Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014017.1 Corchorus olitorius cultivar O-4 contig14050, 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: 17599
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:581 original size:68 final size:69
Alignment explanation
Indices: 452--765 Score: 560
Period size: 68 Copynumber: 4.6 Consensus size: 69
442 CCGAATGCTT
*
452 TAGGCTTTTCCACAAGCCAAACTAGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
517 CATA
66 CATA
*
521 TAGGCTTTTCCACAAGCCAAACTCGTTT-CATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAAC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
585 CATA
66 CATA
589 TAGGCTTTTCCACAAGCCAAACTCGTTT-CATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
*
653 CACA
66 CATA
* *
657 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTTAAGCCTTGGTTTCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
722 CATA
66 CATA
*
726 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
766 AGCCTTACTT
Statistics
Matches: 235, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
68 133 0.57
69 102 0.43
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (69 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
CATA
Found at i:805 original size:137 final size:132
Alignment explanation
Indices: 452--779 Score: 424
Period size: 137 Copynumber: 2.4 Consensus size: 132
442 CCGAATGCTT
* ** *
452 TAGGCTTTTCCACAAGCCAAACTAGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTT-CATACGAGTC----TAAGCCTTACTTCCAACCAAGC
* *
517 CATATAGGCTTTTCCACAAGCCAAACTCGTTTCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
61 CACATAAGCTTTTCCACAAGCCAAACTCGTTTCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
582 AACCATA
126 AACCATA
** *
589 TAGGCTTTTCCACAAGCCAAACTCGTTTCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCATACGAGTC----TAAGCCTTACTTCCAACCAAGCC
* * *
654 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTTAAGCCTTGGTTTCATCCA
62 ACATAAGCTTTTCCACAAGCCAAACTCGTTT-CATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
*
719 AGCCATA
126 AACCATA
*
726 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTC-AAGCCTTACTTCCAA
1 TAGGCTTTTCCACAAGCCAAACTCGTTT-CATACGAGTCTAAGCCTTACTTCCAA
780 GTAGGCTCAA
Statistics
Matches: 180, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
133 12 0.07
136 67 0.37
137 91 0.51
138 10 0.06
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (132 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCATACGAGTCTAAGCCTTACTTCCAACCAAGCCACAT
AAGCTTTTCCACAAGCCAAACTCGTTTCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAACCA
TA
Found at i:1087 original size:167 final size:168
Alignment explanation
Indices: 811--1364 Score: 854
Period size: 167 Copynumber: 3.3 Consensus size: 168
801 TTCCATTTGA
* * * *
811 TAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCACCAAAAATTCATGTTTAAG-TTAAA
1 TAAAACCTCCGGGTACCATTTCATTTCATCAAATTTTTCATCAAAAATTCATGTTTAAGTTTAAA
* * * *
875 ATCCCTGGTCAAGGTCTCTACTCAGAGTTTGCGTTGGTTAGTCCTCCGGGCACAAATTCAGAAAC
66 ATCCTTGTTCAAGGTCTCTACTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAAC
*
940 CTCTGGTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
131 CTCCGGTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
* *
978 TAAAACCTCCGGTTACCATTTCATTTCATCAAGTTTTTCATC-AAAATTCATGTTTAAGTTTAAA
1 TAAAACCTCCGGGTACCATTTCATTTCATCAAATTTTTCATCAAAAATTCATGTTTAAGTTTAAA
* * *
1042 ATCCTTGTTCAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCACAAAGTCAGAAAC
66 ATCCTTGTTCAAGGTCTCTACTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAAC
1107 CTCCGGGTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
131 CTCC-GGTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
*
1146 TAAAACCTCCGGGTACCATTTGATTTCATCAAATTTTTCATC-AAAA---A--TTTAAGTTTAAA
1 TAAAACCTCCGGGTACCATTTCATTTCATCAAATTTTTCATCAAAAATTCATGTTTAAGTTTAAA
* *
1205 ATCCTTGTTTAAGGTCTCTAGTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAAC
66 ATCCTTGTTCAAGGTCTCTACTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAAC
* * *
1270 CTCCAGTAGTAATTTTGATAAGTCCTCTGGGCAATCGG
131 CTCCGGTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
*
1308 TAAAACCTCCGGGTACCATTTGATTTCATCAAATTTTTCATCAAAAATTCATGTTTA
1 TAAAACCTCCGGGTACCATTTCATTTCATCAAATTTTTCATCAAAAATTCATGTTTA
1365 TGAACCTTGT
Statistics
Matches: 357, Mismatches: 22, Indels: 15
0.91 0.06 0.04
Matches are distributed among these distances:
162 73 0.20
163 81 0.23
165 1 0.00
166 17 0.05
167 104 0.29
168 81 0.23
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (168 bp):
TAAAACCTCCGGGTACCATTTCATTTCATCAAATTTTTCATCAAAAATTCATGTTTAAGTTTAAA
ATCCTTGTTCAAGGTCTCTACTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAAC
CTCCGGTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
Found at i:1507 original size:38 final size:38
Alignment explanation
Indices: 1451--1563 Score: 140
Period size: 38 Copynumber: 3.0 Consensus size: 38
1441 ATTCTACTTT
**
1451 ATCAG-TTTATTTCGATCCTGGTTTAGGATCATTGTGTG
1 ATCAGTTTTATTTTAATCCTGGTTTAGGATCATTGT-TG
* * *
1489 AT-TGTTTTATTTTAATCCTGGTTTAGGATCAGTGCTTT
1 ATCAGTTTTATTTTAATCCTGGTTTAGGATCATTG-TTG
*
1527 ATCAGTTTTATTTTAATCCTGGTTGAGGATCATTGTT
1 ATCAGTTTTATTTTAATCCTGGTTTAGGATCATTGTT
1564 TTATGTTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
37 1 0.02
38 33 0.52
39 30 0.47
ACGTcount: A:0.19, C:0.12, G:0.20, T:0.49
Consensus pattern (38 bp):
ATCAGTTTTATTTTAATCCTGGTTTAGGATCATTGTTG
Found at i:1528 original size:30 final size:30
Alignment explanation
Indices: 1489--2109 Score: 542
Period size: 30 Copynumber: 20.3 Consensus size: 30
1479 TCATTGTGTG
*
1489 ATTGTTTTATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
* *
1519 AGTGCTTTATCAGTTTTATTTTAATCCTGGTTGAGGATC
1 ATTGC-TT-T-A----T-T-TTAATCCTGGTTTAGGATC
* * * *
1558 ATTGTTTTATGTTAATCCTGGTTGAGGATT
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
* *
1588 GTTGCTTTATGTTAATCCT-GTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
1618 ATTGCTTTATTTTAATCCT-GTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
* * *
1648 ATTGCTTTATTCTAATCCTGGTTGAGAATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
* * **
1678 GTTGCTTTA-TTCAAT-CTTATTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
* *
1707 ATTGCTTTATGTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
* * * *
1737 ATTGTTTTATGTTAATTCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
* * * *
1767 GTTGCTTTATTATAATCAT-ATTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
*
1797 ATTGCTTTATGTTAATCCT-GTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
* *
1827 ATTGCTTTATGTTAAT-CTTGTTTAAGGATC
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
* * *
1857 ATTGCTTTATGTTGATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
* *
1887 ATTGCTATATGTTAATCCT-GTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
* *
1917 ATTGCTTTATGTTAAT-CTTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTT-AGGATC
* * * *
1947 GTCGCTTTATTTTAGTCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
* *
1977 GTTG-TTTAATTTTCAATCCTGGTTGAGGATC
1 ATTGCTTT-ATTTT-AATCCTGGTTTAGGATC
* *
2008 GTTGCTTTATTATAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
2038 ATTGCTTTATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
* * * *
2068 ATTGCTTTATCAGTTAATCCCGATGTAGGATC
1 ATTGCTTTAT--TTTAATCCTGGTTTAGGATC
*
2100 ATTGCATTAT
1 ATTGCTTTAT
2110 GAATTAATTT
Statistics
Matches: 497, Mismatches: 69, Indels: 48
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.01
29 32 0.06
30 360 0.72
31 43 0.09
32 30 0.06
33 1 0.00
36 1 0.00
37 2 0.00
38 3 0.01
39 21 0.04
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.47
Consensus pattern (30 bp):
ATTGCTTTATTTTAATCCTGGTTTAGGATC
Found at i:1546 original size:39 final size:39
Alignment explanation
Indices: 1447--1567 Score: 149
Period size: 39 Copynumber: 3.2 Consensus size: 39
1437 AACTATTCTA
**
1447 CTTTATCAG-TTTATTTCGATCCTGGTTTAGGATCATTG
1 CTTTATCAGTTTTATTTTAATCCTGGTTTAGGATCATTG
* * *
1485 -TGTGAT-TGTTTTATTTTAATCCTGGTTTAGGATCAGTG
1 CT-TTATCAGTTTTATTTTAATCCTGGTTTAGGATCATTG
*
1523 CTTTATCAGTTTTATTTTAATCCTGGTTGAGGATCATTG
1 CTTTATCAGTTTTATTTTAATCCTGGTTTAGGATCATTG
*
1562 TTTTAT
1 CTTTAT
1568 GTTAATCCTG
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
37 2 0.03
38 32 0.46
39 35 0.51
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (39 bp):
CTTTATCAGTTTTATTTTAATCCTGGTTTAGGATCATTG
Found at i:1607 original size:60 final size:60
Alignment explanation
Indices: 1533--2110 Score: 673
Period size: 60 Copynumber: 9.6 Consensus size: 60
1523 CTTTATCAGT
* * **
1533 TTTATTTTAATCCTGGTTGAGGATCATTGTTTTATGTTAATCCTGGTTGAGGATTGTTGC
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
* * *
1593 TTTATGTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
* * * * **
1653 TTTAT-TCTAATCCTGGTTGAGAATCGTTGCTTTAT-TCAATCTTATTTGAGGATCATTGC
1 TTTATGT-TAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
* * *
1712 TTTATGTTAATCCTGGTTGAGGATCATTGTTTTATGTTAATTCTGGTTGAGGATCGTTGC
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
* ** *
1772 TTTAT-TATAATCATATTTGAGGATCATTGCTTTATGTTAATCCTGTTTGAGGATCATTGC
1 TTTATGT-TAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
* * * *
1832 TTTATGTTAATCTTGTTTAAGGATCATTGCTTTATGTTGATCCTGGTTGAGGATCATTGC
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
* * * * * *
1892 TATATGTTAATCCTGTTTGAGGATCATTGCTTTATGTTAATCTTGTTTGAGGATCGTCGC
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
* * * * *
1952 TTTATTTTAGTCCTGGTTGAGGATCGTTG-TTTAATTTTCAATCCTGGTTGAGGATCGTTGC
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTT-ATGTT-AATCCTGGTTGAGGATCATTGC
* * *
2013 TTTAT-TATAATCCTGGTTTAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATGT-TAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
* * *
2073 TTTATCAGTTAATCC-CGATGTAGGATCATTGCATTATG
1 TTTAT--GTTAATCCTGGTTG-AGGATCATTGCTTTATG
2111 AATTAATTTT
Statistics
Matches: 444, Mismatches: 61, Indels: 24
0.84 0.12 0.05
Matches are distributed among these distances:
59 56 0.13
60 312 0.70
61 51 0.11
62 24 0.05
63 1 0.00
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.46
Consensus pattern (60 bp):
TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCATTGC
Found at i:1686 original size:90 final size:89
Alignment explanation
Indices: 1533--2110 Score: 689
Period size: 90 Copynumber: 6.4 Consensus size: 89
1523 CTTTATCAGT
* * *
1533 TTTATTTTAATCCTGGTTGAGGATCATTGTTTTATGTTAATCCTGGTTGAGGATTGTTGCTTTAT
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCGTTGCTTTAT
1598 GTTAATCCTGTTTGAGGATCATTGC
66 -TTAATCCTGTTTGAGGATCATTGC
* * *
1623 TTTATTTTAATCCTGTTTGAGGATCATTGCTTTAT-TCTAATCCTGGTTGAGAATCGTTGCTTTA
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGT-TAATCCTGGTTGAGGATCGTTGCTTTA
* * *
1687 TTCAATCTTATTTGAGGATCATTGC
65 TTTAATCCTGTTTGAGGATCATTGC
* *
1712 TTTATGTTAATCCTGGTTGAGGATCATTGTTTTATGTTAATTCTGGTTGAGGATCGTTGCTTTAT
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCGTTGCTTTAT
* *
1777 TATAATCATATTTGAGGATCATTGC
66 T-TAATCCTGTTTGAGGATCATTGC
* * * * *
1802 TTTATGTTAATCCTGTTTGAGGATCATTGCTTTATGTTAATCTTGTTTAAGGATCATTGCTTTAT
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCGTTGCTTTAT
* *
1867 GTTGATCCTGGTTGAGGATCATTGC
66 -TTAATCCTGTTTGAGGATCATTGC
* * * * *
1892 TATATGTTAATCCTGTTTGAGGATCATTGCTTTATGTTAATCTTGTTTGAGGATCGTCGCTTTAT
1 TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCGTTGCTTTA-
* * *
1957 TTTAGTCCTGGTTGAGGATCGTTG-
65 TTTAATCCTGTTTGAGGATCATTGC
* * * *
1981 TTTAATTTTCAATCCTGGTTGAGGATCGTTGCTTTAT-TATAATCCTGGTTTAGGATCATTGCTT
1 TTT-ATGTT-AATCCTGGTTGAGGATCATTGCTTTATGT-TAATCCTGGTTGAGGATCGTTGCTT
2045 TATTTTAATCCTGGTTT-AGGATCATTGC
63 TA-TTTAATCCT-GTTTGAGGATCATTGC
* * *
2073 TTTATCAGTTAATCC-CGATGTAGGATCATTGCATTATG
1 TTTAT--GTTAATCCTGGTTG-AGGATCATTGCTTTATG
2111 AATTAATTTT
Statistics
Matches: 425, Mismatches: 49, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
89 83 0.20
90 243 0.57
91 72 0.17
92 25 0.06
93 2 0.00
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.46
Consensus pattern (89 bp):
TTTATGTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCGTTGCTTTAT
TTAATCCTGTTTGAGGATCATTGC
Found at i:2616 original size:27 final size:28
Alignment explanation
Indices: 2586--2661 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
2576 TAGGATCACC
* *
2586 TAGGGGCATTTTGGTCATTTT-TACATT
1 TAGGGGCGTTTTGGTCATTTTGCACATT
2613 TAGGGGCGTTTTGGTCATTTTGCACATT
1 TAGGGGCGTTTTGGTCATTTTGCACATT
*
2641 CAGGGGCGTTTTGGTCATTTT
1 TAGGGGCGTTTTGGTCATTTT
2662 AAGTTTATTG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 20 0.44
28 25 0.56
ACGTcount: A:0.14, C:0.13, G:0.28, T:0.45
Consensus pattern (28 bp):
TAGGGGCGTTTTGGTCATTTTGCACATT
Found at i:5576 original size:21 final size:22
Alignment explanation
Indices: 5551--5591 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5541 TGATTAAATG
*
5551 CAATTTGATCCCTG-CTTTATT
1 CAATTTAATCCCTGACTTTATT
5572 CAATTTAATCCCTGACTTTA
1 CAATTTAATCCCTGACTTTA
5592 GAAATTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.44
Consensus pattern (22 bp):
CAATTTAATCCCTGACTTTATT
Found at i:7335 original size:14 final size:15
Alignment explanation
Indices: 7316--7346 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
7306 CAACTAGGAA
7316 AAATAAATAA-CAAG
1 AAATAAATAAGCAAG
7330 AAATAAATAAGCAAG
1 AAATAAATAAGCAAG
7345 AA
1 AA
7347 TTGAACTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (15 bp):
AAATAAATAAGCAAG
Found at i:7766 original size:24 final size:26
Alignment explanation
Indices: 7731--7781 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 26
7721 CTTCCTTGCA
7731 CTCCATGCTCATC-CAT-TCCATGAT
1 CTCCATGCTCATCTCATGTCCATGAT
7755 CTCCATTG-TCATCTTCATGTCCATGAT
1 CTCCA-TGCTCATC-TCATGTCCATGAT
7782 AAGCCCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 10 0.43
25 2 0.09
26 3 0.13
27 8 0.35
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (26 bp):
CTCCATGCTCATCTCATGTCCATGAT
Found at i:8178 original size:19 final size:17
Alignment explanation
Indices: 8154--8188 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
8144 AAGTTCGTGT
8154 TTGAAGACCATTTGAAGAC
1 TTGAAGA-C-TTTGAAGAC
8173 TTGAAGACTTTGAAGA
1 TTGAAGACTTTGAAGA
8189 TTTATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (17 bp):
TTGAAGACTTTGAAGAC
Found at i:9588 original size:15 final size:15
Alignment explanation
Indices: 9558--9599 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
9548 TTACTTTGTT
9558 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
9574 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
9589 TTGTTTTCTGT
1 TTGTTTTCTGT
9600 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:13961 original size:199 final size:199
Alignment explanation
Indices: 13621--13984 Score: 597
Period size: 199 Copynumber: 1.8 Consensus size: 199
13611 TAAGGACTAG
* * *
13621 ATTGAAATATTAAAAATCTAATTATTTCTGAAATGAGGTACTTGTCAACTTTTGAACCCGCTTGT
1 ATTGAAATACTAAAAATCTAATTAATTCTGAAATGAGGTACTTGTCAACCTTTGAACCCGCTTGT
*
13686 GGAGTCCAAAAACTACACTGACGGTGTATCAAATAATTAACTCAAATGGAAAATAATTAAATACA
66 GGAGTCCAAAAACTACACTGACGGTGTATCAAATAATTAACTAAAATGGAAAATAATTAAATACA
* *
13751 CCTTTAGTGGAGTTTACCAGACTGCACGTGCGGGTCTAAAAGGGTGACATGAGTCCCCTTTGGGG
131 CCATCAGTGGAGTTTACCAGACTGCACGTGCGGGTCTAAAAGGGTGACATGAGTCCCCTTTGGGG
13816 TTAA
196 TTAA
* * *
13820 ATTGAAATACTAAAAATTTAATTAATTCTGAAATGGGGGTATTTGTCAACCTTTGAACCCGCTTG
1 ATTGAAATACTAAAAATCTAATTAATTCTGAAAT-GAGGTACTTGTCAACCTTTGAACCCGCTTG
*
13885 TGGAGTTCC-AAAACTACACTGACGGTGTATCAAATAA-TAATTAAAATGGAAAATAATTAAATA
65 TGGAG-TCCAAAAACTACACTGACGGTGTATCAAATAATTAACTAAAATGGAAAATAATTAAATA
*
13948 CACCATCAGTGGAGTTTAGCAGACTGCACGTGCGGGT
129 CACCATCAGTGGAGTTTACCAGACTGCACGTGCGGGT
13985 TTATTAACAA
Statistics
Matches: 152, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
199 89 0.59
200 60 0.39
201 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (199 bp):
ATTGAAATACTAAAAATCTAATTAATTCTGAAATGAGGTACTTGTCAACCTTTGAACCCGCTTGT
GGAGTCCAAAAACTACACTGACGGTGTATCAAATAATTAACTAAAATGGAAAATAATTAAATACA
CCATCAGTGGAGTTTACCAGACTGCACGTGCGGGTCTAAAAGGGTGACATGAGTCCCCTTTGGGG
TTAA
Done.