Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014929.1 Corchorus olitorius cultivar O-4 contig14962, 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: 89678
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:8646 original size:17 final size:17
Alignment explanation
Indices: 8624--8659 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
8614 TCTGAACTTT
*
8624 AAATTAGAAAGTTTTAG
1 AAATTAGAAAGTTTGAG
*
8641 AAATTAGAATGTTTGAG
1 AAATTAGAAAGTTTGAG
8658 AA
1 AA
8660 GGCGACACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (17 bp):
AAATTAGAAAGTTTGAG
Found at i:9031 original size:27 final size:28
Alignment explanation
Indices: 8991--9046 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
8981 TCCATTCTCG
* *
8991 AGCTCAAGACCTTACTT-AAGGAGAAAT
1 AGCTCAAGAACTTACTTAAAAGAGAAAT
*
9018 AGCTCGAGAACTTACTTAAAAGAGAAAT
1 AGCTCAAGAACTTACTTAAAAGAGAAAT
9046 A
1 A
9047 ATATCGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (28 bp):
AGCTCAAGAACTTACTTAAAAGAGAAAT
Found at i:9088 original size:14 final size:14
Alignment explanation
Indices: 9069--9096 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9059 TTGAACTAAC
9069 CACTTATTAGTAAA
1 CACTTATTAGTAAA
9083 CACTTATTAGTAAA
1 CACTTATTAGTAAA
9097 TAATAGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
CACTTATTAGTAAA
Found at i:16665 original size:2 final size:2
Alignment explanation
Indices: 16658--16691 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16648 TATTACAAGA
16658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16692 GTTAATCACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24408 original size:18 final size:18
Alignment explanation
Indices: 24363--24414 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
24353 AAGCTATTAT
24363 CTTGTTTGTTTGTTTTCAA
1 CTTGTTTG-TTGTTTTCAA
* *
24382 CCTGATTGTTG-TTTCAGA
1 CTTGTTTGTTGTTTTCA-A
*
24400 CTTGTTTGTTATTTT
1 CTTGTTTGTTGTTTT
24415 GCAGTACTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 5 0.19
18 12 0.46
19 9 0.35
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.60
Consensus pattern (18 bp):
CTTGTTTGTTGTTTTCAA
Found at i:26691 original size:15 final size:15
Alignment explanation
Indices: 26673--26702 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26663 ATAATGGATC
*
26673 CGGTTCTTTCAGTTG
1 CGGTGCTTTCAGTTG
26688 CGGTGCTTTCAGTTG
1 CGGTGCTTTCAGTTG
26703 TTTTGGGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.20, G:0.30, T:0.43
Consensus pattern (15 bp):
CGGTGCTTTCAGTTG
Found at i:35819 original size:335 final size:330
Alignment explanation
Indices: 33842--37556 Score: 3660
Period size: 335 Copynumber: 11.3 Consensus size: 330
33832 AACCCTACAA
* * *
33842 TTTTGCATGATTTTTGGCAGAAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAGTC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * * * **
33907 GTATCGAATTTAAGGATTTGATTTCACGAGCATTTGAATCTTGTTTCGATTTAATTATATTTAAA
66 GCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAAA
* *
33972 TTC--GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAACACCCTTCAATTTTTTTTGGCGTTG
131 TTCGGGAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGTCGTTG
* * * * *
34035 AACTATATATATTTTCTAAGTATTGTGGCAAAAAAATTGAGGAAAAAC-TTTCCGTATCAGTTTT
195 AACTATATATTTTTTCTGAGTATTGTGG-TAAAAAATTGAGGAAAAACTTTTCGGT-T-AGTCTT
* * * ***
34099 TCTAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGATTTTGGC-AAAAA-GCTCACCTCGA
257 TC-AAAATTTTAGCCGAAATCGTGTACT-ATCATCACAGTTTTTGGCTAAAAACG-TGTTC-CGA
** **
34162 GGCCCTAGCTTTG
318 GGCCCCGGCTCAG
34175 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * * * ** * *
34240 ACATTGAACTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGAATCGATTTAATTCAG-ATTAA
66 GCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAA-TAAGAAATAA
* * * * *
34304 ATTCGGG-----AA--AAAATCGATATTAGAAACGTG-AAAACTCTTCAATTTTTTTTGGCATTG
130 ATTCGGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGTCGTTG
* *
34361 AACTATATATTTTTTCTGAGTATTGTGGTAAAAAATT-AAGAAAAATTTTTC-G---G-C--TC-
195 AACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTCGGTTAGTCTTTCA
* * *
34417 AATTTTTAGCCGAAATCGTGTAC---CATCAC-GATTTTTGGCTAAAAACGAGTTTCGAGGCCCC
260 AAATTTTAGCCGAAATCGTGTACTATCATCACAG-TTTTTGGCTAAAAACGTGTTCCGAGGCCCC
34478 GGCTCAG
324 GGCTCAG
* * *
34485 TTTTGCATGATTTTTGGCAGAAAGACTTCTTGGAATATCTATATTCATCTAACTAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * *
34550 GCATTGGATTTGAGAATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
66 GCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAAA
* * * *
34615 TTCGGGGAAAAAAAAGGGAAAACGATATTAGAAGCGTAAAAAAACCCTACAATTTTTTATTGTCT
131 TTC-GGG-AAAAAAAGGAAAAACGATATTAGAAGCGT-GAAAAACCCTTCAATTTTTT-TTGTCG
* *
34680 TTGAATTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTCGGGTTAGTTT
192 TTGAACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTC-GGTTAGTCT
* *
34745 TTGCAAAATTTTAGTCGAAATCGTGTACTAT-ATCATAAGTTTTTGGCTAAAAACGTGTTCCG-G
256 TT-CAAAATTTTAGCCGAAATCGTGTACTATCATCA-CAGTTTTTGGCTAAAAACGTGTTCCGAG
*
34808 GACCCCGACTCAG
319 G-CCCCGGCTCAG
* * * * * **
34821 TTTGGCATGATTTTAGGTAGATAGACTCCTTTG-AATATCTATATTCATGTAATTAAATCTCAGC
1 TTTTGCATGATTTTTGGCAGAAAGACTCC-TTGAAATATCTATATTCATCTAACCAAATCTCAGC
** * * * * * * * * *
34885 CATATTGGATCTAAGGATTTGTTTTTTCGAGAATCTAAATTTTGTTTCGATTTAATTACAAATAA
65 CGCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAA
* * *
34950 ATTC-GGAAAAAAAGGAAAAAACAATATTAGAAGCGTGAAAAACCCATCAATTTTGTTTGGT-GT
130 ATTCGGGAAAAAAAGG-AAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTT-TTTTGTCGT
* * * *
35013 TGAACTATATATTTTTTCTGAGTATTGTGG-CAAAAATTAAGAAAAAAATTTTC-G---G-C--T
193 TGAACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTCGGTTAGTCTTT
* * * *
35070 C-AATTTTTAGCCGAAATCGTGTAC-A-CATCACGGTTTTTGGCTAAAAAACGAGTTTCGAGGCC
258 CAAAATTTTAGCCGAAATCGTGTACTATCATCACAGTTTTTGGCT-AAAAACGTGTTCCGAGGCC
35132 CCGGCTCAG
322 CCGGCTCAG
* * * *
35141 TTTTGCATGATTGTTT-ACAGAAAAACGCCTTGAAATATCTATATTCATCTAACCAAATCTCAGT
1 TTTTGCATGATT-TTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
* * * * * **
35205 TG-TTTCGAATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATTATATTTA
65 CGCATT-GGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATA
*
35269 AATTC--GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGT
129 AATTCGGGAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGTCGT
* * * * * * * *
35332 TGAACTATATATATTTTCTAAGTATTGTGGCAAAAAAATTGAGGAAAATCCTTCCGTGTCAGTTT
193 TGAACTATATATTTTTTCTGAGTATTGTGG-TAAAAAATTGAGGAAAAACTTTTCG-GTTAG-TC
* * * * * *
35397 TTTTAAAATTTTAGCCGAAATCGTGTATTAACCATAACAGATTTTGGC-AAAAA-GCT-TACCTC
255 TTTCAAAATTTTAGCCGAAATCGTGTACT-ATCATCACAGTTTTTGGCTAAAAACG-TGT-TC-C
* **
35459 GCGGCCCCGGCTTTG
316 GAGGCCCCGGCTCAG
* *
35474 TTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTATATTCATCTTACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * **
35539 GCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTGAATAAGAACCAAA
66 GCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAAA
* * * * *
35604 TTCGGGTAAAAAAAGGGAAAACGATATTAGTACCGTAAAAAACCCTAT-AATTTTTTATTGTCTT
131 TTCGGG-AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCT-TCAATTTTTT-TTGTCGT
* *
35668 TGAATTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAATAACTTTTCGGGTTAGTCTT
193 TGAACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTC-GGTTAGTCTT
* *
35733 TGCAAAATTTTAGTCGAAATCGTGTACTATCTATCATAGTTTTTGGCTAAAAACGTGTTCCG-GG
257 T-CAAAATTTTAGCCGAAATCGTGTACTATC-ATCACAGTTTTTGGCTAAAAACGTGTTCCGAGG
* *
35797 ACACCGACTCAG
320 -CCCCGGCTCAG
* * * * **
35809 TTTGGCATGATTTTAGGTAGAAAGACTCCTTTG-AATATCTATATTCATGTAATTAAATCTCAGC
1 TTTTGCATGATTTTTGGCAGAAAGACTCC-TTGAAATATCTATATTCATCTAACCAAATCTCAGC
** * * * * * * *
35873 CATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAATTAA
65 CGCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAA
* *
35938 ATTC-GGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTGTTTTGGCGTTG
130 ATTCGGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGTCGTTG
* * * * *
36001 AACTATATATTTTTTCTGAGTATTGTCGCAAAAAATTAAGAAAAAATTTTTC-G---G-C--TC-
195 AACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTCGGTTAGTCTTTCA
* * ** * *
36058 AATTTTTAGCCGAAATC--GTA-TACCATCAC-GATTTTTGGGAAAAAACGAGTTTCGAGGCCCC
260 AAATTTTAGCCGAAATCGTGTACTATCATCACAG-TTTTTGGCTAAAAACGTGTTCCGAGGCCCC
*
36119 AGCTCAG
324 GGCTCAG
* *
36126 TTTTGCATGATTTTTGGCGGAAAGACTCCTTGAAATATCTATATTCATCTTACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * *
36191 GCATTGGATTTGAGAATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
66 GCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAAA
* * * * *
36256 TTCGGGAAAAAAAGGGAAACCGATATTAGAAGCGTAAAAAACCCTACAATTTTTTATTGTCTTTG
131 TTCGGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTT-TTGTCGTTG
* * * * * *
36321 AATTATATAATTCTTCTGAGTATTGTGGTAAAAAATTGAGGAATAACCTTTCGGGTTAGTTTTTT
195 AACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTC-GGTTAG-TCTTT
* * *
36386 GCAAAACTTTAGCCGAAATCGTGTACTATCATCATAGTTTTTGGCTAAAAACGTGTTCCGAGACC
258 -CAAAATTTTAGCCGAAATCGTGTACTATCATCACAGTTTTTGGCTAAAAACGTGTTCCGAGGCC
*
36451 CCGACTCAG
322 CCGGCTCAG
* * * * * * *
36460 TTTGGCATGACTTTTGGTAGATAGACTCCTTTG-AATATCTATATTCTTGTAATCAAATCTCAGC
1 TTTTGCATGATTTTTGGCAGAAAGACTCC-TTGAAATATCTATATTCATCTAACCAAATCTCAGC
** * * * * * * * *
36524 CATATTGGATCTAAGAATTTGTTTTTACGAGCATGTAAATTTTGTTTCGATTTAATTACAAATAA
65 CGCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAA
* * *
36589 ATTCGGAAAAAAAAAGGAAAAACAATATTAGAAGCGTG-AAAACCCTTCAA-TTTTTTTGGCGTT
130 ATTCGG-GAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGTCGTT
* * * *
36652 GAACTATATATTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAAATTTTC---T-G-C--T
194 GAACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAG-GAAAAACTTTTCGGTTAGTCTTT
* * * * *
36710 C-AATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAACGAGTTTCGAGGC
258 CAAAATTTTAGCCGAAATCGTGTACT-ATCATCACAGTTTTTGGCT-AAAAACGTGTTCCGAGGC
36774 CCCGGCTCAG
321 CCCGGCTCAG
* * * **
36784 TTATGCATGATTTTTGGCAGAAAAACTCCTTGAAATACCTATATTCATCTAACCAAATCTCAGTT
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * *
36849 G-TTTCGAATTTAAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAA
66 GCATT-GGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAA
* * * * *
36913 ATTCGGGGAAAAAATGGGAAAACGATATTAGAAGCGT-AAAAACCCTACAATTTTTTATTCTCTT
130 ATTC-GGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTT-TTGTCGT
* * * * * * * * *
36977 TGAATTATATGTATTTTATGAGTATTCTGGTAAAAAATTGAGAAAAAAATTTTAGGGTTAGTTTT
193 TGAACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTT-CGGTTAGTCTT
* * * * *
37042 TACAAAAATTTAGCTGAAATCGTGTACTATCTATCACAGTTTTTGGCTAAAAAACGAGTTTCAAG
257 T-CAAAATTTTAGCCGAAATCGTGTACTATC-ATCACAGTTTTTGGCT-AAAAACGTGTTCCGAG
37107 GCCCCGGCTCAG
319 GCCCCGGCTCAG
* * * *
37119 TTTTGCATGATTTTTGGCAAAAAAAACTCCTTGAAATATCTATATTCATCTAACCATATCTCAGT
1 TTTTGCATGATTTTTGGC-AGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
* * * * * **
37184 TGTATCGAATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAA-ATATATTTA
65 CGCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATA-AGAAATA
* * * * * *
37248 AATT-TGAAAAAAAATGGAAAACCAATATTAGAAGCGTGGAAAACCCTGCAATTTTTTTTGGT-G
129 AATTCGGGAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTT-GTCG
* * * * * * *
37311 CTGAACTATATATATTTTCTAAGTATTGTGGCAAAAAATTGAGGAAAAACTTTCCGTGTCAGTTT
192 TTGAACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTCG-GTTAGTCT
* * * * *
37376 TTCTAAAATTTTAGCCGAAATCGTGTACAAACCATCACAGATTTTAG-TAAAAA-GCTCG-CCTC
256 TTC-AAAATTTTAGCCGAAATCGTGTAC-TATCATCACAGTTTTTGGCTAAAAACG-T-GTTC-C
**
37438 GAGGCCCCGGCTTTG
316 GAGGCCCCGGCTCAG
*
37453 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAAACAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * ** * *
37518 ACATTGGACTTAAATATTTGTTTTTACGAGCATCTGAAT
66 GCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAAT
37557 TATAAGCAAG
Statistics
Matches: 2783, Mismatches: 462, Indels: 274
0.79 0.13 0.08
Matches are distributed among these distances:
309 4 0.00
310 136 0.05
311 8 0.00
312 1 0.00
314 22 0.01
316 6 0.00
317 141 0.05
318 50 0.02
319 114 0.04
320 176 0.06
321 72 0.03
322 68 0.02
323 37 0.01
324 171 0.06
325 33 0.01
326 92 0.03
327 19 0.01
328 2 0.00
329 5 0.00
330 5 0.00
331 110 0.04
332 87 0.03
333 415 0.15
334 252 0.09
335 441 0.16
336 309 0.11
337 7 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (330 bp):
TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
GCATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATAAA
TTCGGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGTCGTTGA
ACTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAACTTTTCGGTTAGTCTTTCAA
AATTTTAGCCGAAATCGTGTACTATCATCACAGTTTTTGGCTAAAAACGTGTTCCGAGGCCCCGG
CTCAG
Found at i:38462 original size:322 final size:321
Alignment explanation
Indices: 37581--38618 Score: 1189
Period size: 322 Copynumber: 3.2 Consensus size: 321
37571 CTCTTCAATT
* * *
37581 TTTTTTTTGGCGTTGAACTATATTTTTTTTCTGAGTATTGTAGCAAAAAATTAAGAAAACATTTT
1 TTTTTATTGGCGTTGAACTATATATTTTTTCTGAGTATTGTAGCAAAAAATTAAGAAAAAATTTT
* *
37646 TCGAGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAACGAGTTTC
66 TCG-GTCATTTTTTAGCCGAAATCGTGTAC--ACCATCACGGTTTTTGGATAAAAAACGAGTTTC
* *
37711 GAGGCCCCGACTCTGTTTTGCATGATTTTTGATGGAAACACACCTTGAAATATCTATATTCATCT
128 GAGGCCCCGACTCAGTTTTGCATGATTTTTG-TGGAAACACTCCTTGAAATATCTATATTCATCT
*
37776 AAACAAATCTCAGCCGCAATGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGAT
192 AAACAAATCTCAGCCGCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGAT
*
37841 TTAATAAGAAACAAATTCGGGAAAAAAAATGGGAAAACGATATTAGAAGCATAAAAAAACCCTAC
257 TTAATAAGAAACAAATTCGGGAAAAAAAATGGGAAAACGATATTAGAAGCGT--AAAAACCCTAC
37906 AA
320 AA
* * * ** * * *
37908 TTTTTTATTGTC-TTAGAATTATATATTTTTTCTGAGTATTAATATAAAAAAATTGAGGAAAAAC
1 -TTTTTATTGGCGTT-GAACTATATATTTTTTCTGAGTATT-GTAGCAAAAAATTAAGAAAAAAT
* *
37972 TTTTCAGGTTAGTTTTTGCAAAAATTTGAGCCGAAATCGTGTACACTATCCATCACAGTTTTT-G
63 TTTTC-GGTCA---TTT-------TTT-AGCCGAAATCGTGT--AC-A-CCATCACGGTTTTTGG
* * * *
38036 ACT-AAAAACGTGTTCCG-GGACCCCGACTCAG-TTTGTCATGATTTTTGGTAGAAAGACTCCTT
112 A-TAAAAAACGAGTTTCGAGG-CCCCGACTCAGTTTTG-CATGATTTTT-GTGGAAACACTCC-T
* * * ** * * * *
38098 TG-AATATCTATATTTATGTAATA-AAACCTCAGCCATATTGGATCTAAGGATTTGTTTTTACGA
172 TGAAATATCTATATTCATCTAA-ACAAATCTCAGCCGCATTGGATTTGAGGATTTGATTTTACAA
* * * * * * *
38161 GCATCTAAATTTTGTTTCGATTTAATTAGAAA-AAATTCGGGAAAAAAAAAGGAAAAACAATATT
236 GCATTTGAATCTTGTTTCGATTTAATAAGAAACAAATTCGGGAAAAAAAATGGGAAAACGATATT
* * *
38225 AGAACCGTGAAAAACCGTTCAA
301 AGAAGCGT-AAAAACCCTACAA
* *
38247 TTTTT-TTGGCGTTGAACTATATATTTTTTTTGAGTATTGTGGCAAAAAATTAAGAAAAAAATTT
1 TTTTTATTGGCGTTGAACTATATATTTTTTCTGAGTATTGTAGCAAAAAATTAAG-AAAAAATTT
*
38311 TTCGCCTCATTTTTTAGCCGAAATCGTGTAC-CCATCACGGTTTTTGGATAAAAAACGAGTTTCG
65 TTCG-GTCATTTTTTAGCCGAAATCGTGTACACCATCACGGTTTTTGGATAAAAAACGAGTTTCG
* *
38375 AGGCCCCGGCTCAGTTTTGCATGATTTTTCGCGGAAACACTCCTTGAAATATCTATATTCATCTA
129 AGGCCCCGACTCAGTTTTGCATGATTTTT-GTGGAAACACTCCTTGAAATATCTATATTCATCTA
*
38440 ACCAAATCTCAGCCGCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATT
193 AACAAATCTCAGCCGCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATT
*
38505 TAATAAGAAACAAATTCGGG-AAAAAAATGGGAACACGATATTAGAAGCGTAAAATACCCTACAA
258 TAATAAGAAACAAATTCGGGAAAAAAAATGGGAAAACGATATTAGAAGCGTAAAA-ACCCTACAA
* * * * *
38569 TTTTTATTGTCTTTGAATTATATATTTTTTCTGAGTATTGTGGTAAAAAA
1 TTTTTATTGGCGTTGAACTATATATTTTTTCTGAGTATTGTAGCAAAAAA
38619 ATGAGGAAAA
Statistics
Matches: 585, Mismatches: 90, Indels: 75
0.78 0.12 0.10
Matches are distributed among these distances:
321 21 0.04
322 159 0.27
323 54 0.09
324 2 0.00
326 14 0.02
327 5 0.01
328 32 0.05
329 24 0.04
330 1 0.00
332 2 0.00
334 3 0.01
336 12 0.02
337 39 0.07
338 7 0.01
339 14 0.02
340 55 0.09
341 120 0.21
342 21 0.04
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (321 bp):
TTTTTATTGGCGTTGAACTATATATTTTTTCTGAGTATTGTAGCAAAAAATTAAGAAAAAATTTT
TCGGTCATTTTTTAGCCGAAATCGTGTACACCATCACGGTTTTTGGATAAAAAACGAGTTTCGAG
GCCCCGACTCAGTTTTGCATGATTTTTGTGGAAACACTCCTTGAAATATCTATATTCATCTAAAC
AAATCTCAGCCGCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAA
TAAGAAACAAATTCGGGAAAAAAAATGGGAAAACGATATTAGAAGCGTAAAAACCCTACAA
Found at i:38813 original size:39 final size:40
Alignment explanation
Indices: 38770--38847 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
38760 TGTTTTGGCG
*
38770 TTGAATTATATATTTTTTCTGAGTATTGT-GACAAAAATA
1 TTGAATTATATATTTTTCCTGAGTATTGTGGACAAAAATA
* *
38809 TTGAATTATATATTTTTCCTGATTATTGTGGCCAAAAAT
1 TTGAATTATATATTTTTCCTGAGTATTGTGGACAAAAAT
38848 TCAGAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 27 0.77
40 8 0.23
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (40 bp):
TTGAATTATATATTTTTCCTGAGTATTGTGGACAAAAATA
Found at i:41280 original size:68 final size:68
Alignment explanation
Indices: 41171--41306 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
41161 AGCGCTGAGT
41171 ACCATGATTATCACCACTACGTCGGAAAACAAAGTCAAAGCAACTTTGCTTCGGTTTTTACCTAT
1 ACCATGATTATCACCACTACGTCGGAAAACAAAGTCAAAGCAACTTTGCTTCGGTTTTTACCTAT
41236 TGC
66 TGC
41239 ACCATGATTATCACCACTACGTCGGAAAACAAAGTCAAAGCAACTTTGCTTCGGTTTTTACCTAT
1 ACCATGATTATCACCACTACGTCGGAAAACAAAGTCAAAGCAACTTTGCTTCGGTTTTTACCTAT
41304 TGC
66 TGC
41307 GATTATATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (68 bp):
ACCATGATTATCACCACTACGTCGGAAAACAAAGTCAAAGCAACTTTGCTTCGGTTTTTACCTAT
TGC
Found at i:48522 original size:45 final size:45
Alignment explanation
Indices: 48458--48594 Score: 213
Period size: 45 Copynumber: 3.0 Consensus size: 45
48448 CCAACCTTCT
* *
48458 CAACTTGAGCTCTTTGTGGCTCTTCAATAGCATTGATGGCTTCAG
1 CAACTTGAGCTCTATGTGGCTCTTCAATAGCATTGACGGCTTCAG
48503 CAACTTGAGCTCTATGTGGCTCTTCAATAGCATTGACGGCTTCAG
1 CAACTTGAGCTCTATGTGGCTCTTCAATAGCATTGACGGCTTCAG
* * *
48548 CAATCAT-AGCTCCATGTGGCTCTTCAATAGCATTGACGACTTCAG
1 CAA-CTTGAGCTCTATGTGGCTCTTCAATAGCATTGACGGCTTCAG
48593 CA
1 CA
48595 TCAATTTGAT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
45 84 0.98
46 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.31
Consensus pattern (45 bp):
CAACTTGAGCTCTATGTGGCTCTTCAATAGCATTGACGGCTTCAG
Found at i:72472 original size:14 final size:13
Alignment explanation
Indices: 72446--72479 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
72436 TACAATAAAG
72446 AAGG-AAAAAGAA
1 AAGGAAAAAAGAA
72458 AAGGAAAAAAGGAA
1 AAGGAAAAAA-GAA
72472 AAGGAAAA
1 AAGGAAAA
72480 GTCAAATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 5 0.25
14 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAGGAAAAAAGAA
Found at i:88700 original size:19 final size:19
Alignment explanation
Indices: 88676--88712 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
88666 CTGTTTAGTA
88676 ACTGTAAAGATGAGATTAC
1 ACTGTAAAGATGAGATTAC
* *
88695 ACTGTACAGATTAGATTA
1 ACTGTAAAGATGAGATTA
88713 GATACTGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (19 bp):
ACTGTAAAGATGAGATTAC
Done.