Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018853.1 Corchorus olitorius cultivar O-4 contig18886, 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: 88797
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:8128 original size:32 final size:32
Alignment explanation
Indices: 8087--8156 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
8077 AACCCTAGTC
8087 TTATGATTTTTAGCCGTCTATGTATGTATGTA
1 TTATGATTTTTAGCCGTCTATGTATGTATGTA
8119 TTATGATTTTTAGCCGTCTATGTATGTATGTA
1 TTATGATTTTTAGCCGTCTATGTATGTATGTA
8151 TGTATG
1 T-TATG
8157 TATGTATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.21, C:0.09, G:0.20, T:0.50
Consensus pattern (32 bp):
TTATGATTTTTAGCCGTCTATGTATGTATGTA
Found at i:8146 original size:4 final size:4
Alignment explanation
Indices: 8137--8198 Score: 124
Period size: 4 Copynumber: 15.5 Consensus size: 4
8127 TTTAGCCGTC
8137 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
8185 TATG TATG TATG TA
1 TATG TATG TATG TA
8199 CAGCTTCTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:10797 original size:32 final size:32
Alignment explanation
Indices: 10756--10827 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
10746 TTCAAAGAAC
* * *
10756 ATTTTGTCCTACTTTGTCAAAATTTGAGGGTT
1 ATTTTGTCCTACTATGTCAAAATTCGAGGGCT
*
10788 ATTTTGTCCTTCTATGTCAAAATTCGAGGGCT
1 ATTTTGTCCTACTATGTCAAAATTCGAGGGCT
10820 ATTTTGTC
1 ATTTTGTC
10828 TATCAATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (32 bp):
ATTTTGTCCTACTATGTCAAAATTCGAGGGCT
Found at i:13835 original size:59 final size:59
Alignment explanation
Indices: 13714--13841 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 59
13704 AACATTTCTT
* ** * * *
13714 GGGGAGAAATTATCCCGATTTTGATAGTTTAAGGGTGAAAGTTTCAAATTAAAAGTAAAA
1 GGGG-GAAATTATCCCGATTTTGATAGTTAAAGACTGAAAGTTCCAAAATAAAAATAAAA
* * * *
13774 GGGGGAAATTGTCCCTATTTTGATAGATTAAAGACTGAAAGTTCCAAAATAAAAATTAAG
1 GGGGGAAATTATCCCGATTTTGATAG-TTAAAGACTGAAAGTTCCAAAATAAAAATAAAA
13834 GGGGGAAA
1 GGGGGAAA
13842 ATGTTCCTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 20 0.35
60 37 0.65
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (59 bp):
GGGGGAAATTATCCCGATTTTGATAGTTAAAGACTGAAAGTTCCAAAATAAAAATAAAA
Found at i:16717 original size:8 final size:8
Alignment explanation
Indices: 16704--16728 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16694 TTTTATATAG
16704 TAGTAAGA
1 TAGTAAGA
16712 TAGTAAGA
1 TAGTAAGA
16720 TAGTAAGA
1 TAGTAAGA
16728 T
1 T
16729 TTTGATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (8 bp):
TAGTAAGA
Found at i:17413 original size:3 final size:3
Alignment explanation
Indices: 17405--17498 Score: 179
Period size: 3 Copynumber: 31.3 Consensus size: 3
17395 ACAATTCCCG
17405 TAT TAT TAT TAT TAT 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
*
17453 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17499 TGCTTTCAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18956 original size:24 final size:25
Alignment explanation
Indices: 18929--18984 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
18919 ACTGTTAAAG
*
18929 TATTCGATC-TTGTGTTTTTGTTTA
1 TATTCGATCGATGTGTTTTTGTTTA
* *
18953 TATT-AAGCGATGTGTTTTTGTTTA
1 TATTCGATCGATGTGTTTTTGTTTA
18977 TATTCGAT
1 TATTCGAT
18985 TCTTAATGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 22 0.88
25 1 0.04
ACGTcount: A:0.18, C:0.07, G:0.18, T:0.57
Consensus pattern (25 bp):
TATTCGATCGATGTGTTTTTGTTTA
Found at i:21934 original size:54 final size:54
Alignment explanation
Indices: 21871--21977 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
21861 AAGTATTATG
* * * * * *
21871 TTTGGTTCGTGGAAAGTATTGGGAAAGTGTGGTAAGTGAGATAAGGAAAATAAC
1 TTTGGTTCGTGAAAAATAGTGGGAAAATGTGATAAATGAGATAAGGAAAATAAC
* *
21925 TTTGGTTCGTGAAAAATAGTGGGAAAATGTGATAAATTAGATAGGGAAAATAA
1 TTTGGTTCGTGAAAAATAGTGGGAAAATGTGATAAATGAGATAAGGAAAATAA
21978 TTTTCCTACG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.39, C:0.03, G:0.30, T:0.28
Consensus pattern (54 bp):
TTTGGTTCGTGAAAAATAGTGGGAAAATGTGATAAATGAGATAAGGAAAATAAC
Found at i:25437 original size:72 final size:72
Alignment explanation
Indices: 25315--25536 Score: 435
Period size: 72 Copynumber: 3.1 Consensus size: 72
25305 GCGTGGGTTG
25315 TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
1 TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
25380 ATACAAT
66 ATACAAT
*
25387 TTGTACCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
1 TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
25452 ATACAAT
66 ATACAAT
25459 TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
1 TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
25524 ATACAAT
66 ATACAAT
25531 TTGTTC
1 TTGTTC
25537 ATAACCAATT
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 148 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (72 bp):
TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
ATACAAT
Found at i:27346 original size:72 final size:72
Alignment explanation
Indices: 27224--27359 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
27214 GTTTCTTCAT
* **
27224 TTAGAAACAAAAATGTTCATGTTTGTCACCTTGGCTTGACCCGTTACATTCTATCAATTTCTTTT
1 TTAGAAACAAAAATGCTCATGTTTGTCACCTTGGCTTGACCCGCGACATTCTATCAATTTCTTTT
27289 ATTAATA
66 ATTAATA
* * * * *
27296 TTAGAAACAAAAATGCTCATGTTTGTCACCTTGGCTTGGCCTGCGGCATTCTTTTAATTTCTTT
1 TTAGAAACAAAAATGCTCATGTTTGTCACCTTGGCTTGACCCGCGACATTCTATCAATTTCTTT
27360 CTTCATAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (72 bp):
TTAGAAACAAAAATGCTCATGTTTGTCACCTTGGCTTGACCCGCGACATTCTATCAATTTCTTTT
ATTAATA
Found at i:58005 original size:102 final size:104
Alignment explanation
Indices: 57747--58006 Score: 398
Period size: 102 Copynumber: 2.5 Consensus size: 104
57737 AGTTTAGCCT
* * *
57747 TAATTTCACTAAGTTTAGCCCGGAATTAAAATTTTATTTTTATTTTAATGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCC-AAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
57812 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
57854 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
57919 ATAA-ATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
57957 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
58007 TAGAAAAATT
Statistics
Matches: 144, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 44 0.31
103 35 0.24
106 44 0.31
107 21 0.15
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:59169 original size:29 final size:27
Alignment explanation
Indices: 59126--59181 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
59116 TAAACCTGTA
*
59126 AGTAGAGGGACGAAATTGATACTTTTTTT
1 AGTAGAAGGACGAAATTGAT--TTTTTTT
*
59155 AGTAGAAGGATGAAATTGATTTTTTTT
1 AGTAGAAGGACGAAATTGATTTTTTTT
59182 GTGAAAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.28
29 18 0.72
ACGTcount: A:0.32, C:0.04, G:0.23, T:0.41
Consensus pattern (27 bp):
AGTAGAAGGACGAAATTGATTTTTTTT
Found at i:63232 original size:22 final size:21
Alignment explanation
Indices: 63180--63233 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
63170 TGTTTCTTGA
63180 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
63201 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
63220 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
63234 CACGAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:64788 original size:20 final size:20
Alignment explanation
Indices: 64751--64789 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
64741 TACTATTATT
64751 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
64771 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
64790 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:64971 original size:22 final size:22
Alignment explanation
Indices: 64943--65174 Score: 157
Period size: 22 Copynumber: 10.5 Consensus size: 22
64933 TGTCTCTGTG
* *
64943 TGGTTATTAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
64965 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* **
64988 -GGTTATCAAAATTCCATAGTT
1 TGGTTATCAAAATTTCATAGGA
* *
65009 TGGTTACCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAGGA
* *
65031 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
* *
65052 AGGTTATCAAAATTGCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
65074 TGGTTACCAAAATTCCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
65096 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* ** *
65120 AGGTTATTGAAATTTTATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* * * *
65142 TGGTTATCACAGTTTTATAGAA
1 TGGTTATCAAAATTTCATAGGA
*
65164 AGGTTATCAAA
1 TGGTTATCAAA
65175 GGGATTATTA
Statistics
Matches: 163, Mismatches: 38, Indels: 18
0.74 0.17 0.08
Matches are distributed among these distances:
21 20 0.12
22 121 0.74
23 5 0.03
24 17 0.10
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:65056 original size:65 final size:66
Alignment explanation
Indices: 64940--65304 Score: 234
Period size: 66 Copynumber: 5.3 Consensus size: 66
64930 TCTTGTCTCT
** * *
64940 GTGTGGTTATTAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATTAAAATTTCATG-GGAAGGTTATCAAAATTCCA
65004 TA
65 TA
* * * *
65006 GTTTGGTTACCAAAATTTCATATGA-AGTTATCAAAATTTCATGGGAAGGTTATCAAAATTGCAT
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATTAAAATTTCATGGGAAGGTTATCAAAATTCCAT
65070 A
66 A
* * * * ** **
65071 GTGTGGTTACCAAAATTCCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTT
1 GTGTGGTTACCAAAATTTCATAAGAT-A-GTTATTAAAATTTCATGGGAAGGTTATCAAAATTCC
65136 ATA
64 ATA
* * * * * * ** *
65139 GTGTGGTTATCACAGTTTTATAGAAAGGTTATCAAAGGGATTATTAAAATGTCATAGCGAGATTA
1 GTGTGGTTACCAAAATTTCAT---AA-G--AT---A--G-TTATTAAAATTTCATGGGAAGGTTA
*
65204 T-AAGAATTTCATA
54 TCAA-AATTCCATA
* * * * * * * *
65217 TTGTGGTTAACAAAATTTCATAAGGA-GGTTACTAATATTTCATGGGGAGGTCATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATAA-GATAGTTATTAAAATTTCATGGGAAGGTTATCAAAATTCCA
65281 TA
65 TA
*
65283 GTGTGGTTATCAAAATTTCATA
1 GTGTGGTTACCAAAATTTCATA
65305 TGAAGGTTAT
Statistics
Matches: 236, Mismatches: 47, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
64 2 0.01
65 55 0.23
66 69 0.29
67 4 0.02
68 48 0.20
71 1 0.00
72 1 0.00
73 1 0.00
74 2 0.01
75 4 0.02
76 1 0.00
77 3 0.01
78 45 0.19
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATTAAAATTTCATGGGAAGGTTATCAAAATTCCAT
A
Found at i:65314 original size:22 final size:22
Alignment explanation
Indices: 65208--65549 Score: 99
Period size: 22 Copynumber: 15.3 Consensus size: 22
65198 AGATTATAAG
* *
65208 AATTTCATATTG-TGGTTAACAA
1 AATTTCATA-TGAAGGTTATCAA
* *
65230 AATTTCATAAGGAGGTTA-CTAA
1 AATTTCATATGAAGGTTATC-AA
* ** * *
65252 TATTTCATGGGGAGGTCATCAA
1 AATTTCATATGAAGGTTATCAA
*
65274 AATTTCATAGTG-TGGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
65296 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* ** *
65317 AAGTCTCAAATTTCAT-AAGGAGCACCAA
1 AA-TTTC--A--T-ATGAAGG-TTATCAA
*
65345 AATTTGATA-GAAGGTTATC-A
1 AATTTCATATGAAGGTTATCAA
* *
65365 AATCTCATA-G-AGTGATTATCGA
1 AATTTCATATGAAG-G-TTATCAA
* * *
65387 AATTTCATAAAGATCAGATCATCAA
1 AATTTCAT-ATGA--AGGTTATCAA
* *
65412 AA-TTCATAAGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
* *
65433 AATTTCA-AAGCGAGGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
65455 AA-TT-ATAT-AATGTGATTATCAA
1 AATTTCATATGAA-G-G-TTATCAA
*
65477 AATTTC--ATGAAGGGGTTAACAA
1 AATTTCATATGAA--GGTTATCAA
*
65499 AATTTTATA-GAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
*
65521 AATTTCATA-AAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
*
65543 ATTTTCA
1 AATTTCA
65550 AAATGTGATT
Statistics
Matches: 246, Mismatches: 39, Indels: 70
0.69 0.11 0.20
Matches are distributed among these distances:
19 3 0.01
20 12 0.05
21 33 0.13
22 149 0.61
23 15 0.06
24 10 0.04
25 8 0.03
26 5 0.02
27 7 0.03
28 4 0.02
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:65476 original size:44 final size:44
Alignment explanation
Indices: 65424--65573 Score: 173
Period size: 44 Copynumber: 3.4 Consensus size: 44
65414 TTCATAAGAA
*
65424 GATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTATATAATGT
1 GATTATCAAAATTTCATAAG-GAGGTTATCAAAATTTTATAATGT
* *
65468 GATTATCAAAATTTCATGAAGG-GGTTAACAAAATTTTATAGA-GA
1 GATTATCAAAATTTCAT-AAGGAGGTTATCAAAATTTTATA-ATGT
* * *
65512 GGTTATCAAAATTTCATAAAGAGGTTATC-AAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAGGAGGTTATCAAAATTTT-ATAATGT
*
65556 GATTACCAAAATTTCATA
1 GATTATCAAAATTTCATA
65574 GTGGTATTTC
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
43 11 0.12
44 74 0.82
45 2 0.02
46 3 0.03
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAGGAGGTTATCAAAATTTTATAATGT
Found at i:65566 original size:66 final size:66
Alignment explanation
Indices: 65402--65574 Score: 165
Period size: 66 Copynumber: 2.6 Consensus size: 66
65392 CATAAAGATC
* * * * *
65402 AGATCATCAAAA-TTCAT-AAGAAGATTATCAAAATTTCAAAGCGAGGTTATCAAAATTATATAA
1 AGATTATCAAAATTTCATAAAG-GGATTAACAAAATTTCATAGAGAGGTTATCAAAATTATATAA
*
65465 TG
65 AG
* * * *
65467 TGATTATCAAAATTTCATGAAGGGGTTAACAAAATTTTATAGAGAGGTTATCAAAATT-TCATAA
1 AGATTATCAAAATTTCATAAAGGGATTAACAAAATTTCATAGAGAGGTTATCAAAATTAT-ATAA
65531 AG
65 AG
* * * *
65533 AGGTTATCAAATTTTCA-AAATGTGATTACCAAAATTTCATAG
1 AGATTATCAAAATTTCATAAA-GGGATTAACAAAATTTCATAG
65575 TGGTATTTCT
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
65 13 0.15
66 71 0.82
67 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAAAGGGATTAACAAAATTTCATAGAGAGGTTATCAAAATTATATAAA
G
Found at i:65702 original size:22 final size:22
Alignment explanation
Indices: 65674--65946 Score: 158
Period size: 22 Copynumber: 12.6 Consensus size: 22
65664 TCAGGGAGGA
65674 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
*
65696 TATCAAAATTTCATAGTTTAA--T
1 TATCAAAATTTCATA--TGAAGGT
* *
65718 TTTCAAAATTTCATA-AAAGGGT
1 TATCAAAATTTCATATGAA-GGT
* *
65740 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
65761 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
65784 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** *
65806 TATCAAAAAATCATAGGGAA-GT
1 TATCAAAATTTCATA-TGAAGGT
*
65828 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
65844 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
65866 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
65889 TATCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
65912 TATCAAAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
65934 TATCAAAATTTCA
1 TATCAAAATTTCA
65947 GAGTGTGATT
Statistics
Matches: 201, Mismatches: 32, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
16 11 0.05
18 2 0.01
19 2 0.01
20 2 0.01
21 5 0.02
22 131 0.65
23 44 0.22
24 4 0.02
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:65731 original size:44 final size:44
Alignment explanation
Indices: 65676--65946 Score: 176
Period size: 44 Copynumber: 6.2 Consensus size: 44
65666 AGGGAGGATA
*
65676 TCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-ATTT
1 TCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGA-TT
*
65720 TCAAAATTTCATA-AAAGGGTTATCAAAATTTCATAGTATGTAGA--
1 TCAAAATTTCATAGGAA-GGTTATCAAAATTTCATAGT-T-TAGATT
* * * * * *
65764 TCAAAATTTCATAGGGAGATTAACAAAATTTCATA-ATGAGGTT
1 TCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGATT
** *
65807 ATCAAAAAATCATAGGGAA-GTTATCAAAATTT-GTAG-TT--A--
1 -TCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGTTTAGATT
* * ** *
65846 TCAAGATTTCATAAGG-AGGTTATCAAAATTTTATAG-GGAGGTTT
1 TCAAAATTTCAT-AGGAAGGTTATCAAAATTTCATAGTTTA-GATT
* *
65890 ATCAAAATTTTATAGGAAGGTTTATCAAAATTTCATAGTGT-GATT
1 -TCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAGTTTAGATT
65935 ATCAAAATTTCA
1 -TCAAAATTTCA
65947 GAGTGTGATT
Statistics
Matches: 176, Mismatches: 29, Indels: 43
0.71 0.12 0.17
Matches are distributed among these distances:
37 1 0.01
38 24 0.14
39 4 0.02
41 2 0.01
42 1 0.01
43 5 0.03
44 87 0.49
45 32 0.18
46 18 0.10
47 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (44 bp):
TCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGATT
Found at i:65833 original size:66 final size:66
Alignment explanation
Indices: 65669--65946 Score: 234
Period size: 66 Copynumber: 4.3 Consensus size: 66
65659 AAATTTCAGG
* * * *
65669 GAGGATATCAAAATTTCATA-TGAAGGTTATCAAAATTTCATAGTTTA-ATTTTCAAAATTTCAT
1 GAGGTTATCAAAATTTCATAGGGAA-GTTATCAAAATTTCATAG-GTAGATTATCAAAATTTCAT
65732 AA-
64 AAT
* * * * * *
65734 AAGGGTTATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCAT
1 GA-GGTTATCAAAATTTCATAGGGAAGT-TATCAAAATTTCATAGGTAGATTATCAAAATTTCAT
65798 AAT
64 AAT
** *
65801 GAGGTTATCAAAAAATCATAGGGAAGTTATCAAAA-TT--T--GTAG-TTATCAAGATTTCATAA
1 GAGGTTATCAAAATTTCATAGGGAAGTTATCAAAATTTCATAGGTAGATTATCAAAATTTCATAA
*
65860 G
66 T
* * * * *
65861 GAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGGTTTATCAAAATTTCAT
1 GAGGTTATCAAAATTTCATAGGGAAG-TTATCAAAATTTCATAGGTA-GATTATCAAAATTTCAT
*
65926 AGT
64 AAT
* *
65929 GTGATTATCAAAATTTCA
1 GAGGTTATCAAAATTTCA
65947 GAGTGTGATT
Statistics
Matches: 169, Mismatches: 31, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
60 37 0.22
61 12 0.07
62 2 0.01
63 1 0.01
64 1 0.01
65 6 0.04
66 74 0.44
67 6 0.04
68 30 0.18
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (66 bp):
GAGGTTATCAAAATTTCATAGGGAAGTTATCAAAATTTCATAGGTAGATTATCAAAATTTCATAA
T
Found at i:65887 original size:82 final size:84
Alignment explanation
Indices: 65763--65922 Score: 200
Period size: 82 Copynumber: 1.9 Consensus size: 84
65753 TAGTATGTAG
* *
65763 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG-TTATCAAAAAATCATAGGGAA-
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATA-GGAAG
65826 G-TTATCAAAATTTGTAGTT
65 GTTTATCAAAATTTGTAGTT
* * * * * ** *
65845 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGGAAGG
65910 TTTATCAAAATTT
66 TTTATCAAAATTT
65923 CATAGTGTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
82 39 0.60
83 14 0.22
84 12 0.18
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (84 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGGAAGG
TTTATCAAAATTTGTAGTT
Found at i:65895 original size:23 final size:23
Alignment explanation
Indices: 65843--66133 Score: 132
Period size: 22 Copynumber: 12.7 Consensus size: 23
65833 AAATTTGTAG
* *
65843 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
*
65865 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* *
65888 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
65911 TTATCAAAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
* * * *
65933 TTATCAAAATTTCAGAGTGTGAT
1 TTATCAAAATTTCATAGGGAGGT
* * *
65956 TACTAACAAATTAACAATTCATATGGAGGT
1 T--TATC--A--AA-ATTTCATAGGGAGGT
* * ** *
65986 TT-TTAAATTTTCATAATGTGG-
1 TTATCAAAATTTCATAGGGAGGT
* * *
66007 TTATCAATATATCATATGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * ***
66029 TTATCAACATCTCATAGTCTTGG-
1 TTATCAAAATTTCATAG-GGAGGT
* *
66052 TTATCAAAATTTCATTGGGAAG-
1 TTATCAAAATTTCATAGGGAGGT
*
66074 TTATCAAAATTTCATAGTGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
66097 CT-TCAAAATTCCTTAGGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
*
66118 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
66134 ATAAGGTTAA
Statistics
Matches: 198, Mismatches: 58, Indels: 26
0.70 0.21 0.09
Matches are distributed among these distances:
21 3 0.02
22 119 0.60
23 58 0.29
25 4 0.02
27 1 0.01
28 1 0.01
29 2 0.01
30 10 0.05
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:66077 original size:45 final size:45
Alignment explanation
Indices: 66004--66091 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
65994 TTTCATAATG
* * *
66004 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTCT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTCT
* *
66049 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGT
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGT
66092 GAGGTCTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTCT
Found at i:66140 original size:22 final size:22
Alignment explanation
Indices: 66115--66177 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
66105 TTCCTTAGGG
*
66115 AGGTTAACAAAATTTCATAATA
1 AGGTTAACAAAATTTCATAAAA
*
66137 AGGTTAAAACAAATTT-ATAAAA
1 AGGTTAACA-AAATTTCATAAAA
** *
66159 AGGTTCTCAAAATTCCATA
1 AGGTTAACAAAATTTCATA
66178 GTGTCGTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 5 0.15
22 22 0.67
23 6 0.18
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAAA
Found at i:81747 original size:2 final size:2
Alignment explanation
Indices: 81740--81766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
81730 TATATTACAG
81740 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 A
81767 GGTGAATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.