Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022781.1 Corchorus olitorius cultivar O-4 contig22814, 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: 53985
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:658 original size:10 final size:10
Alignment explanation
Indices: 645--669 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
635 ATATTAATAC
645 TAATTGATTT
1 TAATTGATTT
655 TAATTGATTT
1 TAATTGATTT
665 TAATT
1 TAATT
670 TGATCAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (10 bp):
TAATTGATTT
Found at i:756 original size:4 final size:4
Alignment explanation
Indices: 747--773 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
737 TATTCAAATT
747 AATC AATC AATC AATC AATC AATC AAT
1 AATC AATC AATC AATC AATC AATC AAT
774 TTAATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
AATC
Found at i:800 original size:77 final size:76
Alignment explanation
Indices: 683--907 Score: 331
Period size: 77 Copynumber: 3.0 Consensus size: 76
673 TCAATATTCA
683 AATCAATCAATCAATTT-ATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATT
1 AATCAATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAA-T
747 AATCAATCAATC
65 AATCAATCAATC
759 AATCAATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTC--A-A
1 AATCAATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATA
821 ATCAATCAATC
66 ATCAATCAATC
*
832 AATCAAT--A--AATTTAATATCATTTTAGTACTAATTGATTCTAATTGGATCAAAATATATTCA
1 AATCAATCAATCAATTTAATATCA--TTAGTACTAATTGATTCTAATTGGATC--AAGATATTCA
893 AATCAATCAATCAAT
62 AAT-AATCAATCAAT
908 TTAATATATA
Statistics
Matches: 139, Mismatches: 1, Indels: 17
0.89 0.01 0.11
Matches are distributed among these distances:
69 12 0.09
71 28 0.20
73 27 0.19
75 2 0.01
76 17 0.12
77 53 0.38
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (76 bp):
AATCAATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATA
ATCAATCAATC
Found at i:833 original size:65 final size:68
Alignment explanation
Indices: 755--907 Score: 231
Period size: 71 Copynumber: 2.2 Consensus size: 68
745 TTAATCAATC
755 AATCAATCAATCAATC-AATTTAATATCA-TTAGTACTAATTGATTCTAATTGGATC-AAGATAT
1 AATCAATCAATCAATCAAATTTAATATCATTTAGTACTAATTGATTCTAATTGGATCAAAGATAT
817 TCA
66 TCA
820 AATCAATCAATCAATCAATAAATTTAATATCATTTTAGTACTAATTGATTCTAATTGGATCAAAA
1 AATCAATCAATCAATC---AAATTTAATATCA-TTTAGTACTAATTGATTCTAATTGGATC-AAA
*
885 TATATTCA
61 GATATTCA
893 AATCAATCAATCAAT
1 AATCAATCAATCAAT
908 TTAATATATA
Statistics
Matches: 79, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
65 16 0.20
69 12 0.15
71 27 0.34
73 24 0.30
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.37
Consensus pattern (68 bp):
AATCAATCAATCAATCAAATTTAATATCATTTAGTACTAATTGATTCTAATTGGATCAAAGATAT
TCA
Found at i:834 original size:69 final size:71
Alignment explanation
Indices: 751--907 Score: 264
Period size: 69 Copynumber: 2.2 Consensus size: 71
741 CAAATTAATC
*
751 AATCAATCAATCAATCAATCAATTTAATATCA-TTAGTACTAATTGATTCTAATTGGATC-AAGA
1 AATCAATCAATCAATCAATAAATTTAATATCATTTAGTACTAATTGATTCTAATTGGATCAAAGA
814 TATTCA
66 TATTCA
820 AATCAATCAATCAATCAATAAATTTAATATCATTTTAGTACTAATTGATTCTAATTGGATCAAAA
1 AATCAATCAATCAATCAATAAATTTAATATCA-TTTAGTACTAATTGATTCTAATTGGATC-AAA
*
885 TATATTCA
64 GATATTCA
893 AATCAATCAATCAAT
1 AATCAATCAATCAAT
908 TTAATATATA
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
69 31 0.38
71 27 0.33
73 24 0.29
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (71 bp):
AATCAATCAATCAATCAATAAATTTAATATCATTTAGTACTAATTGATTCTAATTGGATCAAAGA
TATTCA
Found at i:1039 original size:9 final size:9
Alignment explanation
Indices: 1017--1046 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1007 TACAGTTTTA
1017 ATATATAT-
1 ATATATATG
1025 ATATATATG
1 ATATATATG
1034 ATATATATG
1 ATATATATG
1043 ATAT
1 ATAT
1047 GATTAGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (9 bp):
ATATATATG
Found at i:3730 original size:2 final size:2
Alignment explanation
Indices: 3723--3761 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3713 ATGCTAAAAC
3723 AT AT AT 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 AT AT AT A
3762 CTAGCTAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29016 original size:53 final size:53
Alignment explanation
Indices: 28952--29060 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
28942 AGTACCAGCT
28952 TATCAAAGAGCTCCTCCTGTTAGTCCATGAGAACAAGGAACACAAGGAAATTA
1 TATCAAAGAGCTCCTCCTGTTAGTCCATGAGAACAAGGAACACAAGGAAATTA
*
29005 TATCACAGAGCTCCTCCTGTTAGTCCATGAGAACAAGGAACACAAGGAAATTA
1 TATCAAAGAGCTCCTCCTGTTAGTCCATGAGAACAAGGAACACAAGGAAATTA
29058 TAT
1 TAT
29061 GGCTAGCATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (53 bp):
TATCAAAGAGCTCCTCCTGTTAGTCCATGAGAACAAGGAACACAAGGAAATTA
Found at i:29396 original size:106 final size:102
Alignment explanation
Indices: 29211--29418 Score: 353
Period size: 106 Copynumber: 2.0 Consensus size: 102
29201 GTAACATCCT
29211 AGCAAGCGGATAAAGAAAGAATCTTGATTGAAGGAAAAAAAATAGAGTTAATAAAACTTTGACTA
1 AGCAAGCGGATAAAGAAAGAATCTTGATTGAAGGAAAAAAAATAGAGTTAATAAAACTTTGACTA
29276 TATTGGCGGGTGTGCCAAACCCTCACGGAAGTGCAAAACAA
66 TATTGGCGGGTGTG-C---CCCTCACGGAAGTGCAAAACAA
* *
29317 AGCAAGCGGATCAAGAAAGAATCTTGATTGAAGGAAAAAAAATCGAGTTAATAAAACTTTGACTA
1 AGCAAGCGGATAAAGAAAGAATCTTGATTGAAGGAAAAAAAATAGAGTTAATAAAACTTTGACTA
*
29382 TATTGGCGGTTGTGCCCCTCACGGAAGTGCAAAACAA
66 TATTGGCGGGTGTGCCCCTCACGGAAGTGCAAAACAA
29419 GGGTGACACA
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
102 22 0.22
105 1 0.01
106 76 0.77
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (102 bp):
AGCAAGCGGATAAAGAAAGAATCTTGATTGAAGGAAAAAAAATAGAGTTAATAAAACTTTGACTA
TATTGGCGGGTGTGCCCCTCACGGAAGTGCAAAACAA
Found at i:30609 original size:13 final size:13
Alignment explanation
Indices: 30591--30618 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30581 GTTTCTCCAA
30591 ATCTATACTATAT
1 ATCTATACTATAT
30604 ATCTATACTATAT
1 ATCTATACTATAT
30617 AT
1 AT
30619 AAAAGTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (13 bp):
ATCTATACTATAT
Found at i:31024 original size:22 final size:22
Alignment explanation
Indices: 30996--31228 Score: 147
Period size: 22 Copynumber: 10.5 Consensus size: 22
30986 TGTCTCTGTG
*
30996 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
31018 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
31041 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
31062 TGGTTA-CAAAAACTTCATATGGA
1 TGGTTATC-AAAATTTCATA-GGA
** *
31085 -ACTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
* *
31106 AGGTTATCAAAAATTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* * *
31128 TGCTTACCTAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
31150 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* **
31174 AGGTTATTGAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
31196 TGGTTATCACAATTAT-ATAGAA
1 TGGTTATCAAAATT-TCATAGGA
*
31218 AGGTTATCAAA
1 TGGTTATCAAA
31229 GAGATTATCA
Statistics
Matches: 160, Mismatches: 36, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
21 7 0.04
22 129 0.81
23 8 0.05
24 16 0.10
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:31079 original size:66 final size:65
Alignment explanation
Indices: 30993--31201 Score: 210
Period size: 66 Copynumber: 3.1 Consensus size: 65
30983 CCTTGTCTCT
* *
30993 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTA-CAAAATTTCATAGGATGGTTATTAAAATTTCATGAGGAAGGTTATCAAAATT-CA
31057 TA
64 TA
* ** *
31059 GTGTGGTTACAAAAACTTCATATGGA-ACTTATCAAAATTTCATG-GGAAGGTTATCAAAAATTC
1 GTGTGGTTAC-AAAATTTCATA-GGATGGTTATTAAAATTTCATGAGGAAGGTTATC-AAAATTC
31122 ATA
63 ATA
* * * * *
31125 GTGTGCTTACCTAAATTTCATAGGATCAGGTTATTAAAATTTC-TTAGGAAGGTTATTGAAATTT
1 GTGTGGTTA-CAAAATTTCATAGGAT--GGTTATTAAAATTTCATGAGGAAGGTTA-TCAAAATT
31189 CATA
62 CATA
31193 GTGTGGTTA
1 GTGTGGTTA
31202 TCACAATTAT
Statistics
Matches: 117, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
65 6 0.05
66 62 0.53
67 10 0.09
68 38 0.32
69 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (65 bp):
GTGTGGTTACAAAATTTCATAGGATGGTTATTAAAATTTCATGAGGAAGGTTATCAAAATTCATA
Found at i:31300 original size:22 final size:23
Alignment explanation
Indices: 31233--31301 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
31223 ATCAAAGAGA
*
31233 TTAT-CAAAATGTCAT-AGCGAGG
1 TTATACAAAATTTCATAAG-GAGG
* * *
31255 TTATA-AGAATTTCATAATGTGG
1 TTATACAAAATTTCATAAGGAGG
31277 TTA-ACAAAATTTCATAAGGAGG
1 TTATACAAAATTTCATAAGGAGG
31299 TTA
1 TTA
31302 CTAATATATC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (23 bp):
TTATACAAAATTTCATAAGGAGG
Found at i:31344 original size:22 final size:22
Alignment explanation
Indices: 31319--31672 Score: 175
Period size: 22 Copynumber: 16.0 Consensus size: 22
31309 ATCCCGGGGA
*
31319 GGTTATTAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
**
31341 GGTTATCAAAATTTTTTAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
31363 GGTTATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGTG-T
* *
31385 GGTTAT-AAAAGTCTCAATTTCA-TGA
1 GGTTATCAAAA-TTTC-A--T-AGTGT
* * * **
31410 GGAGTACCAAAATTTGATAG-AA
1 GG-TTATCAAAATTTCATAGTGT
* * *
31432 AGTTATC-AAATCTCATAGAGT
1 GGTTATCAAAATTTCATAGTGT
* * *
31453 GATTATCGAAATTTCATAGAGAT
1 GGTTATCAAAATTTCATAGTG-T
31476 CGGATTATCAAAATTT-ATAG-GT
1 -GG-TTATCAAAATTTCATAGTGT
*
31498 AGATTATCAAAATTTCATAGTGT
1 -GGTTATCAAAATTTCATAGTGT
* * * *
31521 TGTTATCAAAATTTCAAAGCGA
1 GGTTATCAAAATTTCATAGTGT
* *
31543 GGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAGTGT
** * *
31565 TATTATCAGAATTTCATAGAG-
1 GGTTATCAAAATTTCATAGTGT
* * * * * *
31586 GGTCAACAAAATTTTATCGAGG
1 GGTTATCAAAATTTCATAGTGT
** *
31608 GGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATAGTGT
* * *
31630 GGTTATCAAATTTTCAAAATGT
1 GGTTATCAAAATTTCATAGTGT
* *
31652 GATTACCAAAATTTCATAGTG
1 GGTTATCAAAATTTCATAGTG
31673 GTATTTCTGG
Statistics
Matches: 250, Mismatches: 65, Indels: 34
0.72 0.19 0.10
Matches are distributed among these distances:
20 9 0.04
21 40 0.16
22 163 0.65
23 6 0.02
24 5 0.02
25 16 0.06
26 7 0.03
27 4 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:31570 original size:87 final size:88
Alignment explanation
Indices: 31478--31670 Score: 205
Period size: 87 Copynumber: 2.2 Consensus size: 88
31468 ATAGAGATCG
* * * **
31478 GATTATCAAAATTT-ATAGGTA-GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAG
1 GATTATCAAAATTTCATAGG-AGGATCAACAAAATTTCATAGAGGGGTTATCAAAATTTCATAA-
* *
31540 CGAGGTTATCAAAATTACATAATGT
64 AGAGGTTATCAAAATTACAAAATGT
* * * * *
31565 TATTATCAGAATTTCATA-GAGGGTCAACAAAATTTTATCGAGGGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGGAGGATCAACAAAATTTCATAGAGGGGTTATCAAAATTTCATAAAG
* *
31629 AGGTTATCAAATTTTCAAAATGT
66 AGGTTATCAAAATTACAAAATGT
*
31652 GATTACCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
31671 TGGTATTTCT
Statistics
Matches: 85, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
86 1 0.01
87 79 0.93
88 5 0.06
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (88 bp):
GATTATCAAAATTTCATAGGAGGATCAACAAAATTTCATAGAGGGGTTATCAAAATTTCATAAAG
AGGTTATCAAAATTACAAAATGT
Found at i:31597 original size:65 final size:66
Alignment explanation
Indices: 31500--31626 Score: 148
Period size: 65 Copynumber: 1.9 Consensus size: 66
31490 TTATAGGTAG
* * * * *
31500 ATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 ATTATCAAAATTTCATAGAGTGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAATGT
31565 T
66 T
* * ** * *
31566 ATTATCAGAATTTCATAGAG-GGTCAACAAAATTTTATCGAGGGGTTATCAAAATTTCATAA
1 ATTATCAAAATTTCATAGAGTGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAA
31627 AGAGGTTATC
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
65 32 0.64
66 18 0.36
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (66 bp):
ATTATCAAAATTTCATAGAGTGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAATGT
T
Found at i:31802 original size:22 final size:22
Alignment explanation
Indices: 31762--32199 Score: 250
Period size: 22 Copynumber: 20.0 Consensus size: 22
31752 TCAAAATTTG
*
31762 AGGGAGGATATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * *
31784 ATGAAGGTTATTAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** *
31806 AGTTTA-GTTTTCAAAATTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
*
31828 A-AGATGGTTATCAAAATTTCAT
1 AGGGA-GGTTATCAAAATTTCAT
* *
31850 AGGGAGATTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** **
31872 AATGAGGTTATCAAAAAATCAT
1 AGGGAGGTTATCAAAATTTCAT
*
31894 AGGGAGATTATCAAAA-TT--T
1 AGGGAGGTTATCAAAATTTCAT
* *
31913 --GTA-GTTATCAAGATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* *
31932 AAGGAGGTTATCAAAATTTTAT
1 AGGGAGGTTATCAAAATTTCAT
*
31954 AGGGAGGTTTATCAAAATTTTAT
1 AGGGAGG-TTATCAAAATTTCAT
* *
31977 AGGAAGGTTTATTAAAATTTCAT
1 AGGGAGG-TTATCAAAATTTCAT
** * *
32000 AACGAGGTTATTACAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
32022 AGTGTGATTATCAAAATTTCAG
1 AGGGAGGTTATCAAAATTTCAT
* * *
32044 AGTGTGATTA-CTAACAA-TTCAT
1 AGGGAGGTTATC-AA-AATTTCAT
* * * *
32066 ATGGAGGTTTTTAAATTTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** * * *
32088 AACGTGGTTATCAATATATCAT
1 AGGGAGGTTATCAAAATTTCAT
** * **
32110 TTGGAGGTTATCAACATCCCAT
1 AGGGAGGTTATCAAAATTTCAT
**
32132 AGTGTTGGTTATCAAAATTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
* * *
32155 AGTGAGGTCT-TCAAAATTCCTT
1 AGGGAGGT-TATCAAAATTTCAT
*
32177 AGGGAGGTTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
32199 A
1 A
32200 AGAATGTTAA
Statistics
Matches: 313, Mismatches: 85, Indels: 36
0.72 0.20 0.08
Matches are distributed among these distances:
16 8 0.03
17 4 0.01
19 2 0.01
20 1 0.00
21 6 0.02
22 230 0.73
23 62 0.20
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
AGGGAGGTTATCAAAATTTCAT
Found at i:31969 original size:23 final size:23
Alignment explanation
Indices: 31917--31996 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
31907 AAATTTGTAG
* * *
31917 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
31939 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
31962 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
31985 TTATTAAAATTT
1 TTATCAAAATTT
31997 CATAACGAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
22 19 0.37
23 33 0.63
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:32007 original size:23 final size:22
Alignment explanation
Indices: 31764--32292 Score: 229
Period size: 22 Copynumber: 24.3 Consensus size: 22
31754 AAAATTTGAG
* *
31764 GGAGGATATCAAAATTTCATAT
1 GGAGGTTATCAAAATTTCATAA
* *
31786 GAAGGTTATTAAAATTTCAT-A
1 GGAGGTTATCAAAATTTCATAA
* *
31807 GTTTA-GTTTTCAAAATTTCATAA
1 G--GAGGTTATCAAAATTTCATAA
*
31830 -GATGGTTATCAAAATTTCATAG
1 GGA-GGTTATCAAAATTTCATAA
* *
31852 GGAGATTAACAAAATTTCATAA
1 GGAGGTTATCAAAATTTCATAA
* ** *
31874 TGAGGTTATCAAAAAATCATAG
1 GGAGGTTATCAAAATTTCATAA
*
31896 GGAGATTATCAAAA-TT--T--
1 GGAGGTTATCAAAATTTCATAA
* *
31913 GTA-GTTATCAAGATTTCATAA
1 GGAGGTTATCAAAATTTCATAA
* *
31934 GGAGGTTATCAAAATTTTATAG
1 GGAGGTTATCAAAATTTCATAA
*
31956 GGAGGTTTATCAAAATTTTAT-A
1 GGAGG-TTATCAAAATTTCATAA
*
31978 GGAAGGTTTATTAAAATTTCATAA
1 GG-AGG-TTATCAAAATTTCATAA
* * *
32002 CGAGGTTATTACAATTTCAT-A
1 GGAGGTTATCAAAATTTCATAA
* * *
32023 GTGTGATTATCAAAATTTCA-GA
1 G-GAGGTTATCAAAATTTCATAA
* * *
32045 GTGTGATTA-CTAACAA-TTCATAT
1 G-GAGGTTATC-AA-AATTTCATAA
* * *
32068 GGAGGTTTTTAAATTTTCATAA
1 GGAGGTTATCAAAATTTCATAA
* * * * **
32090 CGTGGTTATCAATATATCATTT
1 GGAGGTTATCAAAATTTCATAA
* **
32112 GGAGGTTATCAACATCCCAT-A
1 GGAGGTTATCAAAATTTCATAA
*
32133 GTGTTGGTTATCAAAATTTCAT-A
1 G-G-AGGTTATCAAAATTTCATAA
* * *
32156 GTGAGGTCT-TCAAAATTCCTTAG
1 G-GAGGT-TATCAAAATTTCATAA
*
32179 GGAGGTTAACAAAATTTCATAA
1 GGAGGTTATCAAAATTTCATAA
* * * * *
32201 GAATGTTA-AAAAAATTAATAA
1 GGAGGTTATCAAAATTTCATAA
* * *
32222 -AAGGTTCT-AGATATTTCAT-A
1 GGAGGTTATCA-AAATTTCATAA
* * * *
32242 GTATCGTCATTAAAATTTCAT-A
1 GGA-GGTTATCAAAATTTCATAA
32264 GGAAGGTTATCAAAATTTCATAA
1 GG-AGGTTATCAAAATTTCATAA
32287 GGAGGT
1 GGAGGT
32293 CACAAAAAAT
Statistics
Matches: 380, Mismatches: 93, Indels: 68
0.70 0.17 0.13
Matches are distributed among these distances:
16 8 0.02
17 4 0.01
19 2 0.01
20 8 0.02
21 26 0.07
22 263 0.69
23 67 0.18
24 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTCATAA
Found at i:32300 original size:22 final size:22
Alignment explanation
Indices: 32247--32299 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
32237 TCATAGTATC
*
32247 GTCATTAAAATTTCATAGGAAG
1 GTCATCAAAATTTCATAGGAAG
*
32269 GTTATCAAAATTTCATAAGG-AG
1 GTCATCAAAATTTCAT-AGGAAG
32291 GTCA-CAAAA
1 GTCATCAAAA
32300 AATAGTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (22 bp):
GTCATCAAAATTTCATAGGAAG
Found at i:43793 original size:33 final size:32
Alignment explanation
Indices: 43736--43797 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
43726 TAATAACAAT
*
43736 GGAGGATATGTGCCGCAAATTTGATGAAGCGAC
1 GGAGGATATGTACCGCAAATTTGAT-AAGCGAC
*
43769 GGAGGATTTGTACCGCGAAA-TTGATAAGC
1 GGAGGATATGTACCGC-AAATTTGATAAGC
43798 TGTTTAGCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 4 0.15
33 19 0.73
34 3 0.12
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.23
Consensus pattern (32 bp):
GGAGGATATGTACCGCAAATTTGATAAGCGAC
Found at i:50188 original size:17 final size:18
Alignment explanation
Indices: 50160--50193 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50150 AGGTGAGGCC
*
50160 TTGGGCCTTTAATTGGTT
1 TTGGGCCTTTAAGTGGTT
50178 TTGGG-CTTTAAGTGGT
1 TTGGGCCTTTAAGTGGT
50194 AAGTGGGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.09, G:0.32, T:0.47
Consensus pattern (18 bp):
TTGGGCCTTTAAGTGGTT
Found at i:53535 original size:32 final size:32
Alignment explanation
Indices: 53494--53554 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
53484 AAATATGTTT
*
53494 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
*
53526 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
53555 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Done.