ATTTCGTAAG
*
26927 GAGGTTATC--AAAATTTTATAGG
1 GAGGTTATCAAAAAATTTTATAGC
*
26949 GATGTTTATCAAAAAATTTTCATAGC
1 GA-GGTTATCAAAAAATTTT-ATAGC
26975 GAGGTTATCAAAA
1 GAGGTTATCAAAA
26988 TTTCATAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 2 0.06
23 6 0.19
25 18 0.56
26 6 0.19
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (24 bp):
GAGGTTATCAAAAAATTTTATAGC
Found at i:27036 original size:22 final size:22
Alignment explanation
Indices: 26979--27025 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
26969 CATAGCGAGG
**
26979 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCAGGGTGTGA
27001 TTATCAAAATTTCAGGGTGTGA
1 TTATCAAAATTTCAGGGTGTGA
27023 TTA
1 TTA
27026 CTAACAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGGGTGTGA
Found at i:31139 original size:19 final size:20
Alignment explanation
Indices: 31088--31139 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
31078 ATATGGAATT
31088 TTTAATAA-TAATTATTCAA
1 TTTAATAATTAATTATTCAA
** *
31107 TAAAATAATT-ATTATT-TA
1 TTTAATAATTAATTATTCAA
31125 TTTAATAATTAATTA
1 TTTAATAATTAATTA
31140 ATTTCAGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATAATTAATTATTCAA
Found at i:33098 original size:22 final size:22
Alignment explanation
Indices: 33049--33099 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
33039 AAATATTACC
**
33049 ATAATTATTTTTGACAGCCATA
1 ATAATTATTTTTGACAGAAATA
*
33071 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGAC-AGAAATA
33094 A-AATTA
1 ATAATTA
33100 GGGAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGACAGAAATA
Found at i:48217 original size:19 final size:20
Alignment explanation
Indices: 48166--48217 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
48156 ATATGGTAAT
48166 TTTAATAA-TAATTATTCAA
1 TTTAATAATTAATTATTCAA
** *
48185 TAAAATAATT-ATTATT-TA
1 TTTAATAATTAATTATTCAA
48203 TTTAATAATTAATTA
1 TTTAATAATTAATTA
48218 ATTTCAGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATAATTAATTATTCAA
Found at i:49714 original size:23 final size:23
Alignment explanation
Indices: 49684--49734 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
49674 GGATGAGCAG
49684 AAACCTCACTCTTCACAGTGCAA
1 AAACCTCACTCTTCACAGTGCAA
49707 AAACCTCACTCTTCACAGTGCAA
1 AAACCTCACTCTTCACAGTGCAA
49730 AAACC
1 AAACC
49735 ATGTTTGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.35, G:0.08, T:0.20
Consensus pattern (23 bp):
AAACCTCACTCTTCACAGTGCAA
Found at i:57963 original size:53 final size:53
Alignment explanation
Indices: 57883--57990 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
57873 ACAAATATAT
* *
57883 AGAGTTTAGTGGTCTTTCAAACATGTGGTGGACGGCTCAGATACACTTCCAAA
1 AGAGTTTAGTGGTCTTTCAAACATGTGGTGGACGACTCAAATACACTTCCAAA
57936 AGAGTTTAGTGGTCTTTCAAACATGTGGTGGACGACTCAAATACACTTCCAAA
1 AGAGTTTAGTGGTCTTTCAAACATGTGGTGGACGACTCAAATACACTTCCAAA
57989 AG
1 AG
57991 TGGATCCTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (53 bp):
AGAGTTTAGTGGTCTTTCAAACATGTGGTGGACGACTCAAATACACTTCCAAA
Found at i:59813 original size:19 final size:20
Alignment explanation
Indices: 59777--59814 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
59767 TATTTATAAA
*
59777 TTATTTAATTTACCAATTTT
1 TTATTTAATTTACAAATTTT
59797 TTATTTAA-TTACAAATTT
1 TTATTTAATTTACAAATTT
59815 CCTTGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTTAATTTACAAATTTT
Found at i:61986 original size:19 final size:18
Alignment explanation
Indices: 61962--61997 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
61952 TGAAAACTCA
61962 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
61981 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
61998 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.