Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014132.1 Corchorus olitorius cultivar O-4 contig14165, 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: 76701
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:740 original size:322 final size:321
Alignment explanation
Indices: 120--1955 Score: 2525
Period size: 321 Copynumber: 5.7 Consensus size: 321
110 AACCATCAAT
*** ** *
120 AACGATATTGGAAGCGTG-AAAACACCTTCAATTTTTTTTTGAAGTTGAACAATATGTTTTGT-A
1 AACGATATTGGAAGCGTGAAAAAC-CCTTCAA-TTTTTTTTGGCTTTGAATTATATATTTTGTCA
* * * * * * *
183 GTGTTGTGTGGCAAAAAAAAATGAGAAGAAAGTTTTCTGG-CAACTTTTAGCGGAAATTGTGTAC
64 GAGTAGTGTGG---TAAAAAATGAGAA-AAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTA-
* * ** * *
247 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGAACCCCGGCTCATTTTTGCATGATTTTT
124 CTAACCATCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTT
**
312 GGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG-CACATTTCAATTTAAG
189 GGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCA-ATTTGGATTTAAG
* * * * * *
376 AATTTCTTTCTACGACCATCTGAATTTTGTTTCGATTTAATTACAAATAAATTCGAAAAAAAAAT
253 GATTTCTTT-TACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATT
441 GGAAA
317 GGAAA
* * * *** * *
446 AACAATATTGGAAGCCTGAAAACCCCTTCAATTTTTTTTGAAGTTGAACTATATGTTTTGT-AGA
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTGTCAGA
* * *
510 GTTGTATGGCAAAAAAATGAGAAGAAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTG-ACTAAC
66 GTAGTGTGG-TAAAAAATGAGAA-AAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAAC
* * *
574 CATCACGGTTTTCGGCTAAAATCGTGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
129 CATCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCAG
*
639 GAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTC
194 AAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTC
*
704 GTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAACTCGG-AAAAAATTGGAAA
259 -TTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATTGGAAA
*
767 AACGATATTGGAAGCGTGAAAAACCCTTCAA-TTTTTTTGGCTTTCAATTATATATTTTGTCAGA
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTGTCAGA
* * * *
831 GAAGTGTGGTTAAAAATGAGAAAAAGGTTTTCGGGTCAATTTTTAGCAGAAATTGTGCACTAACC
66 GTAGTGTGGTAAAAAATGAGAAAAA-GTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAACC
* * *
896 ATCACGGTTTTTGGCTAAAATCGCATTTCGGAGCCCCAGCTCAGTTTTGCATGATTTTTGGCAGG
130 ATCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCAGA
961 AAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCT
195 AAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCT
* *
1026 ATTTATGAGCATCTAAATTTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAAAATTGGAAA
260 -TTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATTGGAAA
* * *
1089 AACGATATTGGAATCGTGAAAAATCCTACAA-TTTTTTTGGCTTTGAATTATATATTTT-TCCAG
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTGT-CAG
* *
1152 AGTAGTGTGGTTAAAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCAGAAAACCGTGTACTAA
65 AGTAGTGTGGTAAAAAATGA-GAAAAAGTTTTCGGGTCAATTTTTAGCAG-AAATCGTGTACTAA
* * *
1217 CCATCACTGTTTTTAGCTATAAA-CGCGTTTCGGGGCCCCTGCTCAGTTTTGCATGATTTTTGGC
128 CCATCACGGTTTTTGGCTA-AAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGC
* ** *
1281 AGAAAGACTCCTTGAAATATCTATTTTCATATAACCAAATCTCAGCCAATTTGGATTTATTGATC
192 AGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATT
* * * * *
1346 TCTTTTCACGAGCATTTGAATCTT-TTTCGATTTAATTAAAAATAAATTCGG-AAAAAATATCGA
257 TCTTTT-ACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAT-TGGA
1409 AA
320 AA
*
1411 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTTTCAGA
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTGTCAGA
* * * * **
1476 GTGGTGTGGCAAAAATTGAGAAAAAATTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAATGA
66 GTAGTGTGGTAAAAAATGAGAAAAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAACCA
* * *
1541 TCACGGTTTTTGGCTAAAAACACGTTTCGGGGCCCCAGCTCAGTTTTGCATAATTTTTGGCAGAA
131 TCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCAGAA
* *
1606 AGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCAAATTTCGATTTAAGGATTTCGT
196 AGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTC-T
1671 TTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATTGG-AA
260 TTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATTGGAAA
*
1732 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTCAATTATATATTTT-TCCAG
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTGT-CAG
** *
1796 AGTAGTGTGGTTTAAAATGAGAAAAAAGTTTTCAGGTCAATTTTTAGCAGAAATCGTGTACTAAC
65 AGTAGTGTGGTAAAAAATGAG-AAAAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAAC
* *
1861 CATCACTGTTTTTGGCTAAAAAAT-GCGTTTCGGGGCCCCTGCTCAGTTTTGCATGATTTTTGGC
129 CATCACGGTTTTTGGCT--AAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGC
* *
1925 AGAAAGACTTCTTGAAATATCTATTTTCATA
192 AGAAAGACTCCTTGAAATATCTATATTCATA
1956 CTATATAATT
Statistics
Matches: 1365, Mismatches: 120, Indels: 53
0.89 0.08 0.03
Matches are distributed among these distances:
319 3 0.00
320 69 0.05
321 453 0.33
322 450 0.33
323 298 0.22
324 26 0.02
325 39 0.03
326 23 0.02
327 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (321 bp):
AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTGTCAGA
GTAGTGTGGTAAAAAATGAGAAAAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAACCA
TCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCAGAA
AGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTT
TTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATTGGAAA
Found at i:960 original size:321 final size:319
Alignment explanation
Indices: 120--1955 Score: 2501
Period size: 322 Copynumber: 5.7 Consensus size: 319
110 AACCATCAAT
*** ** *
120 AACGATATTGGAAGCGTG-AAAACACCTTCAATTTTTTTTTGAAGTTGAACAATATGTTTTGT-A
1 AACGATATTGGAAGCGTGAAAAAC-CCTTCAA-TTTTTTTTGGCTTTGAATTATATATTTT-TCA
* * ** * * * *
183 GTGTTGTGTGGCAAAAAAAAATGAGAAGAAAGTTTTCTGG-CAACTTTTAGCGGAAATTGTGTAC
63 GAGTAGTGTGG---TTAAAAATGAGAA-AAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTA-
* * ** * *
247 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGAACCCCGGCTCATTTTTGCATGATTTTT
123 CTAACCATCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTT
**
312 GGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG-CACATTTCAATTTAAG
188 GGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCA-ATTTGGATTTAAG
* * * * * *
376 AATTTCTTTCTACGACCATCTGAATTTTGTTTCGATTTAATTACAAATAAATTCGAAAAAAAAAT
252 GATTTCTTT-TACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCG-GAAAAAATT
441 GGAAA
315 GGAAA
* * * *** * *
446 AACAATATTGGAAGCCTGAAAACCCCTTCAATTTTTTTTGAAGTTGAACTATATGTTTTGT-AGA
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTT-TCAGA
* * **
510 GTTGTATGGCAAAAAAATGAGAAGAAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTG-ACTAAC
65 GTAGTGTGG-TTAAAAATGAGAA-AAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAAC
* * *
574 CATCACGGTTTTCGGCTAAAATCGTGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
128 CATCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCAG
*
639 GAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTC
193 AAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTC
*
704 GTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAACTCGGAAAAAATTGGAAA
258 -TTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATTGGAAA
*
767 AACGATATTGGAAGCGTGAAAAACCCTTCAA-TTTTTTTGGCTTTCAATTATATATTTTGTCAGA
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTT-TCAGA
* * *
831 GAAGTGTGGTTAAAAATGAGAAAAAGGTTTTCGGGTCAATTTTTAGCAGAAATTGTGCACTAACC
65 GTAGTGTGGTTAAAAATGAGAAAAA-GTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAACC
* * *
896 ATCACGGTTTTTGGCTAAAATCGCATTTCGGAGCCCCAGCTCAGTTTTGCATGATTTTTGGCAGG
129 ATCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCAGA
961 AAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCT
194 AAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCT
* *
1026 ATTTATGAGCATCTAAATTTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAAAATTGGAAA
259 -TTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAATTGGAAA
* * *
1089 AACGATATTGGAATCGTGAAAAATCCTACAA-TTTTTTTGGCTTTGAATTATATATTTTTCCAGA
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTT-CAGA
*
1153 GTAGTGTGGTTAAAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCAGAAAACCGTGTACTAAC
65 GTAGTGTGGTTAAAAATGA-GAAAAAGTTTTCGGGTCAATTTTTAGCAG-AAATCGTGTACTAAC
* * *
1218 CATCACTGTTTTTAGCTATAAA-CGCGTTTCGGGGCCCCTGCTCAGTTTTGCATGATTTTTGGCA
128 CATCACGGTTTTTGGCTA-AAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCA
* ** *
1282 GAAAGACTCCTTGAAATATCTATTTTCATATAACCAAATCTCAGCCAATTTGGATTTATTGATCT
192 GAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTT
* * * * *
1347 CTTTTCACGAGCATTTGAATCTT-TTTCGATTTAATTAAAAATAAATTCGGAAAAAATATCGAAA
257 CTTTT-ACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAT-TGGAAA
1411 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTTTCAGA
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATA-TTTTTCAGA
* * * **
1476 GTGGTGTGG-CAAAAATTGAGAAAAAATTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAATG
65 GTAGTGTGGTTAAAAA-TGAGAAAAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAACC
* * *
1540 ATCACGGTTTTTGGCTAAAAACACGTTTCGGGGCCCCAGCTCAGTTTTGCATAATTTTTGGCAGA
129 ATCACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCAGA
* *
1605 AAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCAAATTTCGATTTAAGGATTTCG
194 AAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTC-
1670 TTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATTGG-AA
258 TTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAATTGGAAA
*
1732 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTCAATTATATATTTTTCCAGA
1 AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTT-CAGA
* *
1797 GTAGTGTGGTTTAAAATGAGAAAAAAGTTTTCAGGTCAATTTTTAGCAGAAATCGTGTACTAACC
65 GTAGTGTGGTTAAAAATGAG-AAAAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAACC
* *
1862 ATCACTGTTTTTGGCTAAAAAAT-GCGTTTCGGGGCCCCTGCTCAGTTTTGCATGATTTTTGGCA
129 ATCACGGTTTTTGGCT--AAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCA
* *
1926 GAAAGACTTCTTGAAATATCTATTTTCATA
192 GAAAGACTCCTTGAAATATCTATATTCATA
1956 CTATATAATT
Statistics
Matches: 1367, Mismatches: 116, Indels: 57
0.89 0.08 0.04
Matches are distributed among these distances:
319 3 0.00
320 73 0.05
321 446 0.33
322 459 0.34
323 290 0.21
324 30 0.02
325 39 0.03
326 23 0.02
327 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (319 bp):
AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCTTTGAATTATATATTTTTCAGAG
TAGTGTGGTTAAAAATGAGAAAAAGTTTTCGGGTCAATTTTTAGCAGAAATCGTGTACTAACCAT
CACGGTTTTTGGCTAAAATCGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCAGAAA
GACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTT
TACGAGCATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATTGGAAA
Found at i:25437 original size:22 final size:22
Alignment explanation
Indices: 24695--25438 Score: 558
Period size: 22 Copynumber: 33.8 Consensus size: 22
24685 GGAGTTTATT
* *
24695 AAAATTTCATAG-GTATGTTACA
1 AAAATTTCATAGTG-AGGTTACC
* **
24717 AAAATTTCATAG-GAAAGTTAGG
1 AAAATTTCATAGTG-AGGTTACC
* *
24739 AGAATTTCATAGGGAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
* **
24761 AAAATTTCTTAGAT-ATATTA-C
1 AAAATTTCATAG-TGAGGTTACC
* * *
24782 AAGAATCTCATAG-GAACGTTACA
1 AA-AATTTCATAGTG-AGGTTACC
* * *
24805 AAAATTTTATAGGGAGGTTATC
1 AAAATTTCATAGTGAGGTTACC
* *
24827 AAACTTTCATAGTGAGGTTATC
1 AAAATTTCATAGTGAGGTTACC
*
24849 AAAATTTCATAAG-GAGGTTACT
1 AAAATTTCAT-AGTGAGGTTACC
* * * *
24871 AGAATTTTATTGTAAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
* * *
24893 AAAATATCATAGCGAAGTTACC
1 AAAATTTCATAGTGAGGTTACC
24915 AAAATTTCATAGTGAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
* * *
24937 ATAATTCCATAG-GCAGATTACC
1 AAAATTTCATAGTG-AGGTTACC
* *
24959 AGAATTTCACAGTGAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
*
24981 AGAATTTCATAG-GCAGGTTACC
1 AAAATTTCATAGTG-AGGTTACC
* *
25003 AAAATTTCATAGTAAGGTTACT
1 AAAATTTCATAGTGAGGTTACC
*
25025 AGAATTTCATAGTGAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
** * *
25047 ATGATTTCATAGTGATGTTGCC
1 AAAATTTCATAGTGAGGTTACC
**
25069 CGAATTTCATAG-GAAGGTTACC
1 AAAATTTCATAGTG-AGGTTACC
* *
25091 AAAATTTCATATTGAGGTTACT
1 AAAATTTCATAGTGAGGTTACC
* *
25113 AAAATTTCATAGCGATGTTA-C
1 AAAATTTCATAGTGAGGTTACC
* *
25134 AAAACTTTCATAGCGAGTTTACC
1 AAAA-TTTCATAGTGAGGTTACC
* ** *
25157 AAAATTCCATAACGAAGTTACC
1 AAAATTTCATAGTGAGGTTACC
* * *
25179 AAAATTTTATACTGAGATTACC
1 AAAATTTCATAGTGAGGTTACC
* * *
25201 AAAATTTCATACTGAGATTACT
1 AAAATTTCATAGTGAGGTTACC
* * * *
25223 AGAATATCATAGGGAGATTACC
1 AAAATTTCATAGTGAGGTTACC
* * *
25245 AAAATTCCATAGAGAGCTTACC
1 AAAATTTCATAGTGAGGTTACC
* * *
25267 AAAATTTCATAAG-GTGGTAACT
1 AAAATTTCAT-AGTGAGGTTACC
* * *
25289 AGAATTTTATACTGAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
* * * * *
25311 AGAATATCACAGCGAGATTACC
1 AAAATTTCATAGTGAGGTTACC
* *
25333 AGAATTTCATAGGGAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
*
25355 AAAATTTCATAGTGAGGTTATC
1 AAAATTTCATAGTGAGGTTACC
*
25377 AGAAA-TTCATAGGGAGGTTACC
1 A-AAATTTCATAGTGAGGTTACC
* *
25399 AAAATTTTATAGCGAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
*
25421 AAAATTTAATAGTGAGGT
1 AAAATTTCATAGTGAGGT
25439 AACCTCCCTA
Statistics
Matches: 572, Mismatches: 129, Indels: 42
0.77 0.17 0.06
Matches are distributed among these distances:
21 15 0.03
22 539 0.94
23 18 0.03
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (22 bp):
AAAATTTCATAGTGAGGTTACC
Found at i:27069 original size:5 final size:5
Alignment explanation
Indices: 27055--27084 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
27045 TTCTATGCCA
27055 ATTT- ATTTG ATTTG ATTTG ATTTG ATTTG A
1 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG A
27085 AGTGTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (5 bp):
ATTTG
Found at i:35207 original size:20 final size:20
Alignment explanation
Indices: 35158--35209 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
35148 AACCGTTGAC
35158 ATTTTTTCTTCTCTCTTTTCT
1 ATTTTTT-TTCTCTCTTTTCT
35179 -TTTTGTTTTCTCTCTTTAT-T
1 ATTTT-TTTTCTCTCTTT-TCT
35199 ATTTTTTTTCT
1 ATTTTTTTTCT
35210 TTAGTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (20 bp):
ATTTTTTTTCTCTCTTTTCT
Found at i:58801 original size:45 final size:45
Alignment explanation
Indices: 58737--58828 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
58727 TTTGTTAAAA
58737 TAAAGACGTATAAATCTCTTTGATATATATTTCTACATTTTAACT
1 TAAAGACGTATAAATCTCTTTGATATATATTTCTACATTTTAACT
58782 TAAAGACGTATAAATCTCTTTGATATATATTTCTACATTTTAACT
1 TAAAGACGTATAAATCTCTTTGATATATATTTCTACATTTTAACT
58827 TA
1 TA
58829 TAATTTTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (45 bp):
TAAAGACGTATAAATCTCTTTGATATATATTTCTACATTTTAACT
Found at i:62400 original size:31 final size:31
Alignment explanation
Indices: 62359--62432 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
62349 TTTATCGATT
* * *
62359 AGACTCAATTGACTCGATCTTATAAGTACAA
1 AGACTAAATTGACCCAATCTTATAAGTACAA
* * *
62390 GGACTAAATTGACCCAATCTTATGAGTAGAA
1 AGACTAAATTGACCCAATCTTATAAGTACAA
62421 AGACTAAATTGA
1 AGACTAAATTGA
62433 TCGTTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (31 bp):
AGACTAAATTGACCCAATCTTATAAGTACAA
Found at i:69172 original size:7 final size:7
Alignment explanation
Indices: 69160--69185 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
69150 ATCAAAATCA
69160 GAAAATT
1 GAAAATT
69167 GAAAATT
1 GAAAATT
69174 GAAAATT
1 GAAAATT
69181 GAAAA
1 GAAAA
69186 CAGAAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (7 bp):
GAAAATT
Found at i:69191 original size:14 final size:14
Alignment explanation
Indices: 69153--69192 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
69143 GAGGAAAATC
69153 AAAATCAGAAAATTG
1 AAAA-CAGAAAATTG
**
69168 AAAATTGAAAATTG
1 AAAACAGAAAATTG
69182 AAAACAGAAAA
1 AAAACAGAAAA
69193 GGAAGGGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.17
Consensus pattern (14 bp):
AAAACAGAAAATTG
Found at i:70424 original size:15 final size:14
Alignment explanation
Indices: 70406--70435 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
70396 ATAATTAATA
70406 ATTAATATATTATAT
1 ATTAATAT-TTATAT
70421 ATTAATATTTATAT
1 ATTAATATTTATAT
70435 A
1 A
70436 AAGTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTAATATTTATAT
Found at i:70434 original size:21 final size:21
Alignment explanation
Indices: 70395--70435 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
70385 TATAGTGATC
70395 TATAATTAATAATTAATATAT
1 TATAATTAATAATTAATATAT
*
70416 TATATATTAAT-ATTTATATA
1 TATA-ATTAATAATTAATATA
70436 AAGTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATAATTAATAATTAATATAT
Found at i:73625 original size:2 final size:2
Alignment explanation
Indices: 73618--73667 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
73608 TGAACATAAA
73618 AT AT AT AT AT AT AT -T AT AT -T AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73657 A- AT AT A- AT AT A
1 AT AT AT AT AT AT A
73668 GTAATAGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
1 5 0.12
2 38 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73643 original size:20 final size:20
Alignment explanation
Indices: 73617--73682 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
73607 ATGAACATAA
73617 AATATATATAT-ATATTATAT
1 AATATATATATAATA-TATAT
*
73637 TATATATATATAATATATAT
1 AATATATATATAATATATAT
*
73657 AATATA-ATATAGTA-ATAGT
1 AATATATATATAATATATA-T
73676 AATATAT
1 AATATAT
73683 TATCATGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.08
19 14 0.35
20 20 0.50
21 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATATATATAATATATAT
Found at i:73678 original size:14 final size:12
Alignment explanation
Indices: 73617--73682 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 12
73607 ATGAACATAA
73617 AATATATATATAT
1 AATATA-ATATAT
* *
73630 ATTATATTATAT
1 AATATAATATAT
73642 ATATATAATATATAT
1 A-ATAT-A-ATATAT
73657 AATATAATATAGT
1 AATATAATATA-T
73670 AATAGTAATATAT
1 AATA-TAATATAT
73683 TATCATGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.25
13 15 0.34
14 12 0.27
15 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
AATATAATATAT
Found at i:75032 original size:11 final size:11
Alignment explanation
Indices: 75008--75042 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
74998 TTGACAGTGC
75008 AACAAAAACAA
1 AACAAAAACAA
* *
75019 AACGAAAACGA
1 AACAAAAACAA
75030 AACAAAAACAA
1 AACAAAAACAA
75041 AA
1 AA
75043 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:75312 original size:11 final size:11
Alignment explanation
Indices: 75291--75338 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
75281 AAAAATTGAC
*
75291 AACACAACAAA
1 AACAAAACAAA
*
75302 AATAAAACAAA
1 AACAAAACAAA
*
75313 AACGAAACAAA
1 AACAAAACAAA
75324 AACAGAAACAGAA
1 AACA-AAACA-AA
75337 AA
1 AA
75339 ACGAAAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 21 0.70
12 5 0.17
13 4 0.13
ACGTcount: A:0.75, C:0.17, G:0.06, T:0.02
Consensus pattern (11 bp):
AACAAAACAAA
Found at i:75322 original size:25 final size:25
Alignment explanation
Indices: 75294--75344 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
75284 AATTGACAAC
*
75294 ACAACAAAAATAAA-ACAAAAACGAA
1 ACAA-AAAAAGAAACACAAAAACGAA
* *
75319 ACAAAAACAGAAACAGAAAAACGAA
1 ACAAAAAAAGAAACACAAAAACGAA
75344 A
1 A
75345 AAGATGTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.75, C:0.16, G:0.08, T:0.02
Consensus pattern (25 bp):
ACAAAAAAAGAAACACAAAAACGAA
Found at i:75325 original size:12 final size:11
Alignment explanation
Indices: 75296--75344 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
75286 TTGACAACAC
**
75296 AACAAAAATAA
1 AACAAAAACGA
75307 AACAAAAACGA
1 AACAAAAACGA
75318 AACAAAAACAGA
1 AACAAAAAC-GA
75330 AACAGAAAAACGA
1 AAC--AAAAACGA
75343 AA
1 AA
75345 AAGATGTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 18 0.55
12 5 0.15
13 4 0.12
14 6 0.18
ACGTcount: A:0.76, C:0.14, G:0.08, T:0.02
Consensus pattern (11 bp):
AACAAAAACGA
Found at i:75325 original size:288 final size:293
Alignment explanation
Indices: 74783--75355 Score: 745
Period size: 288 Copynumber: 2.0 Consensus size: 293
74773 GTTTGGCAGG
*
74783 CTGTTTCCGTTTTCAAAAATTTTGGAAACAGAAACAGTGTTTTAGAAAAAGTGAAAGTAAGAATT
1 CTGTTTCCGTTTTCAAAAATTTTGGAAACAGAAACAGTGTTTTAGAAAAAGTGAAAGTAAAAATT
* *
74848 TTGTGTTTTCATGTTTTTCCAAAAAACTTCCAAAACACAGAAGCACAATGATGAATAGTAACTTA
66 TTGTGTTTTCATGTTTTTCC-AAAAACAT-CAAAACACAGAAGCACAA-GATCAATAGT-ACTTA
*
74913 CATGCTTTTTAACCATTTTTTAAACTTTTTTATTTAAAAACATACAACCAAATTGTTTATCTAAA
127 CATGCTTTTTAACCATTTTTT-AACTTTTTTATTTAAAAACATACAACCAAATTATTTATCTAAA
* * *** *
74978 TATGTTTTTGTTTTCAAAAATTGACAGTGCAACAAAAACAAAACGAAAACGAAACAAAAACAAAA
191 CATGTTTTTGTTTTAAAAAATTGACAACACAACAAAAACAAAACAAAAACGAAACAAAAAC-AAA
*
75043 AACAGAAAAACGAAAACGATGCCAAACGACCCTAGCAAA
255 AACAGAAAAACGAAAAAGATGCCAAACGACCCTAGCAAA
* * * *
75082 CTGTTTCCGTTTTCAAAAATTTTGGAAACCGAAGCCGTGTTTTGGAAAAAAGGTGAAAGTAAAAA
1 CTGTTTCCGTTTTCAAAAATTTTGGAAACAGAAACAGTGTTTTAG-AAAAA-GTGAAAGTAAAAA
* * *
75147 TTTTGTGTTTTCATGTTTTTCC-AAAACAT-AGAAACACA-ATG-ATAA-A-CAATA-T-TTTAC
64 TTTTGTGTTTTCATGTTTTTCCAAAAACATCA-AAACACAGAAGCACAAGATCAATAGTACTTAC
* * * *
75204 ATGTTTTTTCACCATTTTTT-ACTTTTTTTATTTAAAAATATACAACCAAATTATATTTTC-AAA
128 ATGCTTTTTAACCATTTTTTAAC-TTTTTTATTTAAAAACATACAACCAAATTAT-TTATCTAAA
* *
75267 CATG-TTTTGTTTTAAAAAATTGACAACACAACAAAAATAAAACAAAAACGAAACAAAAACAGAA
191 CATGTTTTTGTTTTAAAAAATTGACAACACAACAAAAACAAAACAAAAACGAAACAAAAACAAAA
*
75331 ACAGAAAAACGAAAAAGATGTCAAA
256 ACAGAAAAACGAAAAAGATGCCAAA
75356 TAACACCTAA
Statistics
Matches: 244, Mismatches: 25, Indels: 22
0.84 0.09 0.08
Matches are distributed among these distances:
287 26 0.11
288 52 0.21
289 35 0.14
290 26 0.11
292 1 0.00
293 4 0.02
294 1 0.00
296 3 0.01
297 3 0.01
298 7 0.03
299 47 0.19
300 5 0.02
301 34 0.14
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (293 bp):
CTGTTTCCGTTTTCAAAAATTTTGGAAACAGAAACAGTGTTTTAGAAAAAGTGAAAGTAAAAATT
TTGTGTTTTCATGTTTTTCCAAAAACATCAAAACACAGAAGCACAAGATCAATAGTACTTACATG
CTTTTTAACCATTTTTTAACTTTTTTATTTAAAAACATACAACCAAATTATTTATCTAAACATGT
TTTTGTTTTAAAAAATTGACAACACAACAAAAACAAAACAAAAACGAAACAAAAACAAAAACAGA
AAAACGAAAAAGATGCCAAACGACCCTAGCAAA
Found at i:75405 original size:21 final size:22
Alignment explanation
Indices: 75379--75420 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
75369 TACAATACAC
75379 GTATAGAGAATATAT-ATATAT
1 GTATAGAGAATATATAATATAT
*
75400 GTATAGATAATATATAATATA
1 GTATAGAGAATATATAATATA
75421 ATATAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (22 bp):
GTATAGAGAATATATAATATAT
Found at i:75421 original size:5 final size:5
Alignment explanation
Indices: 75411--75475 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
75401 TATAGATAAT
* * * *
75411 ATATA ATATA ATATA ATATA AT-TAA ATGTT ATATA ATATT TTATA ATAATA
1 ATATA ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA ATATA AT-ATA
75462 ATAATA ATATA ATA
1 AT-ATA ATATA ATA
75476 CTGCTAGTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
4 1 0.02
5 37 0.74
6 12 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:75425 original size:21 final size:21
Alignment explanation
Indices: 75380--75425 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
75370 ACAATACACG
*
75380 TATAGAGAATATATATATATG
1 TATAGAGAATATATATATATA
*
75401 TATAGATAATATATA-ATATAA
1 TATAGAGAATATATATATAT-A
75422 TATA
1 TATA
75426 ATATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (21 bp):
TATAGAGAATATATATATATA
Found at i:76006 original size:15 final size:15
Alignment explanation
Indices: 75986--76016 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
75976 TCACTGACAG
*
75986 TGTATTGTATGATTT
1 TGTATTGTATAATTT
76001 TGTATTGTATAATTT
1 TGTATTGTATAATTT
76016 T
1 T
76017 CCTATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (15 bp):
TGTATTGTATAATTT
Done.