Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014267.1 Corchorus olitorius cultivar O-4 contig14300, 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: 94160
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:615 original size:333 final size:334
Alignment explanation
Indices: 6--1648 Score: 2379
Period size: 333 Copynumber: 4.9 Consensus size: 334
1 ACTGT
* *
6 TTTTGGCTAAAAATGCGTTTCGGGGCCTTGGCTCAGTTTTGCATAATTTTTGGCA-AAATGACTT
1 TTTTGGCTAAAAATGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAAA-GACTT
* * * * * * * *
70 ATCGAATTATCCATAGTCATCTAATCAATTCTCTCAGCCACAATGCATTTACGGATTTATTTTTA
65 CTCGAAATATCTATATTCATCTAATCAA--ATCTCAGCCACATTGGATTTACGGATTTGTTTTTA
* ** * ** * *
135 CAAGTTTCCGAATCTTGTTCCGATATAATTAGAAATAAATTCAGACAAAAAATGGAAAAACGATA
128 CGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATA
200 TTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTG
193 TTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTG
* * *
265 GCCAAAAATTGGGGAAAAACTTGTCGGGTCAGTTTTTTGCAAAATTTTAGCCG-AAATCGTGTAC
258 GCAAAAAATTTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAAATCGTGTAC
329 T-ACCATCACAG
323 TAACCATCACAG
* *
340 TTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCC
1 TTTTGGCTAAAAATGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTTC
*
405 TCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGTTTTTACGA
66 TCGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTACGGATTTGTTTTTACGA
470 GCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAATAATGGAAAAACGATATT
131 GCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAA-AATGGAAAAACGATATT
* *
535 AGAAGCGTGAAATACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC
195 AGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC
* *
600 AAGAAATTTGGGAAAAACTTTTCAGGTCAGTTTTTTGCAAAATTTTAG-CGAAAATCGTGTACTA
260 AAAAAATTTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAAATCGTGTACTA
*
664 ACCATCACGG
325 ACCATCACAG
* ** * *
674 TTTTCGGCTAAAAATGCGTTTCGGGGCCCTCACTCAGTTTTGCATGATTTTTGGTAGAAAGGCTT
1 TTTT-GGCTAAAAATGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTT
*
739 CTCGAAATATCTATATTGATCTAATCAAATCTCTCAGCCACATTGGATTTACGGATTTGTTTTTA
65 CTCGAAATATCTATATTCATCTAATCAAA--TCTCAGCCACATTGGATTTACGGATTTGTTTTTA
* *
804 CGAGCATCTGAATCTTATTAAAATTTAATTAGAAATAAATTCAGAAAAAAAAAATGGAAAAACGA
128 CGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAG--AAAAAAAATGGAAAAACGA
* * *
869 TATTAGAAGCGTGAAAAACCCTAAAATAATTTTGGAGTTGAATTATATGAATTTTCTGAGTATTG
191 TATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTG
* *
934 TGG-AAAAAAATTGGAGAAAAACTTTTCGGGTCAGTTTATTGCAAAATTTTAGCCG-AAATCGTG
256 TGGCAAAAAATTTGG-GAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAAATCGTG
* *
997 ---T-A-CAT--GAT
320 TACTAACCATCACAG
* * *
1005 TTTTGGCTAAAAACGCGTTTCGGGGCTATGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCC
1 TTTTGGCTAAAAATGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTTC
*
1070 TCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGA-TT-TTTTTACGA
66 TCGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTACGGATTTGTTTTTACGA
1133 GCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATATTA
131 GCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATATTA
** *
1198 GAAGCGTG-AAAACTTTAAAATATTTTTGG-GATTGAATTATATGATTTTTCTGAGTATTGTGGC
196 GAAGCGTGAAAAACCCTAAAATAGTTTTGGCG-TTGAATTATATGATTTTTCTGAGTATTGTGGC
* ** *
1261 AAGAAATTTGGGAAAAACTTTTCATGTCTAGTTTTTAGTCAAAATTTTAG-CGAAAATCGTGTAC
260 AAAAAATTTGGGAAAAACTTTTCGGGTC-AGTTTTTTG-CAAAATTTTAGCCGAAAATCGTGTAC
*
1325 TAACCATCACGG
323 TAACCATCACAG
* ** * * *
1337 TTTTCGGCTAAAAATGCGTTTCGGGGCCCTCACTAAGTTTTGCATGATTTTTGGTAGAAAGGCTT
1 TTTT-GGCTAAAAATGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTT
*
1402 CTTGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACATTGGATTTACGGATTTGTTTTTA
65 CTCGAAATATCTATATTCATCTAATCAAA--TCTCAGCCACATTGGATTTACGGATTTGTTTTTA
* *
1467 CGAGCATCTGAATCTTATTAAAATTTAATTAGAAATAAATTCAGATAAAAAAATGGAAAAAACGA
128 CGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGA-AAAAAAATGG-AAAAACGA
*
1532 TAATAGAAGCGT-AAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTG
191 TATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTG
* *
1596 TGGAAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGC
256 TGGCAAAAAATTTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGC
1649 TGAAGTCCGA
Statistics
Matches: 1177, Mismatches: 99, Indels: 62
0.88 0.07 0.05
Matches are distributed among these distances:
322 1 0.00
323 63 0.05
324 50 0.04
325 19 0.02
326 48 0.04
327 2 0.00
328 25 0.02
329 1 0.00
330 82 0.07
331 4 0.00
332 79 0.07
333 216 0.18
334 93 0.08
335 108 0.09
336 2 0.00
337 145 0.12
338 138 0.12
339 100 0.08
340 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (334 bp):
TTTTGGCTAAAAATGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTTC
TCGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTACGGATTTGTTTTTACGA
GCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATATTA
GAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCA
AAAAATTTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAAATCGTGTACTAA
CCATCACAG
Found at i:1378 original size:663 final size:667
Alignment explanation
Indices: 4--1648 Score: 2727
Period size: 663 Copynumber: 2.5 Consensus size: 667
1 ACT
* * ** * * *
4 GTTTTTGGCTAAAAATGCGTTTCGGGGCCTTGGCTCAGTTTTGCATAATTTTTGGCA-AAATGAC
1 GTTTTCGGCTAAAAATGCGTTTCGGGGCCCTCACTCAGTTTTGCATGATTTTTGGTAGAAA-GGC
* * * * * * * *
68 TTATCGAATTATCCATAGTCATCTAATCAATTCTCTCAGCCACAATGCATTTACGGATTTATTTT
65 TTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACATTGGATTTACGGATTTGTTTT
* ** * * *** * *
133 TACAAGTTTCCGAATCTTGTTCCGATATAATTAGAAATAAATTCAG-ACAAAAAATGGAAAAACG
130 TACGAGCATCTGAATCTTATTAAAATTTAATTAGAAATAAATTCAGAAAAAAAAATGGAAAAACG
197 ATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATT
195 ATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATT
** *
262 GTGGCCAAAAATTGGGGAAAAACTTGTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGT
260 GTGGAAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTG-
327 ACTACCATCACAGTTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTG
324 A-TACCAT-ACAGTTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTG
392 GCAGAAAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGA
387 GCAGAAAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGA
457 TTTGTTTTTACGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAATAATG
452 TTTGTTTTTACGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAATAATG
522 GAAAAACGATATTAGAAGCGTGAAATACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTTC
517 GAAAAACGATATTAGAAGCGTGAAATACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTTC
*
587 TGAGTATTGTGGCAAGAAATTTGGGAAAAACTTTTCAGGTCAGTTTTTTGCAAAATTTTAGCGAA
582 TGAGTATTGTGGCAAGAAATTTGGGAAAAACTTTTCAGGTCAGTTTTTAGCAAAATTTTAGCGAA
652 AATCGTGTACTAACCATCACG
647 AATCGTGTACTAACCATCACG
673 GTTTTCGGCTAAAAATGCGTTTCGGGGCCCTCACTCAGTTTTGCATGATTTTTGGTAGAAAGGCT
1 GTTTTCGGCTAAAAATGCGTTTCGGGGCCCTCACTCAGTTTTGCATGATTTTTGGTAGAAAGGCT
*
738 TCTCGAAATATCTATATTGATCTAATCAAATCTCTCAGCCACATTGGATTTACGGATTTGTTTTT
66 TCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACATTGGATTTACGGATTTGTTTTT
803 ACGAGCATCTGAATCTTATTAAAATTTAATTAGAAATAAATTCAGAAAAAAAAAATGGAAAAACG
131 ACGAGCATCTGAATCTTATTAAAATTTAATTAGAAATAAATTCAG-AAAAAAAAATGGAAAAACG
* * *
868 ATATTAGAAGCGTGAAAAACCCTAAAATAATTTTGGAGTTGAATTATATGAATTTTCTGAGTATT
195 ATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATT
* *
933 GTGGAAAAAAATTGGAGAAAAACTTTTCGGGTCAGTTTATTGCAAAATTTTAGCCGAAATCGTG-
260 GTGGAAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGA
* * *
997 TA-CAT-GATTTTTGGCTAAAAACGCGTTTCGGGGCTATGGCTCAGTTTTGCATGATTTTTGGCA
325 TACCATACAGTTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCA
1060 GAAAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGA-TT
390 GAAAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTT
1124 -TTTTTACGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAA-AATGGAA
455 GTTTTTACGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAATAATGGAA
**
1187 AAACGATATTAGAAGCGTGAAA-ACTTTAAAATATTTTTGG-GATTGAATTATATGATTTTTCTG
520 AAACGATATTAGAAGCGTGAAATACCCTAAAATATTTTTGGCG-TTGAATTATATGATTTTTCTG
*
1250 AGTATTGTGGCAAGAAATTTGGGAAAAACTTTTCATGTCTAGTTTTTAGTCAAAATTTTAGCGAA
584 AGTATTGTGGCAAGAAATTTGGGAAAAACTTTTCAGGTC-AGTTTTTAG-CAAAATTTTAGCGAA
1315 AATCGTGTACTAACCATCACG
647 AATCGTGTACTAACCATCACG
*
1336 GTTTTCGGCTAAAAATGCGTTTCGGGGCCCTCACTAAGTTTTGCATGATTTTTGGTAGAAAGGCT
1 GTTTTCGGCTAAAAATGCGTTTCGGGGCCCTCACTCAGTTTTGCATGATTTTTGGTAGAAAGGCT
*
1401 TCTTGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACATTGGATTTACGGATTTGTTTTT
66 TCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACATTGGATTTACGGATTTGTTTTT
*
1466 ACGAGCATCTGAATCTTATTAAAATTTAATTAGAAATAAATTCAGATAAAAAAATGGAAAAAACG
131 ACGAGCATCTGAATCTTATTAAAATTTAATTAGAAATAAATTCAGAAAAAAAAATGG-AAAAACG
*
1531 ATAATAGAAGCGT-AAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATT
195 ATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATT
1595 GTGGAAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGC
260 GTGGAAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGC
1649 TGAAGTCCGA
Statistics
Matches: 918, Mismatches: 51, Indels: 21
0.93 0.05 0.02
Matches are distributed among these distances:
660 1 0.00
661 75 0.08
662 148 0.16
663 283 0.31
664 2 0.00
665 117 0.13
667 3 0.00
668 2 0.00
669 146 0.16
670 3 0.00
671 138 0.15
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (667 bp):
GTTTTCGGCTAAAAATGCGTTTCGGGGCCCTCACTCAGTTTTGCATGATTTTTGGTAGAAAGGCT
TCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACATTGGATTTACGGATTTGTTTTT
ACGAGCATCTGAATCTTATTAAAATTTAATTAGAAATAAATTCAGAAAAAAAAATGGAAAAACGA
TATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTG
TGGAAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGAT
ACCATACAGTTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAG
AAAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTG
TTTTTACGAGCATCTGAATCTTGTTAAGATTTAATTAGAAATAAATTCAGAAAAAATAATGGAAA
AACGATATTAGAAGCGTGAAATACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTTCTGAG
TATTGTGGCAAGAAATTTGGGAAAAACTTTTCAGGTCAGTTTTTAGCAAAATTTTAGCGAAAATC
GTGTACTAACCATCACG
Found at i:3859 original size:99 final size:99
Alignment explanation
Indices: 3696--3930 Score: 303
Period size: 99 Copynumber: 2.4 Consensus size: 99
3686 AAAGCAAGAA
* * *
3696 AAAATGGGGACTATGCTAAGCGAAATGTATGCAAGGCAAGATGAAGCAAAGATGAAGGAAATGGA
1 AAAATGGGGACTATGCTAAGCGAAATCTATGAAAGGCAAGACGAAGCAAAGATGAAGGAAATGGA
* *
3761 AGAAACTATGAAGCAAATTC-TGGCCCAGCAAATG
66 AGAAACTATGAA-CAAAATCTTGGCCCAGCAAATC
** * * *
3795 AACGTGGGGACTAGGCTAAGCGAAATCTATGAAAGGCAAGACGAAGGAAAGATGAAGGAGATGGA
1 AAAATGGGGACTATGCTAAGCGAAATCTATGAAAGGCAAGACGAAGCAAAGATGAAGGAAATGGA
* * *
3860 AGAAACTGTGAACAAAATCTTGGCCGATCAAATC
66 AGAAACTATGAACAAAATCTTGGCCCAGCAAATC
* *
3894 AAAATGGGG-CATATGCTATGGGAAATCTATGAAAGGC
1 AAAATGGGGAC-TATGCTAAGCGAAATCTATGAAAGGC
3931 GAGAAGCTAA
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
98 7 0.06
99 109 0.94
ACGTcount: A:0.42, C:0.13, G:0.29, T:0.17
Consensus pattern (99 bp):
AAAATGGGGACTATGCTAAGCGAAATCTATGAAAGGCAAGACGAAGCAAAGATGAAGGAAATGGA
AGAAACTATGAACAAAATCTTGGCCCAGCAAATC
Found at i:4044 original size:24 final size:24
Alignment explanation
Indices: 4012--4061 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4002 AATTCTGGCC
4012 AAACTTGGAGAGATGGAAAAGAAA
1 AAACTTGGAGAGATGGAAAAGAAA
*
4036 AAACTTGGAGAGATGGACAAGAAA
1 AAACTTGGAGAGATGGAAAAGAAA
4060 AA
1 AA
4062 TGAATATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.28, T:0.12
Consensus pattern (24 bp):
AAACTTGGAGAGATGGAAAAGAAA
Found at i:6868 original size:99 final size:99
Alignment explanation
Indices: 6697--6875 Score: 295
Period size: 99 Copynumber: 1.8 Consensus size: 99
6687 AAAGCAAGAA
* *
6697 AAAATGGGGACTATGCTAAGCGAAATCTACCAAAGGCAAGATGTAGAAAAGATGAAGGAAATGGA
1 AAAATGGGGACTATGCTAAGCGAAATCTACCAAAGGCAAGATGAAGAAAAGATGAAGGAAATAGA
6762 AGAAACTATGAAGAAAATTCTGGCCGATCAAATG
66 AGAAACTATGAAGAAAATTCTGGCCGATCAAATG
* * * * *
6796 AAAATGGGGACTATGCTAAGCGAAATTTATCAAAGGCAAGATGAAGCAAAGATGAGGGAGATAGA
1 AAAATGGGGACTATGCTAAGCGAAATCTACCAAAGGCAAGATGAAGAAAAGATGAAGGAAATAGA
6861 AGAAACTATGAAGAA
66 AGAAACTATGAAGAA
6876 CTATCAAAGG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 73 1.00
ACGTcount: A:0.46, C:0.11, G:0.26, T:0.17
Consensus pattern (99 bp):
AAAATGGGGACTATGCTAAGCGAAATCTACCAAAGGCAAGATGAAGAAAAGATGAAGGAAATAGA
AGAAACTATGAAGAAAATTCTGGCCGATCAAATG
Found at i:6910 original size:54 final size:54
Alignment explanation
Indices: 6823--6929 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
6813 AAGCGAAATT
*
6823 TATCAAAGGCAAGATGAAGCAAAGATGAGGGAGATAGAAGAAACTATGAAGAAC
1 TATCAAAGGCAAGATGAAGCAAAGATGAAGGAGATAGAAGAAACTATGAAGAAC
*
6877 TATCAAAGGCAAGATGAAGCAAAGATGAAGGAGATGGAAGAAACTATGAAGAA
1 TATCAAAGGCAAGATGAAGCAAAGATGAAGGAGATAGAAGAAACTATGAAGAA
6930 AATTCTGGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.50, C:0.08, G:0.28, T:0.13
Consensus pattern (54 bp):
TATCAAAGGCAAGATGAAGCAAAGATGAAGGAGATAGAAGAAACTATGAAGAAC
Found at i:8807 original size:78 final size:78
Alignment explanation
Indices: 8717--8865 Score: 237
Period size: 78 Copynumber: 1.9 Consensus size: 78
8707 AGGCAAGAAC
8717 AAATGGGGACTATGCTAAGCCAAATCTATGC-AAGGCCAGATGAAGCAAACACGAAGGAAATGGA
1 AAATGGGGACTATGCTAAGCCAAATCTAT-CAAAGGCCAGATGAAGCAAACACGAAGGAAATGGA
8781 AGAAACTGTGAAGA
65 AGAAACTGTGAAGA
* * * * *
8795 AAATGGGGACTATGCTAAGCGAAATTTATCAAAGGCCAGATGAATCAAAGACGAAGGAAGTGGAA
1 AAATGGGGACTATGCTAAGCCAAATCTATCAAAGGCCAGATGAAGCAAACACGAAGGAAATGGAA
8860 GAAACT
66 GAAACT
8866 ATATTGAAGC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 1 0.02
78 64 0.98
ACGTcount: A:0.44, C:0.14, G:0.27, T:0.15
Consensus pattern (78 bp):
AAATGGGGACTATGCTAAGCCAAATCTATCAAAGGCCAGATGAAGCAAACACGAAGGAAATGGAA
GAAACTGTGAAGA
Found at i:8997 original size:102 final size:100
Alignment explanation
Indices: 8793--9009 Score: 327
Period size: 96 Copynumber: 2.2 Consensus size: 100
8783 AAACTGTGAA
*
8793 GAAAATGGGGACTATGCTAAGCGAAATTTATCAAAGGCCAGATGAATCAAAGACGAAGGAAGTGG
1 GAAAATGGGGACTATGCTAAGCGAAAGTTATCAAAGGCCA-ATGAATCAAAGACGAAGGAAGTGG
* *
8858 AAGAAACTATATTGAAGCAAATTCTGGCCGATCAAAT
65 AAGAAAC-ATATTGAAGAAAATTCAGGCCGATCAAAT
*
8895 GAAAATGGGGACTATGCTAAGCGAAAGTTATCAAAGG-C-ATGAATCCAAGACGAAGGGAA-TGG
1 GAAAATGGGGACTATGCTAAGCGAAAGTTATCAAAGGCCAATGAATCAAAGACGAA-GGAAGTGG
*
8957 AAGAAAC-TA-TGAAGAAAATTCAGGCGGATCAAAT
65 AAGAAACATATTGAAGAAAATTCAGGCCGATCAAAT
8991 GAAAATGGGGACTATGCTA
1 GAAAATGGGGACTATGCTA
9010 CGCCAAATCC
Statistics
Matches: 109, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
96 41 0.38
97 2 0.02
99 25 0.23
100 4 0.04
101 1 0.01
102 36 0.33
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.18
Consensus pattern (100 bp):
GAAAATGGGGACTATGCTAAGCGAAAGTTATCAAAGGCCAATGAATCAAAGACGAAGGAAGTGGA
AGAAACATATTGAAGAAAATTCAGGCCGATCAAAT
Found at i:9203 original size:29 final size:30
Alignment explanation
Indices: 9143--9222 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
9133 GCTAAATACC
*
9143 CAAAAAAATCCCTTATGTTTCACTTTCGGGA
1 CAAAATAATCCCTTATGTTT-ACTTTCGGGA
* *
9174 CAAAATAATCCCTTATGTTT-TTTTTGGGA
1 CAAAATAATCCCTTATGTTTACTTTCGGGA
* *
9203 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
9223 CAAAAGTGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 25 0.57
31 19 0.43
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTACTTTCGGGA
Found at i:11083 original size:27 final size:28
Alignment explanation
Indices: 11027--11093 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 28
11017 AGCTAGTTTT
*
11027 GAGAAAGATGATGAGCAAGATTTGGCAGAA
1 GAGAAAGATGATGAGCAAGATCT-G-AGAA
11057 GAGAAAGATGATGAGCAAGATCT-AGAA
1 GAGAAAGATGATGAGCAAGATCTGAGAA
11084 GA-AATAGATG
1 GAGAA-AGATG
11094 CTGCAGAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
30 22 0.63
ACGTcount: A:0.46, C:0.06, G:0.31, T:0.16
Consensus pattern (28 bp):
GAGAAAGATGATGAGCAAGATCTGAGAA
Found at i:14683 original size:29 final size:30
Alignment explanation
Indices: 14646--14719 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
14636 CTCACTTTTG
* *
14646 AAACTTAAGGGATTAATTTGTCCCTAAA-A
1 AAACATAAGGGATTAATTTGTCCCGAAAGA
* *
14675 AAACATAAGGGATTATTTTGTCCCGAAAGTG
1 AAACATAAGGGATTAATTTGTCCCGAAAG-A
14706 AAACATAAGGGATT
1 AAACATAAGGGATT
14720 TTTTTGGGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 25 0.64
31 14 0.36
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCGAAAGA
Found at i:15134 original size:1 final size:1
Alignment explanation
Indices: 15128--15161 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
15118 ATGGAAAAGT
* *
15128 AAAAAAAAATAAAAAAAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15162 CCGAGGCCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.03, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:15140 original size:10 final size:10
Alignment explanation
Indices: 15122--15161 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
15112 TGGGAAATGG
*
15122 AAAAGTAAAA
1 AAAAATAAAA
15132 AAAAATAAAA
1 AAAAATAAAA
15142 AAAAA-AAAA
1 AAAAATAAAA
*
15151 AAAAACAAAA
1 AAAAATAAAA
15161 A
1 A
15162 CCGAGGCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.90, C:0.03, G:0.03, T:0.05
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:15485 original size:89 final size:89
Alignment explanation
Indices: 15333--15599 Score: 464
Period size: 89 Copynumber: 3.0 Consensus size: 89
15323 AGATTCATAT
*
15333 TAGGTATTGTACATGAGATTTGAAATGAAGATTACACTTAAACTTCGTTTGACCGGGATATCAAT
1 TAGGTATTGTACATGAGATTTGAAATGAAGATTACACTTAAACTTCGTTTGACCGGGACATCAAT
*
15398 GTACCGGCCCAACGACTGATGTAC
66 GCACCGGCCCAACGACTGATGTAC
* * *
15422 TAGGTATTGTAGATGAGATTTGAAATGAAGATTATACTTAAACTTCGTTTGACCGGAACATCAAT
1 TAGGTATTGTACATGAGATTTGAAATGAAGATTACACTTAAACTTCGTTTGACCGGGACATCAAT
* *
15487 GCACCGGTCCAACGACTGATGTAG
66 GCACCGGCCCAACGACTGATGTAC
15511 TAGGTATTGTACATGAGATTTGAAATGAAGATTACACTTAAACTTCGTTTGACCGGGACATCAAT
1 TAGGTATTGTACATGAGATTTGAAATGAAGATTACACTTAAACTTCGTTTGACCGGGACATCAAT
15576 GCACC-GCCCAACGACTGATGTAC
66 GCACCGGCCCAACGACTGATGTAC
15599 T
1 T
15600 GACACATTAT
Statistics
Matches: 166, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
88 17 0.10
89 149 0.90
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (89 bp):
TAGGTATTGTACATGAGATTTGAAATGAAGATTACACTTAAACTTCGTTTGACCGGGACATCAAT
GCACCGGCCCAACGACTGATGTAC
Found at i:43311 original size:24 final size:24
Alignment explanation
Indices: 43279--43351 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
43269 AGTGAAGCTG
43279 CAGTCAACCTTCCTAGACAAGATT
1 CAGTCAACCTTCCTAGACAAGATT
43303 CAGTCAACCTTCCTAGACAAGATT
1 CAGTCAACCTTCCTAGACAAGATT
*
43327 CAGTCAACCTTCCAAGACAAGATT
1 CAGTCAACCTTCCTAGACAAGATT
43351 C
1 C
43352 TGATTTATCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.23
Consensus pattern (24 bp):
CAGTCAACCTTCCTAGACAAGATT
Found at i:50276 original size:3 final size:3
Alignment explanation
Indices: 50268--50307 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
50258 TTCAGTGAAA
* * *
50268 AAT AAT AAT AAT AAC AAT AAT TAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
50308 GTTAAGTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:50288 original size:15 final size:15
Alignment explanation
Indices: 50268--50307 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
50258 TTCAGTGAAA
50268 AATAATAATAATAAC
1 AATAATAATAATAAC
*
50283 AATAATTATAATAAC
1 AATAATAATAATAAC
50298 AATAATAATA
1 AATAATAATA
50308 GTTAAGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:68597 original size:12 final size:12
Alignment explanation
Indices: 68580--68605 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
68570 AGCTACGTAT
68580 ATCACTAGAAAG
1 ATCACTAGAAAG
68592 ATCACTAGAAAG
1 ATCACTAGAAAG
68604 AT
1 AT
68606 TGTTAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (12 bp):
ATCACTAGAAAG
Found at i:74358 original size:26 final size:26
Alignment explanation
Indices: 74322--74374 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
74312 TGCAAACATA
74322 TGAGGTAGAAAAGCATATAATGATTC
1 TGAGGTAGAAAAGCATATAATGATTC
74348 TGAGGTAGAAAAGCATATAATGATTC
1 TGAGGTAGAAAAGCATATAATGATTC
74374 T
1 T
74375 CAGTGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (26 bp):
TGAGGTAGAAAAGCATATAATGATTC
Found at i:82521 original size:63 final size:63
Alignment explanation
Indices: 82351--82534 Score: 289
Period size: 67 Copynumber: 2.9 Consensus size: 63
82341 ACACAATTTC
* * * *
82351 CATTTTCCAATTTCCCACAAAGGGAGAAGTTCTAATTACATCCCAAAAAGGCCAAATCTATGG
1 CATTTTCCAGTATCCCACAAAGGGAGAAGTTCTATTTACATCCCAAAAAGGCCAAATCTAAGG
82414 CATTTTTCCAGTAGTATCCCACAAAGGGAGAAGTTCTATTTACATCCCAAAAAGGCCAAATCTAA
1 CA-TTTTCC---AGTATCCCACAAAGGGAGAAGTTCTATTTACATCCCAAAAAGGCCAAATCTAA
82479 GG
62 GG
82481 CATTTTCCAGTATCCCACAAAGGGAGAAGTTCTATTTACATCCC-AAAAGGCCAA
1 CATTTTCCAGTATCCCACAAAGGGAGAAGTTCTATTTACATCCCAAAAAGGCCAA
82535 CTAACTATGG
Statistics
Matches: 113, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
62 10 0.09
63 38 0.34
64 6 0.05
66 6 0.05
67 53 0.47
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (63 bp):
CATTTTCCAGTATCCCACAAAGGGAGAAGTTCTATTTACATCCCAAAAAGGCCAAATCTAAGG
Found at i:89825 original size:39 final size:39
Alignment explanation
Indices: 89771--89851 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
89761 AGGACGAAGT
89771 TGATGCTTTTGGGCTCATAATAGGCGATCTAACTGGAGG
1 TGATGCTTTTGGGCTCATAATAGGCGATCTAACTGGAGG
89810 TGATGCTTTTGGGCTCATAATAGGCGATCTAACTGGAGG
1 TGATGCTTTTGGGCTCATAATAGGCGATCTAACTGGAGG
89849 TGA
1 TGA
89852 CTTAGAAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (39 bp):
TGATGCTTTTGGGCTCATAATAGGCGATCTAACTGGAGG
Done.