Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019478.1 Corchorus olitorius cultivar O-4 contig19511, 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: 20662
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Found at i:2487 original size:22 final size:22
Alignment explanation
Indices: 2459--2595 Score: 111
Period size: 22 Copynumber: 6.3 Consensus size: 22
2449 TGTCTCTGTG
2459 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
2481 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* * *
2504 -GGTTATTAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
2525 TGGTTACCAAAATTTCATAAGGA
1 TGGTTATCAAAATTTCATAA-GA
* **
2548 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
2569 AGGTTATCAAAATTTCAT-AGG
1 TGGTTATCAAAATTTCATAAGA
2590 TGGTTA
1 TGGTTA
2596 CTTTCATAAG
Statistics
Matches: 90, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 8 0.09
22 76 0.84
23 4 0.04
24 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:2562 original size:66 final size:65
Alignment explanation
Indices: 2456--3659 Score: 254
Period size: 66 Copynumber: 18.6 Consensus size: 65
2446 TCTTGTCTCT
* * * *
2456 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATTAAAATTCCAT
1 GTGTGGTTATCAAAATTTCATAAGA-AGTTATCAAAATTTCATGAGGAGGTTATTAAAATTTCAT
2521 A
65 A
* *
2522 GTGTGGTTACCAAAATTTCATAAGGAAGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTTCA
1 GTGTGGTTATCAAAATTTCATAA-GAAGTTATCAAAATTTCATGAGG-AGGTTATTAAAATTTCA
2586 TA
64 TA
* * *
2588 G-GTGGTTA-C----TTTCATAAGATCAGGTTATTAAAATTTC-TTAGGAAGGTTATTGAAATTT
1 GTGTGGTTATCAAAATTTCATAAGA--A-GTTATCAAAATTTCATGAGG-AGGTTATTAAAATTT
*
2646 TATA
62 CATA
* * * * * *
2650 GTGTGATTATCACAATTTTATAAAAAGGTTATC--AA----A-GA-GA--TTATCAAAATGTCAT
1 GTGTGGTTATCAAAATTTCATAAGAA-GTTATCAAAATTTCATGAGGAGGTTATTAAAATTTCAT
2705 A
65 A
* * * ** * * * * *
2706 GCGAGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAGGTTACTAATATTTTA
1 GTGTGGTTATCAA-AATTTCATA-AGAAGTTATCAAAATTTCATGAGGAGGTTATTAAAATTTCA
2770 TA
64 TA
* * * ** * * *
2772 GGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAAATTT--TTAGTGTGGTTATCAAAATTTC
1 GTGTGGTTATCAAAATTTCATA-AGAAGTTATC-AAAATTTCATGAG-GAGGTTATTAAAATTTC
2835 ATA
63 ATA
* * * * * * * * *
2838 -TGAAGGTTATAAAAGTCTCAATTTCATGAGGAG-TACCAAAATTTGAT-AGAAGATTA-TCAAA
1 GTG-TGGTTAT-CAA-----AATTTCATAAGAAGTTATCAAAATTTCATGAGGAGGTTATTAAAA
*
2899 TCTCATA
59 TTTCATA
* * * * * *
2906 GAGTGATTATCGAAATTTCATAGAGATCGGATTATCAAAATTT-AT-AGGAAGATTATCAAAATT
1 GTGTGGTTATCAAAATTTCATA-AGA--AG-TTATCAAAATTTCATGAGG-AGGTTATTAAAATT
2969 TCATA
61 TCATA
* * * * * * * *
2974 GTGTTGTTATCAAAATTTCA-AAGCAAGGTTATCAAAATTACATAATGTGATTATCATAATTTCA
1 GTGTGGTTATCAAAATTTCATAAG-AA-GTTATCAAAATTTCATGAGGAGGTTATTAAAATTTCA
3038 TA
64 TA
* * * * * * * * * * * *
3040 GAGGGGTCAACAAAATTTTATAGAGATGTTATCAAAATTTCATAAAGAGTTTATCAAATTTTCAA
1 GTGTGGTTATCAAAATTTCATA-AGAAGTTATCAAAATTTCATGAGGAGGTTATTAAAATTTCAT
3105 A
65 A
* * ** ** * *
3106 ATGTGATTGCCAAAATTTCAT----AGTGGT----ATTTC-TGGGGAGGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATAAGAAGTTATCAAAATTTCATGAGGAGGTTATTAAAATTTCATA
* * * * * * * * *
3162 GTTTAGTTTTCAAAGTTTCATAAGAGTGTTATCAAAATTTCAT-AGTATGTAAATCAAAATTTCA
1 GTGTGGTTATCAAAATTTCATAAGA-AGTTATCAAAATTTCATGAGGAGGT-TATTAAAATTTCA
3226 TA
64 TA
* * * * * * ** *
3228 GGGAGATTAACAAAATTTCATAATGAGGTTATAAAAAAATCAT-AGGGAGGTTATCAAAA--T--
1 GTGTGGTTATCAAAATTTCATAA-GAAGTTATCAAAATTTCATGA-GGAGGTTATTAAAATTTCA
3288 T-
64 TA
** * * * *
3289 -TGTAATTATCAAGATTTCATAAGGAGGTTTATCAAAATTTTAT-AGGATGGTTTATCAAAATTT
1 GTGTGGTTATCAAAATTTCATAA-GAAG-TTATCAAAATTTCATGAGGA-GG-TTATTAAAATTT
3352 CATA
62 CATA
* * * ** * * *
3356 GCGAGGTTATCACAATTTCAT-AGTGTGATTATCAACATTTCA--AGGTGTGATTACTAACAA-T
1 GTGTGGTTATCAAAATTTCATAAG-AAG-TTATCAAAATTTCATGAGGAG-G-TTATTAA-AATT
3417 TCATA
61 TCATA
* ** * ** * * * * *
3422 -TGGAGGTT-TTTAAATTATCATAGCGGGGTTATCAATATATCAT-ATGGAGGTTATCAACATCT
1 GT-GTGGTTATCAAAATT-TCATA-AGAAGTTATCAAAATTTCATGA-GGAGGTTATTAAAATTT
3484 CATA
62 CATA
** *
3488 GTGTTGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCAT-AGTGAGGTCT-TCAAAA-TT
1 GTG-TGGTTATCAAAATTTCA-TAAGAAGTTATCAAAATTTCATGAG-GAGGT-TATTAAAATTT
3550 CATTA
62 CA-TA
**** * * ** * * ** * * *
3555 AAAAGGTTAACAAAATTTCGTAAGAAGGTTAAAAAAATTTTA-AAAAAGGTTCTCAAAATTCCAT
1 GTGTGGTTATCAAAATTTCATAAGAA-GTTATCAAAATTTCATGAGGAGGTTATTAAAATTTCAT
3619 A
65 A
* * * *
3620 GTATCGTTATTAAAATTTCATAGGAAGGTTATCAAAATTT
1 GTGTGGTTATCAAAATTTCATAAGAA-GTTATCAAAATTT
3660 TATAAAGAAG
Statistics
Matches: 832, Mismatches: 212, Indels: 189
0.67 0.17 0.15
Matches are distributed among these distances:
55 1 0.00
56 64 0.08
57 5 0.01
58 3 0.00
59 3 0.00
60 33 0.04
61 22 0.03
62 52 0.06
63 9 0.01
64 9 0.01
65 87 0.10
66 343 0.41
67 98 0.12
68 75 0.09
69 12 0.01
70 5 0.01
71 3 0.00
72 8 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (65 bp):
GTGTGGTTATCAAAATTTCATAAGAAGTTATCAAAATTTCATGAGGAGGTTATTAAAATTTCATA
Found at i:2574 original size:44 final size:44
Alignment explanation
Indices: 2461--2587 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 44
2451 TCTCTGTGTG
* * * * *
2461 GTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAG
1 GTTATCAAAATTTCATGAGATGGTTATCAAAATTTCATAAGGAA
* * * *
2505 GTTATTAAAATTCCAT-AGTGTGGTTACCAAAATTTCATAAGGAA
1 GTTATCAAAATTTCATGAG-ATGGTTATCAAAATTTCATAAGGAA
* *
2549 GTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATA
1 GTTATCAAAATTTCATGAGATGGTTATCAAAATTTCATA
2588 GGTGGTTACT
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 2 0.03
44 64 0.96
45 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (44 bp):
GTTATCAAAATTTCATGAGATGGTTATCAAAATTTCATAAGGAA
Found at i:2624 original size:24 final size:22
Alignment explanation
Indices: 2597--2645 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
2587 AGGTGGTTAC
2597 TTTCATAAGATCAGGTTATTAAAA
1 TTTCATAAGA--AGGTTATTAAAA
* * *
2621 TTTCTTAGGAAGGTTATTGAAA
1 TTTCATAAGAAGGTTATTAAAA
2643 TTT
1 TTT
2646 TATAGTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (22 bp):
TTTCATAAGAAGGTTATTAAAA
Found at i:2726 original size:22 final size:22
Alignment explanation
Indices: 2690--3130 Score: 220
Period size: 22 Copynumber: 19.9 Consensus size: 22
2680 ATCAAAGAGA
* *
2690 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
2712 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
2734 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
2756 TTA-CTAATATTTTATAGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
2778 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
2800 TTATCAAAAATTT-TTAGTGTGG
1 TTATC-AAAATTTCATAGTGAGG
2822 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
2844 TTAT-AAAAGTCTCAATTTCA-TGAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * * *
2869 AGTACCAAAATTTGATAG-AAGA
1 -TTATCAAAATTTCATAGTGAGG
* * * *
2891 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
2912 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
2936 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
**
2958 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* **
2980 TTATCAAAATTTCAAAGCAAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
3002 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
3024 TTATCATAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
3046 TCAACAAAATTTTATAGAGATG
1 TTATCAAAATTTCATAGTGAGG
** *
3068 TTATCAAAATTTCATAAAGAGT
1 TTATCAAAATTTCATAGTGAGG
* * * * *
3090 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
**
3112 TTGCCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
3131 GTATTTCTGG
Statistics
Matches: 319, Mismatches: 75, Indels: 50
0.72 0.17 0.11
Matches are distributed among these distances:
20 9 0.03
21 40 0.13
22 221 0.69
23 16 0.05
24 6 0.02
25 16 0.05
26 7 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:3444 original size:172 final size:170
Alignment explanation
Indices: 3141--3456 Score: 367
Period size: 172 Copynumber: 1.8 Consensus size: 170
3131 GTATTTCTGG
** *
3141 GGAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAGTTTCATAAGAGTGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATAGGATAGTTTTCAAAATTTCATAAGAGTGTTATCAAAATTTCATA
3206 GTATGTAAATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTATAAAAAAATCAT
66 GTATGTAAATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTATAAAAAAATCAT
3271 AG-GGAGGTTATCAAAATTTGTAATTATCAAGATTTCATAA
131 AGCGG-GGTTATCAAAATTTGTAATTATCAAGATTTCATAA
* * * *
3311 GGAGGTTTATCAAAATTTTATAGGATGGTTTATCAAAATTTCATAGCGAG-GTTATCACAATTTC
1 GGAGG-TTATCAAAATTTCATAGGATAGTTT-TCAAAATTTCATA-AGAGTGTTATCAAAATTTC
* * * * * *
3375 ATAGTGTG-ATTATCAACATTTCA-AGGTGTGATT-ACTAACAA-TTCAT-ATGGAGGTTTTTAA
63 ATAGTATGTA-AATCAAAATTTCATAGG-GAGATTAAC-AA-AATTTCATAAT-GAGGTTATAAA
**
3435 ATTATCATAGCGGGGTTATCAA
123 AAAATCATAGCGGGGTTATCAA
3457 TATATCATAT
Statistics
Matches: 122, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
170 5 0.04
171 29 0.24
172 81 0.66
173 7 0.06
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (170 bp):
GGAGGTTATCAAAATTTCATAGGATAGTTTTCAAAATTTCATAAGAGTGTTATCAAAATTTCATA
GTATGTAAATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTATAAAAAAATCAT
AGCGGGGTTATCAAAATTTGTAATTATCAAGATTTCATAA
Found at i:3520 original size:45 final size:45
Alignment explanation
Indices: 3448--3535 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
3438 ATCATAGCGG
* * *
3448 GGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGTT
* *
3493 GGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 GGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
3536 AGGTCTTCAA
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:0.11, G:0.18, T:0.38
Consensus pattern (45 bp):
GGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGTT
Found at i:3650 original size:22 final size:22
Alignment explanation
Indices: 3143--3659 Score: 195
Period size: 22 Copynumber: 23.7 Consensus size: 22
3133 ATTTCTGGGG
**
3143 AGGTTATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG-GA
* * *
3166 A-GTTTTCAAAGTTTCATAAG-
1 AGGTTATCAAAATTTCATAGGA
*
3186 AGTGTTATCAAAATTTCATA-GT
1 AG-GTTATCAAAATTTCATAGGA
* * *
3208 ATGTAAATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * *
3231 AGATTAACAAAATTTCATAATG-
1 AGGTTATCAAAATTTCAT-AGGA
* ** *
3253 AGGTTATAAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATAGGA
*
3275 AGGTTATCAAAA-TT--T-GTA
1 AGGTTATCAAAATTTCATAGGA
*
3293 A--TTATCAAGATTTCATAAGG-
1 AGGTTATCAAAATTTCAT-AGGA
*
3313 AGGTTTATCAAAATTTTATAGGA
1 AGG-TTATCAAAATTTCATAGGA
*
3336 TGGTTTATCAAAATTTCATAGCG-
1 AGG-TTATCAAAATTTCATAG-GA
*
3359 AGGTTATCACAATTTCATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* * *
3381 TGATTATCAACATTTCA-AGG-
1 AGGTTATCAAAATTTCATAGGA
*
3401 TGTGATTA-CTAACAA-TTCATATGG-
1 AG-G-TTATC-AA-AATTTCATA-GGA
**
3425 AGGTT-TTTAAATTATCATAGCG-
1 AGGTTATCAAAATT-TCATAG-GA
* * *
3447 GGGTTATCAATATATCATATGG-
1 AGGTTATCAAAATTTCATA-GGA
* * *
3469 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATAG-GA
* *
3492 TGGTTATCAAAATTTCATTGGGA
1 AGGTTATCAAAATTTCA-TAGGA
3515 A-GTTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
**
3536 AGGTCT-TCAAAA-TTCATTAAAA
1 AGGT-TATCAAAATTTCA-TAGGA
* * *
3558 AGGTTAACAAAATTTCGTAAGA
1 AGGTTATCAAAATTTCATAGGA
** * **
3580 AGGTTAAAAAAATTTTA-AAAA
1 AGGTTATCAAAATTTCATAGGA
* * *
3601 AGGTTCTCAAAATTCCATAGTA
1 AGGTTATCAAAATTTCATAGGA
** *
3623 TCGTTATTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
3645 AGGTTATCAAAATTT
1 AGGTTATCAAAATTT
3660 TATAAAGAAG
Statistics
Matches: 372, Mismatches: 82, Indels: 81
0.70 0.15 0.15
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
19 2 0.01
20 7 0.02
21 37 0.10
22 241 0.65
23 67 0.18
24 6 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:5277 original size:22 final size:22
Alignment explanation
Indices: 5252--5368 Score: 105
Period size: 22 Copynumber: 5.4 Consensus size: 22
5242 TGGAGTAATC
5252 AAAATTTCATAGGGAGGTTATT
1 AAAATTTCATAGGGAGGTTATT
* * *
5274 AAAATTTCATATGAAGGTTATC
1 AAAATTTCATAGGGAGGTTATT
* *
5296 AAAATTTGATAGGTAGGTTATT
1 AAAATTTCATAGGGAGGTTATT
* **
5318 GAAATTTCATAGTTTA-GTT-TT
1 AAAATTTCATAG-GGAGGTTATT
*
5339 CAAAATTTCATAGGG-GGTTATC
1 -AAAATTTCATAGGGAGGTTATT
*
5361 AGAATTTC
1 AAAATTTC
5369 CGTATGTAGA
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
21 12 0.16
22 62 0.82
23 2 0.03
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGTTATT
Found at i:5279 original size:44 final size:43
Alignment explanation
Indices: 5225--5400 Score: 169
Period size: 44 Copynumber: 4.1 Consensus size: 43
5215 ATTAGAAAGT
* * * *
5225 TTATTTAAATTTTATTATGGAGTAATCAAAATTTCATAGGGAGG
1 TTATTAAAATTTCA-TATGTAGTTATCAAAATTTCATAGGGAGG
* * *
5269 TTATTAAAATTTCATATGAAGGTTATCAAAATTTGATAGGTAGG
1 TTATTAAAATTTCATATGTA-GTTATCAAAATTTCATAGGGAGG
* * *
5313 TTATTGAAATTTCATAGTTTAGTTTTCAAAATTTCATAGGG-GG
1 TTATTAAAATTTCATA-TGTAGTTATCAAAATTTCATAGGGAGG
* * * *
5356 TTATCAGAATTTCCGTATGTAG--ATCAAAATTTCATAGGGAAG
1 TTATTAAAATTT-CATATGTAGTTATCAAAATTTCATAGGGAGG
5398 TTA
1 TTA
5401 ACAGAATTTC
Statistics
Matches: 109, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
41 16 0.15
42 4 0.04
43 20 0.18
44 67 0.61
45 2 0.02
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (43 bp):
TTATTAAAATTTCATATGTAGTTATCAAAATTTCATAGGGAGG
Found at i:7328 original size:44 final size:44
Alignment explanation
Indices: 7202--7397 Score: 207
Period size: 44 Copynumber: 4.5 Consensus size: 44
7192 TTTCACTTGT
* * * *
7202 AGGTTATCAAAATTCCATTGGATGGTTATCAAAATTTTATTGGG
1 AGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTTATAGGG
* * *
7246 AGGTTATCGAAATTTTATA-G-AGGTTTTCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTTATAGGG
* * *
7288 AGGTTAACAAAATTTCATAGGAAGGTTATCGAAATTTTATAGAG
1 AGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTTATAGGG
* * * *
7332 AGGTTTTCAAAATTTCATAGGGAGGTTAACAAAATTTTCATAGTG
1 AGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTT-ATAGGG
* ** *
7377 TGACTATCATAATTTCATAGG
1 AGGTTATCAAAATTTCATAGG
7398 GAGATTATAA
Statistics
Matches: 125, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
42 35 0.28
43 2 0.02
44 67 0.54
45 21 0.17
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTTATAGGG
Found at i:7368 original size:22 final size:22
Alignment explanation
Indices: 7202--7414 Score: 182
Period size: 22 Copynumber: 9.7 Consensus size: 22
7192 TTTCACTTGT
* *
7202 AGGTTATCAAAATTCCAT-TGG
1 AGGTTATCAAAATTTCATAGGG
* *
7223 ATGGTTATCAAAATTTTATTGGG
1 A-GGTTATCAAAATTTCATAGGG
* *
7246 AGGTTATCGAAATTTTATA--G
1 AGGTTATCAAAATTTCATAGGG
* *
7266 AGGTTTTCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGGG
* *
7288 AGGTTAACAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGG
* * *
7310 AGGTTATCGAAATTTTATAGAG
1 AGGTTATCAAAATTTCATAGGG
*
7332 AGGTTTTCAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGGG
* *
7354 AGGTTAACAAAATTTTCATAGTG
1 AGGTTATCAAAA-TTTCATAGGG
* ** *
7377 TGACTATCATAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGGG
*
7399 AGATTAT-AACAATTTC
1 AGGTTATCAA-AATTTC
7415 GTAGTGTGGT
Statistics
Matches: 154, Mismatches: 32, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
20 18 0.12
21 2 0.01
22 115 0.75
23 19 0.12
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGG
Found at i:8508 original size:42 final size:44
Alignment explanation
Indices: 8457--8550 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
8447 AGTGCATTAC
* *
8457 CTAA-ATTCTA-C-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAA
8498 CTAATATTCTACTCTTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTAC-CTTCCATCTCTAGATAATTCATCAAAATAAAA
8543 CTAATATT
1 CTAATATT
8551 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 36 0.77
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:9437 original size:107 final size:105
Alignment explanation
Indices: 9326--9590 Score: 392
Period size: 107 Copynumber: 2.5 Consensus size: 105
9316 TATTTTAGAT
*
9326 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCTCAAACTAAAATTTTATTTTTAT
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCC-CAAATTAAAATTTTATTTTTA-
*
9391 TTTAAGGGTAAATTTTAAAT-TTAATAATTTATTGTTATAGGG
64 TTTAAGGGTAAA-TTCAAATATTAATAATTTATTGTTATAGGG
*
9433 TTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTAT
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTAT
* *
9498 TTAAGGGTAAATTCCATTATTAATAATTTATTGTTATAGGG
65 TTAAGGGTAAATTCAAATATTAATAATTTATTGTTATAGGG
* * * *
9539 -TCTAGAAATAAAATATATAACTAA-TTAACTAAGTTTAGTCCAAATTAAAATT
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATT
9591 AAAATTTAAT
Statistics
Matches: 146, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
103 13 0.09
104 13 0.09
105 25 0.17
106 34 0.23
107 59 0.40
108 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (105 bp):
TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATT
TAAGGGTAAATTCAAATATTAATAATTTATTGTTATAGGG
Found at i:13081 original size:29 final size:29
Alignment explanation
Indices: 13048--13106 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
13038 ACCTACTTGG
*
13048 ATTATTATATGCTTTAAGAACATATGATC
1 ATTATTATATGCTTTAAGAACATAGGATC
13077 ATTATTATATGCTTTAAGAACATAGGATC
1 ATTATTATATGCTTTAAGAACATAGGATC
13106 A
1 A
13107 ACTGATGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
ATTATTATATGCTTTAAGAACATAGGATC
Found at i:13416 original size:44 final size:45
Alignment explanation
Indices: 13343--13427 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
13333 ATTTTGTATG
*
13343 GCGAAGGCTTGTTATTCCTTGTTGCCGGATGATTTGACAGAGGAA
1 GCGAAAGCTTGTTATTCCTTGTTGCCGGATGATTTGACAGAGGAA
*
13388 GCGAAAGCTT-TTA-TCCATTGTTGTCGGATGATTTGACAGA
1 GCGAAAGCTTGTTATTCC-TTGTTGCCGGATGATTTGACAGA
13428 TCCTCAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 3 0.08
44 25 0.68
45 9 0.24
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (45 bp):
GCGAAAGCTTGTTATTCCTTGTTGCCGGATGATTTGACAGAGGAA
Found at i:13466 original size:45 final size:45
Alignment explanation
Indices: 13405--13490 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
13395 CTTTTATCCA
*
13405 TTGTTGTCGGATGATTTGACAGATCCTCAAAGAAGCGGTTGTATC
1 TTGTTGCCGGATGATTTGACAGATCCTCAAAGAAGCGGTTGTATC
* * *
13450 TTGTTGCCGGATGATTTGACAGATGCTCTAAGTAGCGGTTG
1 TTGTTGCCGGATGATTTGACAGATCCTCAAAGAAGCGGTTG
13491 GGTTGGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (45 bp):
TTGTTGCCGGATGATTTGACAGATCCTCAAAGAAGCGGTTGTATC
Found at i:14909 original size:17 final size:17
Alignment explanation
Indices: 14883--14918 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
14873 TTAATCTTTT
*
14883 TTTTTTTGAAAATATTA
1 TTTTTGTGAAAATATTA
14900 TTTTTGTGAAAATATTA
1 TTTTTGTGAAAATATTA
14917 TT
1 TT
14919 ACTATAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTTTGTGAAAATATTA
Found at i:16374 original size:23 final size:23
Alignment explanation
Indices: 16344--16389 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16334 GAAAAATCCG
16344 ACGCAAATGCGCGGAGATAATAT
1 ACGCAAATGCGCGGAGATAATAT
16367 ACGCAAATGCGCGGAGATAATAT
1 ACGCAAATGCGCGGAGATAATAT
16390 CTAGTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (23 bp):
ACGCAAATGCGCGGAGATAATAT
Found at i:17671 original size:2 final size:2
Alignment explanation
Indices: 17664--17695 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17654 AATCACTTAC
17664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17696 CTAGATTCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18525 original size:43 final size:44
Alignment explanation
Indices: 18473--18567 Score: 133
Period size: 46 Copynumber: 2.2 Consensus size: 44
18463 AGTGCATTGC
* *
18473 CTAA-ATTCTACT-T-CATCTCTAGGTAATTTATCAAAATAGAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATA-AAG
18515 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
18560 CTAATATT
1 CTAATATT
18568 AATTGTTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
42 4 0.09
43 8 0.17
45 12 0.26
46 23 0.49
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Done.