Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017980.1 Corchorus olitorius cultivar O-4 contig18013, 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: 129979
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:607 original size:333 final size:330
Alignment explanation
Indices: 1--1918 Score: 2831
Period size: 333 Copynumber: 5.8 Consensus size: 330
*
1 CTCAATTTTTTGCCGCAATAATCGTATAAAATATATAACTCAACGTCAAAAAG-TTTTGAGGGCT
1 CTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTT-AGGGCT
* *
65 TTTTACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAGTCGTATTGGAAAAC
65 TTTCACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAATCGTATTGGAAAAC
130 GATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATAC
130 GATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATAC
* *
195 ATATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGGCTCCGAAACGCGTT
195 AGATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGGC-CCGGAACGCGTT
260 TTGAGCCAAAAACCGTGATAATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAA
259 TTGAGCCAAAAACCGTGAT--TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAA
325 ACTTTTGCG
322 ACTTTTGCG
* * *
334 CTCAATTTTTTTCCACAATAATCGTATAAAATATATAAGTCAATGTCAAAAAGATTTTAGGGCTT
1 CTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCTT
* *
399 TTAACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAATCGTATTAGAAAACG
66 TTCACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAATCGTATTGGAAAACG
* * * *
464 ACTCTGATGCTCGTAAAAACAAAACCTTAAGTCCATTGTGGCTGACATTTCGATAGATGAATACA
131 ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATACA
* * **
529 GATATTTTAATGAGTCTTGACGCAAAAAATCATGCAAGACTGAGCCAGGAACCCGGAACGCGTTT
196 GATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAGCC-GGGGCCCGGAACGCGTTT
*
594 TGAGCCAAAAACCGTGATGATTAGTACACGATTTTGGCTAAAATTTTGCAAAAATTGACCCGAAA
260 TGAGCCAAAAACCGTGAT--TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
*
659 CTTTTACG
323 CTTTTGCG
*
667 CTCAATTTTTTGCCACAATAATCGTATAAAATATATAACACAACGTCAAAAAGATTTTAGGGCTT
1 CTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCTT
* * *
732 TTCACGCTTCTAATATCATTTTTCCAATTTTTTCTAAATTAAAATTCTAATCGTATTAGAAAACG
66 TTCACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAATCGTATTGGAAAACG
* ***
797 ATTCTGATGCTCATAAAAACAAATAAATAAATCCATTGTGGCTGAGATTTCGATAGATGAATACA
131 ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATACA
* *
862 GATATTTTAATGAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGTAACGCGTTT
196 GATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGG-CCCGGAACGCGTTT
927 TGAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
260 TGAGCCAAAAACCGTGAT--TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
*
992 GTTTTGCG
323 CTTTTGCG
* * *
1000 CTCAATTTTTTGCCCCAATAATCGTATAAAATATATAACACAACGTCAAAAAGATTTTAGGGATT
1 CTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCTT
** * * * *** * *
1065 TTCACGATTCTAATGTCATTTTTCCAATTTTTTCTAAACTAAAATTCTAATTAAATCGGAAAAAG
66 TTCACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAATCGTATTGGAAAACG
* * * * *
1130 ATTTTGACGCTCGTAAAAACAAATCCTTATATCCATTGTTGCTAAGATTTCGATAGATGAATACA
131 ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATACA
* * *
1195 TATATTTTAATAAGTCTTGACTCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTT
196 GATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGG-CCCGGAACGCGTTT
*
1260 TGAGCCAAAAACC--------G--CACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGT
260 TGAGCCAAAAACCGTGATTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAACT
1315 TTTGCG
325 TTTGCG
* * *
1321 CTCAATTTTTTGCCACAATAATCGTATCAAATATATAACTCAACATCAAAAAGATATTAGGGCTT
1 CTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCTT
*
1386 TTAACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAATCGTATTGGAAAACG
66 TTCACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAATCGTATTGGAAAACG
* * *
1451 ATTCTGATGCTCGTAAAAATAAATCCTTAAATCCATTGTGTCTGAGATTTCGATAGATGAATAAA
131 ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATACA
* * *
1516 TATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAACCGGGGCCCCGAACGCGTTTT
196 GATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGGCCCGGAACGCGTTTT
* * *
1581 GAGCC--AAA-C--------GTACACGATTTTGGCTAAAATTTTGTAAAAATTGATCCGAAACTT
261 GAGCCAAAAACCGTGATTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAACTT
1635 TTGCG
326 TTGCG
* *
1640 CTCAATTTTTCGCCACAATAATCTTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGAC-
1 CTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGG-CT
* * * *
1704 TTTCACGCTTCTACTATGATTTTTCCAA-TCTTTTCTGAATTAAAATTCTAATCGTATTGGAAAA
65 TTTCACGCGTCTAATATCATTTTTCCAAGT-TTTTCTAAATTAAAATTCTAATCGTATTGGAAAA
* * *
1768 CGATTATTATGTTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATA
129 CGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATA
* *
1833 CAGATATTTTAATGATTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGGCCTCGGAACGCGT
194 CAGATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGGCC-CGGAACGCGT
* *
1898 TTTAAACCAAAAACCGTGATT
258 TTTGAGCCAAAAACCGTGATT
1919 AACGTAATTT
Statistics
Matches: 1445, Mismatches: 123, Indels: 38
0.90 0.08 0.02
Matches are distributed among these distances:
317 2 0.00
318 4 0.00
319 266 0.18
320 34 0.02
321 265 0.18
322 3 0.00
323 2 0.00
332 2 0.00
333 860 0.60
334 7 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (330 bp):
CTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCTT
TTCACGCGTCTAATATCATTTTTCCAAGTTTTTCTAAATTAAAATTCTAATCGTATTGGAAAACG
ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATACA
GATATTTTAATAAGTCTTGACGCAAAAAATCATGCAAAACTGAGCCGGGGCCCGGAACGCGTTTT
GAGCCAAAAACCGTGATTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAACTT
TTGCG
Found at i:3236 original size:334 final size:334
Alignment explanation
Indices: 2617--3247 Score: 1002
Period size: 334 Copynumber: 1.9 Consensus size: 334
2607 TCGCACCCTC
* *
2617 TACATGATTTCGGGTAAAATTTTGCAAAAATTCACCCAAAACTTTTCTGCTCAATTTTTTGCCAC
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTCACCCAAAACTTTTCTGCTCAATTTTTTGCCAC
* *
2682 AATAATCTTATAAAATATATAACTCAACGTCAAAAATATTTTAGGGACTTTCACGCTTCTAATAT
66 AATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGACTTTCACGCTTCTAATAT
* *
2747 CATTTTTCCAATTTTTTCTGAAATTAAAAATCTAATTAAATCGGAAAAAGATTATGATGCTCATA
131 CATTTTTCCAATCTTTTCTGAAATTAAAAATCTAATTAAATCAGAAAAAGATTATGATGCTCATA
** * *
2812 AAAACATGTCCTTAAATCCATTGTGGTTGAGTTTTCAATAGATGAATACGGATATTTTAATGAGT
196 AAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCAATAGATGAATACGGATATTTTAATGAGT
*
2877 CTTGACGCAAAAAATCATACAAAACTGAG-TCGGAGCTCCGGAACGCGTTTTTAGCAAAAAACCG
261 CTTGACGCAAAAAATAATACAAAACTGAGCT-GGAGCTCCGGAACGCGTTTTTAGCAAAAAACCG
2941 TGATGGTTAG
325 TGATGGTTAG
* *
2951 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGTTTTGC-GCTCAATTTTTTTGCC
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTCACCCAAAACTTTT-CTGCTCAA-TTTTTTGCC
* *
3015 ACAATAATCGTATAAAATATATAACTCAATGTCAAAAAGATTTTAGGGTCTTTCACGCTTCTAAT
64 ACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGACTTTCACGCTTCTAAT
* * * *
3080 ATCATTTTTCCAATCTTTTCTG-AATTAAAATTCTTATTAAATCAGAAAAAGATTCTGATGCTCG
129 ATCATTTTTCCAATCTTTTCTGAAATTAAAAATCTAATTAAATCAGAAAAAGATTATGATGCTCA
3144 TAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCAATAGATGAATACAGG-TATTTTAATG
194 TAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCAATAGATGAATAC-GGATATTTTAATG
*
3208 AGAT-TTGACGCAAAAAATAATGCAAAACTGAGCTGGAGCT
258 AG-TCTTGACGCAAAAAATAATACAAAACTGAGCTGGAGCT
3248 AGGGATGGCA
Statistics
Matches: 272, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
334 176 0.65
335 96 0.35
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (334 bp):
TACACGATTTCGGCTAAAATTTTGCAAAAATTCACCCAAAACTTTTCTGCTCAATTTTTTGCCAC
AATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGACTTTCACGCTTCTAATAT
CATTTTTCCAATCTTTTCTGAAATTAAAAATCTAATTAAATCAGAAAAAGATTATGATGCTCATA
AAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCAATAGATGAATACGGATATTTTAATGAGT
CTTGACGCAAAAAATAATACAAAACTGAGCTGGAGCTCCGGAACGCGTTTTTAGCAAAAAACCGT
GATGGTTAG
Found at i:5054 original size:338 final size:333
Alignment explanation
Indices: 3742--5028 Score: 1987
Period size: 338 Copynumber: 3.9 Consensus size: 333
3732 CTGGGGCCCC
* ** ** * *
3742 GGAACGCGTTTTGAGCCAAAAACTGTGATGGTTAGTACAGGATTTCGGCTAAAATTTTGCAAAAA
1 GGAACGCGTTTTAAGCCAAAAACCATGATACTTAGTACACGATTTCGCCTAAAATTTTGC-AAAA
* *
3807 TTGACCCGAAACTTTTGCGCTCAATTTTTTGCCAAAATAATCGTATAAAATATATAACTCAACGT
65 TTGACCCGAAACATTTGCGCTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGT
* *
3872 CAAAAAAGATTTTAGGGGCTTTCATGCTTCTAATATCATTTTTCCAATTTTTCCTGAATTAAAAT
130 CAAAAAA-ATTTTAGGGACTTTCATGCTTCTAATATCATTTTTCCAATTTTTTCTGAATTAAAAT
* ** *
3937 TCTAATTTAATCGGAAAAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGTTGA
194 TCTAATTAAATCGGAAAAAGATAATGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
** * *
4002 GATTTCGATTGATGAATACAGATATTTTAATGAGTCTTGACGC-AAAAAATCATGCAAAGCTGAG
259 GATTTCGACAGATAAATACAGATATTTTAATGAGTCTTGACGCAAAAAAATCATGCAAAACTGAG
* * * *
4066 CTGGGGCCCC
324 CCGAGACCCT
* * * * * *
4076 GGAATGCATTTTGAA-CCAAAAACC--G-TA-ATGGTACACGATTTCGGCTAAAATTTTGAAAAA
1 GGAACGCGTTTT-AAGCCAAAAACCATGATACTTAGTACACGATTTCGCCTAAAATTTTG-CAAA
* ** * *
4136 ATTGACCCGAAACTTTTGCGCTCAATTTTTTGCCACTGTACTCGTATAAAATATATAACTCAGCG
64 ATTGACCCGAAACATTTGCGCTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACG
* * * *
4201 TCAAAAAGATTTTAGAGCCTTTCACGCTTCTAATATCATTTTTCCAATTTTTTCTGAATTAAAAT
129 TCAAAAAAATTTTAGGGACTTTCATGCTTCTAATATCATTTTTCCAATTTTTTCTGAATTAAAAT
*
4266 TCTAATTAAATCGGAAAAA-ATAATGATGCTCGTAAAAACAAATCTTTAAATCCATTGTGGCTGA
194 TCTAATTAAATCGGAAAAAGATAATGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
4330 GATTTCGACAGATAAATACAGATATTTTAATGAGTCTTGACGCAAAAAAATCATGCAAAACTGAG
259 GATTTCGACAGATAAATACAGATATTTTAATGAGTCTTGACGCAAAAAAATCATGCAAAACTGAG
4395 CCGAGACCCT
324 CCGAGACCCT
4405 GGAACGCGTTTTAAGCCAAAAACCATGATACTTAGTACACGATTTCGCCTAAAATTTTGCAAAAT
1 GGAACGCGTTTTAAGCCAAAAACCATGATACTTAGTACACGATTTCGCCTAAAATTTTGCAAAAT
*
4470 TGACCCGAAACATTTGTGACTTCAATTTTTTGCCACAATAATACGTATAAAATATATAA-TCAAC
66 TGACCCGAAACATTTGCG-C-TCAATTTTTTGCCACAATAAT-CGTATAAAATATATAACTCAAC
4534 GTACAAAAAAATTTTTAGGGACTTTCATGCTTCTAATATCATTTTTCCAATTTTTTCTGAATTAA
128 GT-CAAAAAAA-TTTTAGGGACTTTCATGCTTCTAATATCATTTTTCCAATTTTTTCTGAATTAA
*
4599 AATTCTAATTAAATCGGAAAAAAGATAATGATGCTCGTAAAAACAAATCTTTAAATCCATTGTGG
191 AATTCTAATTAAATCGG-AAAAAGATAATGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGG
4664 CTGAGATTTCGACAGATAAATACAGATATTTTAATGAGTCTTGACGCAAAAAAATCATGCAAAAC
255 CTGAGATTTCGACAGATAAATACAGATATTTTAATGAGTCTTGACGCAAAAAAATCATGCAAAAC
4729 TGAGCCGAGACCCT
320 TGAGCCGAGACCCT
4743 GGAACGCGTTTTAAGCCAAAAACCATGATACTTAGTACACGATTTCGCCTAAAATTTTGCAAAAT
1 GGAACGCGTTTTAAGCCAAAAACCATGATACTTAGTACACGATTTCGCCTAAAATTTTGCAAAAT
* *
4808 TGACCCGAAACATTTGTGCTCAATTTTTTGCCACAATAATCGTATAAAATATATAATTCAACGTC
66 TGACCCGAAACATTTGCGCTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTC
4873 AAAAAAATTTTAGGGACTTTCATGCTTCTAATATCATTTTTCCAATTTTTTCTGAATTAAAATTC
131 AAAAAAATTTTAGGGACTTTCATGCTTCTAATATCATTTTTCCAATTTTTTCTGAATTAAAATTC
** *
4938 TAATTAAATCGGAAAAAGATTTTGATGCTCGTAAAAACAAATCCTTAAATCCATTATGGCTGAGA
196 TAATTAAATCGGAAAAAGATAATGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGA
* * *
5003 TTTTGATAGATGAATACAGATATTTT
261 TTTCGACAGATAAATACAGATATTTT
5029 GTTTTTAAAT
Statistics
Matches: 882, Mismatches: 55, Indels: 33
0.91 0.06 0.03
Matches are distributed among these distances:
328 83 0.09
329 116 0.13
330 95 0.11
331 2 0.00
332 24 0.03
333 98 0.11
334 112 0.13
335 48 0.05
336 95 0.11
337 6 0.01
338 203 0.23
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (333 bp):
GGAACGCGTTTTAAGCCAAAAACCATGATACTTAGTACACGATTTCGCCTAAAATTTTGCAAAAT
TGACCCGAAACATTTGCGCTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCAACGTC
AAAAAAATTTTAGGGACTTTCATGCTTCTAATATCATTTTTCCAATTTTTTCTGAATTAAAATTC
TAATTAAATCGGAAAAAGATAATGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGA
TTTCGACAGATAAATACAGATATTTTAATGAGTCTTGACGCAAAAAAATCATGCAAAACTGAGCC
GAGACCCT
Found at i:5754 original size:335 final size:328
Alignment explanation
Indices: 5045--5922 Score: 988
Period size: 335 Copynumber: 2.6 Consensus size: 328
5035 AAATCCTTAA
* * * *
5045 TGGCAAAAAATTGACCGCAAAATTTTCAAGTCAATTTTTGTAAAATTTTAGCTGAAATCGTGTAC
1 TGGCAAAAAATTGACCGCAAAACTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT--
* * *
5110 AAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGC-CT--CGGCTCAGTTTTGCATGATTT
63 --ACCATCACGGTTTTTGGCTAAAAACGCGTTCTG-GGCACTCCCGACTCAATTTTGCATGA-TT
* * * * *
5172 TTTTACGTCAAGGCTCATTAAAATATTTGTATTCATCTAACAAAATACCAGGTCCAGTCACATTG
124 TTTTGCGTCAAGACTCATTAAAATATATGTATTCATCTAACGAAAT--C---T-CAGCCACATTG
* *
5237 GATTTAAGGATTTGTTTTTATAAGCATCAGAATCTTTTTTCGATTTAATTAGAAATTAATTCAGA
183 GATTTAAGGATTTGTTTTTAAAAGCATCAGAATCTTTTTCCGATTTAATTAGAAATTAATTCAGA
*
5302 AAAATAGGAAAAATGATATTAAAAGCATGAAAGGCCCTAAAATATTTTTGATGTTGAGTTATATA
248 AAAATAGGAAAAATGATATTAAAAGCATGAAAGGCCCTAAAATATTTTTGACGTTGAGTTATATA
5367 TTTTACACGATTATTG
313 TTTTACACGATTATTG
* *
5383 TGGCAAAAAATTGACCGCAAAATTTTCGGATCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAC
1 TGGCAAAAAATTGACCGCAAAACTTTCGG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
*
5448 CATCACGGTTTTTGGCTCAAAACGCGTTCTGGGTCCCCACTCCCCGACTCAATTTTGCATGATTT
65 CATCACGGTTTTTGGCTAAAAACGCGTTCTGGG----CACT-CCCGACTCAATTTTGCATGATTT
* * * * *
5513 TTTGCGTCAAGACGCATTAAAATATATGTATTCATCTATCGAAATCTTAGCCACATTAGACTTAA
125 TTTGCGTCAAGACTCATTAAAATATATGTATTCATCTAACGAAATCTCAGCCACATTGGATTTAA
*
5578 GGATTTGTTTTTAAAAGCATCAGAATCTTTTTCCGATTTAATTAGAATTTTAATTCAGAAAAAAT
190 GGATTTGTTTTTAAAAGCATCAGAATCTTTTTCCGATTTAATTAGAA-ATTAATTCAG-AAAAAT
* * * *
5643 TGG-AAAATGATATTATAAG-AGTGAAAGGCCCTAAAATATTTTTTACGTTGAGTTGTGA-ACTT
253 AGGAAAAATGATATTAAAAGCA-TGAAAGGCCCTAAAATATTTTTGACGTTGAGTTAT-ATA-TT
* *
5705 TT-TATGATTATTG
315 TTACACGATTATTG
* * *
5718 TGGTAAAAAATTGAGCG-AAAGACTTTCGCGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTA
1 TGGCAAAAAATTGACCGCAAA-ACTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
* * * ** *
5782 CTAATCATCACGGTTTTTGGCAAAAAAAG-GTATTCTGGGGAC-CTGGTC-CAATTTTGCATGAT
64 C----CATCACGGTTTTTGGCTAAAAACGCG--TTCTGGGCACTCCCGACTCAATTTTGCATGAT
* * * * *
5844 TTTTTGCGCCAAGACTCATTAAAATATCTAT-TTTATCTACCGAAATCTCAGCCACATTGGATTT
123 TTTTTGCGTCAAGACTCATTAAAATATATGTATTCATCTAACGAAATCTCAGCCACATTGGATTT
5908 AAGGATTTGTTTTTA
188 AAGGATTTGTTTTTA
5923 CGAGCAGCTC
Statistics
Matches: 469, Mismatches: 49, Indels: 50
0.83 0.09 0.09
Matches are distributed among these distances:
332 43 0.09
333 43 0.09
334 97 0.21
335 121 0.26
336 16 0.03
337 2 0.00
338 61 0.13
339 21 0.04
340 49 0.10
341 16 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (328 bp):
TGGCAAAAAATTGACCGCAAAACTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACC
ATCACGGTTTTTGGCTAAAAACGCGTTCTGGGCACTCCCGACTCAATTTTGCATGATTTTTTGCG
TCAAGACTCATTAAAATATATGTATTCATCTAACGAAATCTCAGCCACATTGGATTTAAGGATTT
GTTTTTAAAAGCATCAGAATCTTTTTCCGATTTAATTAGAAATTAATTCAGAAAAATAGGAAAAA
TGATATTAAAAGCATGAAAGGCCCTAAAATATTTTTGACGTTGAGTTATATATTTTACACGATTA
TTG
Found at i:12234 original size:15 final size:14
Alignment explanation
Indices: 12205--12238 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
12195 ACTTGTTATG
12205 AAGAA-ATAAAATT
1 AAGAAGATAAAATT
12218 AAGAAGATAAGAATT
1 AAGAAGATAA-AATT
12233 AAGAAG
1 AAGAAG
12239 GCATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 4 0.21
15 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (14 bp):
AAGAAGATAAAATT
Found at i:12249 original size:17 final size:15
Alignment explanation
Indices: 12212--12251 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
12202 ATGAAGAAAT
12212 AAAATTAAGAAGATA
1 AAAATTAAGAAGATA
*
12227 AGAATTAAGAAGGCATA
1 AAAATTAAGAA-G-ATA
12244 AAAATTAA
1 AAAATTAA
12252 AAATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 10 0.48
16 1 0.05
17 10 0.48
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.20
Consensus pattern (15 bp):
AAAATTAAGAAGATA
Found at i:18021 original size:19 final size:19
Alignment explanation
Indices: 17997--18059 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
17987 GTAATGTACT
17997 AGCACAAAATAATGCAAAA
1 AGCACAAAATAATGCAAAA
** *
18016 AGCACAAAATTGCTACAAATAA
1 AGCACAAAA-TAATGC-AA-AA
18038 CAGCACAAAATAATGCAAAA
1 -AGCACAAAATAATGCAAAA
18058 AG
1 AG
18060 AAAACTGCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 11 0.32
20 5 0.15
21 4 0.12
22 5 0.15
23 9 0.26
ACGTcount: A:0.59, C:0.17, G:0.11, T:0.13
Consensus pattern (19 bp):
AGCACAAAATAATGCAAAA
Found at i:19088 original size:14 final size:14
Alignment explanation
Indices: 19069--19111 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
19059 GTCAAATCAT
19069 ATACTGTGTAGTAC
1 ATACTGTGTAGTAC
19083 ATACTGTGTGTAGTAC
1 ATAC--TGTGTAGTAC
* *
19099 CTGCTGTGTAGTA
1 ATACTGTGTAGTA
19112 TAGTATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.52
16 12 0.48
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (14 bp):
ATACTGTGTAGTAC
Found at i:28584 original size:1 final size:1
Alignment explanation
Indices: 28580--28609 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
28570 CTTTTTTTTT
28580 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28610 CTTTTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32451 original size:76 final size:76
Alignment explanation
Indices: 32325--32476 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
32315 TCCTTCTCAA
32325 ATGCTTTCTGTTTAGTAAAATTTCTTCCATTTCTGGTCAGGCGAGATAATCAATTTTCTTATTTC
1 ATGCTTTCTGTTTAGTAAAATTTCTTCCATTTCTGGTCAGGCGAGATAATCAATTTTCTTATTTC
32390 TGCTTCTTGAC
66 TGCTTCTTGAC
32401 ATGCTTTCTGTTTAGTAAAATTTCTTCCATTTCTGGTCAGGCGAGATAATCAATTTTCTTATTTC
1 ATGCTTTCTGTTTAGTAAAATTTCTTCCATTTCTGGTCAGGCGAGATAATCAATTTTCTTATTTC
32466 TGCTTCTTGAC
66 TGCTTCTTGAC
32477 CCTGACTCTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.46
Consensus pattern (76 bp):
ATGCTTTCTGTTTAGTAAAATTTCTTCCATTTCTGGTCAGGCGAGATAATCAATTTTCTTATTTC
TGCTTCTTGAC
Found at i:37457 original size:23 final size:23
Alignment explanation
Indices: 37427--37473 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
37417 ATTTTACCAA
* *
37427 ATCATTATTTTATTATTATATAT
1 ATCATTATTATATTATAATATAT
37450 ATCATTATTATATTATAATATAT
1 ATCATTATTATATTATAATATAT
37473 A
1 A
37474 CTAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
ATCATTATTATATTATAATATAT
Found at i:38247 original size:19 final size:19
Alignment explanation
Indices: 38223--38259 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38213 ATACAGTACC
38223 TAATCTAATATGTACAGTG
1 TAATCTAATATGTACAGTG
* *
38242 TAATCTCATTTGTACAGT
1 TAATCTAATATGTACAGT
38260 TACTAAATAG
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:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (19 bp):
TAATCTAATATGTACAGTG
Found at i:39743 original size:24 final size:24
Alignment explanation
Indices: 39709--39779 Score: 81
Period size: 26 Copynumber: 2.9 Consensus size: 24
39699 GGGTCCGGAT
* *
39709 TACACAAACTAATTTGCAATTAAA
1 TACACACACTAATTTGCAATAAAA
*
39733 TACACACACTAATTAGACTCAA-AAAA
1 TACACACACTAATTTG---CAATAAAA
39759 TACACACACTAATTTGCAATA
1 TACACACACTAATTTGCAATA
39780 TACACGCTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 3 0.08
24 15 0.38
26 18 0.46
27 3 0.08
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.25
Consensus pattern (24 bp):
TACACACACTAATTTGCAATAAAA
Found at i:40250 original size:8 final size:8
Alignment explanation
Indices: 40237--40283 Score: 80
Period size: 8 Copynumber: 6.1 Consensus size: 8
40227 CCTTTCCTTT
40237 GTTGAAGA
1 GTTGAAGA
40245 GTTGAAGA
1 GTTGAAGA
40253 GTTGAAGA
1 GTTGAAGA
40261 G-TGAAGA
1 GTTGAAGA
40268 GTTGAAGA
1 GTTGAAGA
40276 G-TGAAGA
1 GTTGAAGA
40283 G
1 G
40284 AGGATCATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 14 0.37
8 24 0.63
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.21
Consensus pattern (8 bp):
GTTGAAGA
Found at i:40267 original size:15 final size:15
Alignment explanation
Indices: 40237--40283 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
40227 CCTTTCCTTT
40237 GTTGAAGAGTTGAAGA
1 GTTGAAGAG-TGAAGA
40253 GTTGAAGAGTGAAGA
1 GTTGAAGAGTGAAGA
40268 GTTGAAGAGTGAAGA
1 GTTGAAGAGTGAAGA
40283 G
1 G
40284 AGGATCATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.21
Consensus pattern (15 bp):
GTTGAAGAGTGAAGA
Found at i:40269 original size:23 final size:22
Alignment explanation
Indices: 40239--40283 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
40229 TTTCCTTTGT
40239 TGAAGAGTTGAAGAGTTGAAGAG
1 TGAAGAGTTGAAGAG-TGAAGAG
40262 TGAAGAGTTGAAGAGTGAAGAG
1 TGAAGAGTTGAAGAGTGAAGAG
40284 AGGATCATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (22 bp):
TGAAGAGTTGAAGAGTGAAGAG
Found at i:65575 original size:2 final size:2
Alignment explanation
Indices: 65559--65592 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
65549 ATTAATATTA
*
65559 AT AT AT AA AT A- 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 A
65593 ATGATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:73059 original size:69 final size:69
Alignment explanation
Indices: 72979--73289 Score: 354
Period size: 69 Copynumber: 4.5 Consensus size: 69
72969 GTCCATTTAC
* * * ** * *
72979 TTTTGCAGATTCTGTTCCAAGCACCCCTTCCTACACGGATAACATGTTTTATGGGAAGAGCTCGT
1 TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTATACAGATAACATGTTCAAGGGGAAGAGCTCAT
73044 CTAA
66 CTAA
** * * * *
73048 TTTTGTGGATTCTGTTCCGAGCACCCCTGCTTATACTGATAACCTGTTCAAGGGGAAGAGCTCAT
1 TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTATACAGATAACATGTTCAAGGGGAAGAGCTCAT
*
73113 CTAT
66 CTAA
* * * * * * *
73117 TTTTGCAGATTCTGTTCCAAGCACTCCTGCGTATTCAGATAGCATGTTCAAGGGGCAGGGTTCAT
1 TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTATACAGATAACATGTTCAAGGGGAAGAGCTCAT
*
73182 C-CA
66 CTAA
* * *
73185 TATTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAAAGCTCA
1 T-TTTGCAGATTCTGTTCCAAGCACCCCTGCCTATACAGATAACATGTTCAAGGGGAAGAGCTCA
*
73250 TCTAT
65 TCTAA
* *
73255 TTTTGCTGATTCTGTTCCAAGCACCCCTGCGTATA
1 TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTATA
73290 ATTATGGGAG
Statistics
Matches: 200, Mismatches: 40, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
68 1 0.00
69 198 0.99
70 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (69 bp):
TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTATACAGATAACATGTTCAAGGGGAAGAGCTCAT
CTAA
Found at i:80382 original size:7 final size:7
Alignment explanation
Indices: 80369--80409 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
80359 AGAAGCGCCT
80369 TGCCAAA
1 TGCCAAA
*
80376 CGCCAAA
1 TGCCAAA
80383 TGCCAAA
1 TGCCAAA
80390 TGCCAAA
1 TGCCAAA
*
80397 CGCCAAA
1 TGCCAAA
80404 TGCCAA
1 TGCCAA
80410 TGGTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.34, G:0.15, T:0.10
Consensus pattern (7 bp):
TGCCAAA
Found at i:80395 original size:21 final size:21
Alignment explanation
Indices: 80369--80409 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
80359 AGAAGCGCCT
80369 TGCCAAACGCCAAATGCCAAA
1 TGCCAAACGCCAAATGCCAAA
80390 TGCCAAACGCCAAATGCCAA
1 TGCCAAACGCCAAATGCCAA
80410 TGGTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.34, G:0.15, T:0.10
Consensus pattern (21 bp):
TGCCAAACGCCAAATGCCAAA
Found at i:88734 original size:22 final size:22
Alignment explanation
Indices: 88688--88741 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
88678 ATGACCTCCT
* * *
88688 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTAATAACCATAC
*
88710 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTAATAACCATAC
*
88732 TATAAAATTT
1 TATGAAATTT
88742 CGAAATTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTAATAACCATAC
Found at i:88820 original size:22 final size:21
Alignment explanation
Indices: 88795--89447 Score: 198
Period size: 22 Copynumber: 30.3 Consensus size: 21
88785 ATTTTTTATG
88795 ACCTCCTTATGAAATTTTGATA
1 ACCTCC-TATGAAATTTTGATA
*
88817 ACCTTCCTATGAAATTTTAATA
1 ACC-TCCTATGAAATTTTGATA
* * * * *
88839 ACGATACTATAAAATTTCGAGA
1 AC-CTCCTATGAAATTTTGATA
** *
88861 ACCTTTTTAT-AATTTTTTG-TA
1 ACC-TCCTATGAA-ATTTTGATA
* *
88882 ACCTTCTTATGAAATTTTGTTA
1 ACC-TCCTATGAAATTTTGATA
* *
88904 ACCTCCCTAAGGAATTTTGA-A
1 ACCT-CCTATGAAATTTTGATA
*
88925 GACCTCACTAT-ATAATTTTGATT
1 -ACCTC-CTATGA-AATTTTGATA
* * *
88948 ACTTCCCAATAAAATTTTGATA
1 ACCT-CCTATGAAATTTTGATA
* * *
88970 ACCAACACTATGAGATGTTGATA
1 ACC-TC-CTATGAAATTTTGATA
88993 ACCTCCATATG--A--TTGATA
1 ACCTCC-TATGAAATTTTGATA
* * * * *
89011 ACCACGTTATGAAAATTTAAAA
1 ACCTC-CTATGAAATTTTGATA
*
89033 ACCTCCATATGAAATGTT-AGTA
1 ACCTCC-TATGAAATTTTGA-TA
* * *
89055 ATCACACTCTGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
* * *** *
89077 ATCACACTGCAAAATTGTGATA
1 ACCTC-CTATGAAATTTTGATA
*
89099 AGCTCGCTATGAAATTTTGATGA
1 ACCTC-CTATGAAATTTTGAT-A
89122 ACCTTCCTAT-AAAGTTTTGATAA
1 ACC-TCCTATGAAA-TTTTGAT-A
*
89145 ACCTCCCTATAAAATTTTGATAA
1 ACCT-CCTATGAAATTTTGAT-A
*
89168 ACCTCCCTATAAAATTTTGATA
1 ACCT-CCTATGAAATTTTGATA
*
89190 A----CTA-CAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
**
89206 ACCTCCCTATGATTTTTTGATA
1 ACCT-CCTATGAAATTTTGATA
* * *
89228 ATCTCATTATGAAATTTTGTTA
1 ACCTC-CTATGAAATTTTGATA
* *
89250 ATCTCCGTATGAAATTTTGATTT
1 ACCTCC-TATGAAATTTTGA-TA
* * *
89273 ACATACTATGAAATTTTGGTA
1 ACCTCCTATGAAATTTTGATA
* *** *
89294 ACCCTCTTATGAAATTAAAAAA
1 A-CCTCCTATGAAATTTTGATA
* *
89316 AACTAAGCTATGAAATTTTGATA
1 ACCT--CCTATGAAATTTTGATA
* *
89339 ACCTTCATATGAAATTTTGGTA
1 ACC-TCCTATGAAATTTTGATA
* * * *
89361 TCCTCC-CTGAAATGTTGATT
1 ACCTCCTATGAAATTTTGATA
* * *
89381 A-CTCCATAATAAAAGTTTAATA
1 ACCTCC-T-ATGAAATTTTGATA
*
89403 ACCTTCC--T--AA-TTTGGTA
1 ACC-TCCTATGAAATTTTGATA
*
89420 ACCATACTATGAAATTTTGATA
1 ACC-TCCTATGAAATTTTGATA
89442 ACCTCC
1 ACCTCC
89448 CCATAAATAC
Statistics
Matches: 465, Mismatches: 113, Indels: 107
0.68 0.16 0.16
Matches are distributed among these distances:
16 12 0.03
17 13 0.03
18 16 0.03
19 5 0.01
20 13 0.03
21 36 0.08
22 268 0.58
23 93 0.20
24 9 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
ACCTCCTATGAAATTTTGATA
Found at i:88829 original size:114 final size:114
Alignment explanation
Indices: 88629--88858 Score: 460
Period size: 114 Copynumber: 2.0 Consensus size: 114
88619 ATATTCATAT
88629 GAAATTATGATAACCTCCCTATTAAATTATGATAATTACACTATTTTTTATGACCTCCTTATGAA
1 GAAATTATGATAACCTCCCTATTAAATTATGATAATTACACTATTTTTTATGACCTCCTTATGAA
88694 ATTTTGATAACCTTCCTATGAAATTTTAATAACGATACTATAAAATTTC
66 ATTTTGATAACCTTCCTATGAAATTTTAATAACGATACTATAAAATTTC
88743 GAAATTATGATAACCTCCCTATTAAATTATGATAATTACACTATTTTTTATGACCTCCTTATGAA
1 GAAATTATGATAACCTCCCTATTAAATTATGATAATTACACTATTTTTTATGACCTCCTTATGAA
88808 ATTTTGATAACCTTCCTATGAAATTTTAATAACGATACTATAAAATTTC
66 ATTTTGATAACCTTCCTATGAAATTTTAATAACGATACTATAAAATTTC
88857 GA
1 GA
88859 GAACCTTTTT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (114 bp):
GAAATTATGATAACCTCCCTATTAAATTATGATAATTACACTATTTTTTATGACCTCCTTATGAA
ATTTTGATAACCTTCCTATGAAATTTTAATAACGATACTATAAAATTTC
Found at i:89139 original size:23 final size:23
Alignment explanation
Indices: 89087--89190 Score: 138
Period size: 23 Copynumber: 4.6 Consensus size: 23
89077 ATCACACTGC
* * *
89087 AAAATTGTGAT-AAGCTCGCTAT
1 AAAATTTTGATAAACCTCCCTAT
* * *
89109 GAAATTTTGATGAACCTTCCTAT
1 AAAATTTTGATAAACCTCCCTAT
*
89132 AAAGTTTTGATAAACCTCCCTAT
1 AAAATTTTGATAAACCTCCCTAT
89155 AAAATTTTGATAAACCTCCCTAT
1 AAAATTTTGATAAACCTCCCTAT
89178 AAAATTTTGATAA
1 AAAATTTTGATAA
89191 CTACAAATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
22 9 0.13
23 62 0.87
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (23 bp):
AAAATTTTGATAAACCTCCCTAT
Found at i:89488 original size:22 final size:22
Alignment explanation
Indices: 89458--89630 Score: 91
Period size: 22 Copynumber: 7.9 Consensus size: 22
89448 CCATAAATAC
* * *
89458 CATTATGAAATTTTGGTAATCA
1 CATTTTGAAATTTTGATAACCA
* *
89480 CATTTTGAAAATTTGATAACCT
1 CATTTTGAAATTTTGATAACCA
* *
89502 C-TTTATGAAATTTTGTTAACCT
1 CATTT-TGAAATTTTGATAACCA
* * * * *
89524 C-TCTGTAAAATTTTGTTGA-CT
1 CAT-TTTGAAATTTTGATAACCA
* *
89545 CATCTATGAAATTTTGATAATCA
1 CAT-TTTGAAATTTTGATAACCA
* * * *
89568 CATTATGTAGTTTTGATAACCT
1 CATTTTGAAATTTTGATAACCA
** *
89590 CGCTTTGAAATTTTGATAACAA
1 CATTTTGAAATTTTGATAACCA
* *
89612 CATTATGAAAATTTGATAA
1 CATTTTGAAATTTTGATAA
89631 TCTTCCTATA
Statistics
Matches: 117, Mismatches: 30, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
21 6 0.05
22 106 0.91
23 5 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
CATTTTGAAATTTTGATAACCA
Found at i:89510 original size:44 final size:44
Alignment explanation
Indices: 89460--89630 Score: 145
Period size: 44 Copynumber: 3.9 Consensus size: 44
89450 ATAAATACCA
* *
89460 TTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTC-T
1 TTATGAAATTTTGATAA-CACATTATGAAAATTTGATAACCTCAT
* * * *
89504 TTATGAAATTTTGTTAAC-C-TCTCTGTAAAATTTTGTTGA-CTCAT
1 TTATGAAATTTTGATAACACAT-TATG-AAAA-TTTGATAACCTCAT
* * ** **
89548 CTATGAAATTTTGATAATCACATTATGTAGTTTTGATAACCTCGC
1 TTATGAAATTTTGATAA-CACATTATGAAAATTTGATAACCTCAT
89593 TT-TGAAATTTTGATAACAACATTATGAAAATTTGATAA
1 TTATGAAATTTTGATAAC-ACATTATGAAAATTTGATAA
89631 TCTTCCTATA
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 9 0.09
44 75 0.75
45 6 0.06
46 4 0.04
47 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (44 bp):
TTATGAAATTTTGATAACACATTATGAAAATTTGATAACCTCAT
Found at i:89574 original size:66 final size:66
Alignment explanation
Indices: 89465--89632 Score: 169
Period size: 66 Copynumber: 2.5 Consensus size: 66
89455 TACCATTATG
* * * * * * *
89465 AAATTTTGGTAATC-ACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGTTAACCTCTCTG
1 AAATTTTGATAA-CAACATTATGAAAATTTGATAATCACATTATGAAATTTTGATAACCTCGCTG
89529 TA
65 TA
* * * * * * *
89531 AAATTTTGTTGAC-TCATCTATGAAATTTTGATAATCACATTATGTAGTTTTGATAACCTCGCTT
1 AAATTTTGATAACAACAT-TATGAAAATTTGATAATCACATTATGAAATTTTGATAACCTCGCTG
*
89595 TG
65 TA
89597 AAATTTTGATAACAACATTATGAAAATTTGATAATC
1 AAATTTTGATAACAACATTATGAAAATTTGATAATC
89633 TTCCTATAAA
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
65 4 0.05
66 75 0.91
67 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (66 bp):
AAATTTTGATAACAACATTATGAAAATTTGATAATCACATTATGAAATTTTGATAACCTCGCTGT
A
Found at i:89766 original size:22 final size:22
Alignment explanation
Indices: 89753--89847 Score: 86
Period size: 22 Copynumber: 4.3 Consensus size: 22
89743 AACCTTCATC
89753 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCACACTA
* * * *
89775 TGAAATTTTGATAATCTCCCCA
1 TGAAATTTTGATAACCACACTA
* * *
89797 TAAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCACAC-TA
*
89819 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCACACTA
89841 TGAAATT
1 TGAAATT
89848 CTTATAATCT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
21 2 0.04
22 54 0.95
23 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACTA
Found at i:89863 original size:22 final size:22
Alignment explanation
Indices: 89838--89879 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
89828 GTTAACCACA
89838 CTATGAAATTCTT-ATAATCTTG
1 CTATGAAATT-TTGATAATCTTG
*
89860 CTATGACATTTTGATAATCT
1 CTATGAAATTTTGATAATCT
89880 CTTTGATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTTG
Found at i:90522 original size:44 final size:43
Alignment explanation
Indices: 90472--90596 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 43
90462 TATCCAAAAA
* *
90472 GAAATTTTGGTAACCACACTATGAAATTTTGATAACTTTCC-CAT
1 GAAATTTTGATAACCACA-TATGAAATTTTGATAAC-CTCCTCAT
*
90516 GAAATTTTGACAACTTC-CATATGAAATTTTGATAACCTCCTCAT
1 GAAATTTTGATAAC--CACATATGAAATTTTGATAACCTCCTCAT
* * *
90560 GAAATTATAATAACCATCTTATGAAATTTTGATAACC
1 GAAATTTTGATAACCA-CATATGAAATTTTGATAACC
90597 ACATAGAGAC
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.04
44 62 0.90
45 2 0.03
46 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (43 bp):
GAAATTTTGATAACCACATATGAAATTTTGATAACCTCCTCAT
Found at i:90572 original size:22 final size:22
Alignment explanation
Indices: 90472--90597 Score: 98
Period size: 22 Copynumber: 5.7 Consensus size: 22
90462 TATCCAAAAA
* *
90472 GAAATTTTGGTAACCA-CACTAT
1 GAAATTTTGATAACCATCTC-AT
** *
90494 GAAATTTTGATAACTTTCCCAT
1 GAAATTTTGATAACCATCTCAT
* *
90516 GAAATTTTGACAA-CTTC-CATAT
1 GAAATTTTGATAACCATCTC--AT
90538 GAAATTTTGATAACC-TCCTCAT
1 GAAATTTTGATAACCAT-CTCAT
* * *
90560 GAAATTATAATAACCATCTTAT
1 GAAATTTTGATAACCATCTCAT
90582 GAAATTTTGATAACCA
1 GAAATTTTGATAACCA
90598 CATAGAGACA
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 75 0.88
23 5 0.06
24 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
GAAATTTTGATAACCATCTCAT
Found at i:91097 original size:15 final size:13
Alignment explanation
Indices: 91043--91098 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
91033 TATAATTCGG
91043 TTTA-AATTGAAAT
1 TTTATAATT-AAAT
*
91056 TTTATAATTAATT
1 TTTATAATTAAAT
91069 TTTA-AATATAAAT
1 TTTATAAT-TAAAT
91082 TTTAATAATGTAAAT
1 TTT-ATAAT-TAAAT
91097 TT
1 TT
91099 AGGAATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 3 0.08
13 18 0.50
14 5 0.14
15 10 0.28
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (13 bp):
TTTATAATTAAAT
Found at i:92144 original size:20 final size:20
Alignment explanation
Indices: 92099--92145 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
92089 ATTTAAAACA
**
92099 AAATAAAAGCTACCCATTTT
1 AAATAAAAGCTACCCATTAC
92119 AAATAAAA-CTACCCATTAC
1 AAATAAAAGCTACCCATTAC
92138 AAGATAAA
1 AA-ATAAA
92146 TATAAGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.23
Consensus pattern (20 bp):
AAATAAAAGCTACCCATTAC
Found at i:101704 original size:2 final size:2
Alignment explanation
Indices: 101697--101721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
101687 TAACTTAGTG
101697 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
101722 TATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:102538 original size:7 final size:7
Alignment explanation
Indices: 102526--102554 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
102516 CCTGTTCCTG
102526 CTTCATA
1 CTTCATA
102533 CTTCATA
1 CTTCATA
102540 CTTCATA
1 CTTCATA
102547 CTTCATA
1 CTTCATA
102554 C
1 C
102555 ATACATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (7 bp):
CTTCATA
Found at i:117478 original size:17 final size:16
Alignment explanation
Indices: 117440--117480 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
117430 CCGGTGACCG
*
117440 GTGATCTTACATCACT
1 GTGATCTTAAATCACT
117456 GTTGATCTTAAATCACT
1 G-TGATCTTAAATCACT
117473 AGTGATCT
1 -GTGATCT
117481 GGGGGTGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (16 bp):
GTGATCTTAAATCACT
Found at i:118467 original size:1 final size:1
Alignment explanation
Indices: 118461--118489 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
118451 CAAAGTTCTC
118461 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
118490 GTATTCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:122295 original size:3 final size:3
Alignment explanation
Indices: 122287--122326 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
122277 CCACAAGAGC
*
122287 AAG AAG AAG AAG AAG AAG ACG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
122327 TGCGGTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:129945 original size:2 final size:2
Alignment explanation
Indices: 129938--129979 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
129928 AGAAGCAGAA
129938 AT AT AT AT 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 AT AT AT AT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.