Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007759.1 Kokia drynarioides strain JFW-HI SEQ_122392, 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: 14305
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1416 original size:29 final size:28
Alignment explanation
Indices: 1365--1880 Score: 176
Period size: 29 Copynumber: 17.6 Consensus size: 28
1355 CTCGGGGGTG
*
1365 AAATGGTAATTTTGGGAAAATTCGGGGTTAA
1 AAATGG-AATTTTTGG--AATTCGGGGTTAA
* *
1396 AAATGGAATTTTTAGACATTCGGGGGTAA
1 AAATGGAATTTTTGGA-ATTCGGGGTTAA
* * * * * **
1425 AAA-GGTAA-ATTTGAGAGTTTTGAGATCGA
1 AAATGG-AATTTTTG-GA-ATTCGGGGTTAA
* *
1454 AAATGGAGTTTTTGGACATCCGAGGG--AA
1 AAATGGAATTTTTGGA-ATTCG-GGGTTAA
*
1482 AAATGGTAATTTTTGGAGGTTTCGGGGTTAA
1 AAATGG-AATTTTTGGA--ATTCGGGGTTAA
* * * *
1513 AAATGGGATTTTTGAAAGTTTAGGGG-TAG
1 AAATGGAATTTTTGGAA--TTCGGGGTTAA
* *
1542 AAATGGAATTTTTAGAAGTTTTGGGG-TAA
1 AAATGGAATTTTTGGAA--TTCGGGGTTAA
* * * * *
1571 AAATGGGATTTTCGAAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAA-TTCGGGGTTAA
* *
1600 AAAT-GAGATTTTTGGAAGTTTTGGGGTCAA
1 AAATGGA-ATTTTTGGAA--TTCGGGGTTAA
*
1630 AAATGGGATTTTTGGAAGTTCGAGGG-TAA
1 AAATGGAATTTTTGGAA-TTCG-GGGTTAA
* *
1659 AAATGGAATTTTTGGGAGTTTCGGGGTCAA
1 AAATGGAATTTTT-GGA-ATTCGGGGTTAA
** * * *
1689 AAATGGGGTTTTTGGTAGTTCGAGAG-TGA
1 AAATGGAATTTTTGG-AATTCG-GGGTTAA
*
1718 AAATGGAATTTTTGGAAATTTAGGGG-TAA
1 AAATGGAATTTTTGG-AA-TTCGGGGTTAA
* * *
1747 AAATGAAATTTTTGGGAGTTTCGAGGTTAA
1 AAATGGAATTTTT-GGA-ATTCGGGGTTAA
*
1777 AAAT-GAGAGTTTTGGAAGTTCGAGGG-TAA
1 AAATGGA-ATTTTTGGAA-TTCG-GGGTTAA
* * * *
1806 AAACGGATTTTTTGGAAGTTTCGAGGTCAAA
1 AAATGGAATTTTTGGAA--TTCGGGGT-TAA
** * *
1837 AAATGGGGTTTTTTGAAGTTCGGGG-TGA
1 AAATGGAATTTTTGGAA-TTCGGGGTTAA
*
1865 AAACGGAATTTTTGGA
1 AAATGGAATTTTTGGA
1881 TAGTTTAGGG
Statistics
Matches: 359, Mismatches: 93, Indels: 69
0.69 0.18 0.13
Matches are distributed among these distances:
28 34 0.09
29 184 0.51
30 111 0.31
31 30 0.08
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (28 bp):
AAATGGAATTTTTGGAATTCGGGGTTAA
Found at i:1525 original size:59 final size:60
Alignment explanation
Indices: 1365--1885 Score: 343
Period size: 59 Copynumber: 8.8 Consensus size: 60
1355 CTCGGGGGTG
* ** * * * * *
1365 AAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATGGAATTTTTAGACA-TTCGGGGGTAA
1 AAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAAGTTCGAGGGTAA
* * * * * * *
1425 AAA-GGTAA-ATTT-GAGAGTTTTGAGATCGAAAAT-GGAGTTTTTGGACA-TCCGAGGG-AA
1 AAATGG-AATTTTTGGA-AGTTTCGGGGTCAAAAATGGGA-TTTTTGGAAAGTTCGAGGGTAA
* * * *
1482 AAATGGTAATTTTTGGAGGTTTCGGGGTTAAAAATGGGATTTTT-GAAAGTT-TAGGGGTAG
1 AAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAAGTTCGA-GGGTAA
* * * * *
1542 AAATGGAATTTTTAGAAGTTTTGGGGT-AAAAATGGGA-TTTTCGAAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAAGTTCGAGGGTAA
*
1600 AAAT-GAGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGG-AAGTTCGAGGGTAA
1 AAATGGA-ATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAAGTTCGAGGGTAA
* * * * *
1659 AAATGGAATTTTTGGGAGTTTCGGGGTCAAAAATGGGGTTTTTGG-TAGTTCGAGAGTGA
1 AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAAGTTCGAGGGTAA
* * ** * *
1718 AAATGGAATTTTTGGAAATTTAGGGGT-AAAAATGAAATTTTTGG-GAGTTTCGAGGTTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAAG-TTCGAGGGTAA
* *
1777 AAAT-GAGAGTTTTGGAAG-TTCGAGGGT-AAAAA-CGGATTTTTTGG-AAGTTTCGA-GGTCAA
1 AAATGGA-ATTTTTGGAAGTTTCG-GGGTCAAAAATGGGA-TTTTTGGAAAG-TTCGAGGGT--A
1836 A
60 A
** * * * * *
1837 AAATGGGGTTTTTTGAAG-TTCGGGGT-GAAAACGGAATTTTTGGATAGTT
1 AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAAGTT
1886 TAGGGACCTC
Statistics
Matches: 371, Mismatches: 66, Indels: 49
0.76 0.14 0.10
Matches are distributed among these distances:
57 15 0.04
58 106 0.29
59 205 0.55
60 44 0.12
61 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33
Consensus pattern (60 bp):
AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAAGTTCGAGGGTAA
Found at i:1721 original size:88 final size:88
Alignment explanation
Indices: 1452--1831 Score: 332
Period size: 88 Copynumber: 4.3 Consensus size: 88
1442 TTTTGAGATC
*
1452 GAAAAT-GGAGTTTTTGGACA-TCCGAGGG-AAAAATGGTAATTTTT-GGAGGTTTCGGGGTTAA
1 GAAAATGGGA-TTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTTGGGA-GTTTCGGGGTTAA
* *
1513 AAATGGGATTTTTGAAAGTT-TAGGG-
62 AAATGGGATTTTTGGAAGTTCGAGGGT
* * * * * ** *
1538 GTAGAAATGGAATTTTTAGAAGTTTTG-GGGTAAAAATGGGATTTTCGAAAGTTT-GGGGGTAAA
1 G-A-AAATGGGATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGGAGTTTCGGGGTTAAA
* *
1601 AATGAGATTTTTGGAAGTTTTG-GGGT
63 AATGGGATTTTTGGAAG-TTCGAGGGT
* *
1627 CAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAGTTTCGGGGTCAAAAA
1 -GAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAGTTTCGGGGTTAAAAA
* * *
1692 TGGGGTTTTTGGTAGTTCGAGAGT
65 TGGGATTTTTGGAAGTTCGAGGGT
* * * * *
1716 GAAAATGGAATTTTTGGAAATT-TAGGGGTAAAAATGAAATTTTTGGGAGTTTCGAGGTTAAAAA
1 GAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGGAGTTTCGGGGTTAAAAA
* *
1780 TGAGAGTTTTGGAAGTTCGAGGGT
65 TGGGATTTTTGGAAGTTCGAGGGT
**
1804 -AAAAACGGATTTTTTGGAAGTTTCGAGG
1 GAAAATGGGA-TTTTTGGAAG-TTCGAGG
1832 TCAAAAAATG
Statistics
Matches: 232, Mismatches: 44, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
86 1 0.00
87 35 0.15
88 153 0.66
89 42 0.18
90 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33
Consensus pattern (88 bp):
GAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAGTTTCGGGGTTAAAAAT
GGGATTTTTGGAAGTTCGAGGGT
Found at i:1761 original size:117 final size:117
Alignment explanation
Indices: 1361--1781 Score: 351
Period size: 117 Copynumber: 3.6 Consensus size: 117
1351 GATTCTCGGG
* * * *
1361 GGTG-AAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATGGAATTTTTAGACA-TTCGGGGGTA
1 GGTGAAAATGGTAATTTTTGGAAATTTCGGGGTTAAAAATGGAATTTTTGGA-AGTTCGAGGGTA
* * * * * * * *
1424 AAAA-GGTAA-ATTTGAGAGTTTTGAGATCGAAAATGGAGTTTTTGGACATCCGA
65 AAAATGG-AATTTTTGGGAGTTTTGGGGTCAAAAATGGGGTTTTTGGA-GTTCGA
** * * *
1477 GG-GAAAAATGGTAATTTTTGGAGGTTTCGGGGTTAAAAATGGGATTTTTGAAAGTT-TAGGGGT
1 GGTG-AAAATGGTAATTTTTGGAAATTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGA-GGGT
* * * * * * * *
1540 AGAAATGGAATTTTTAGAAGTTTTGGGGT-AAAAATGGGATTTTCGAAAGTTTGGG
64 AAAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAATGGGGTTTTTG-GAG-TTCGA
* * * * *
1595 GGTAAAAAT-G-AGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
1 GGTGAAAATGGTA-ATTTTTGGAAATTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
*
1658 AAAATGGAATTTTTGGGAGTTTCGGGGTCAAAAATGGGGTTTTTGGTAGTTCGA
65 AAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAATGGGGTTTTTGG-AGTTCGA
* * * *
1712 GAGTGAAAATGG-AATTTTTGGAAATTTAGGGG-TAAAAATGAAATTTTTGGGAGTTTCGAGGTT
1 G-GTGAAAATGGTAATTTTTGGAAATTTCGGGGTTAAAAATGGAATTTTTGGAAG-TTCGAGGGT
1775 AAAAATG
64 AAAAATG
1782 AGAGTTTTGG
Statistics
Matches: 241, Mismatches: 48, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
115 1 0.00
116 4 0.02
117 154 0.64
118 80 0.33
119 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (117 bp):
GGTGAAAATGGTAATTTTTGGAAATTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAA
AAATGGAATTTTTGGGAGTTTTGGGGTCAAAAATGGGGTTTTTGGAGTTCGA
Found at i:1885 original size:29 final size:28
Alignment explanation
Indices: 1453--1885 Score: 307
Period size: 29 Copynumber: 14.8 Consensus size: 28
1443 TTTGAGATCG
* *
1453 AAAATGGAGTTTTTGGACA-TCCGAGGG-A
1 AAAATGGAATTTTTGGA-AGTTCG-GGGTA
*
1481 AAAATGGTAATTTTTGGAGGTTTCGGGGTTA
1 AAAATGG-AATTTTTGGAAG-TTCGGGG-TA
* * *
1512 AAAATGGGATTTTTGAAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAG-TTCGGGGTA
* * *
1541 GAAATGGAATTTTTAGAAGTTTTGGGGTA
1 AAAATGGAATTTTTGGAAG-TTCGGGGTA
* * * *
1570 AAAATGGGATTTTCGAAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAG-TTCGGGGTA
*
1599 AAAAT-GAGATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGA-ATTTTTGGAAG-TTCGGGGT-A
*
1629 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCG-GGGTA
*
1658 AAAATGGAATTTTTGGGAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGT-A
** * * *
1688 AAAATGGGGTTTTTGGTAGTTCGAGAGTG
1 AAAATGGAATTTTTGGAAGTTCG-GGGTA
* *
1717 AAAATGGAATTTTTGGAAATTTAGGGGTA
1 AAAATGGAATTTTTGG-AAGTTCGGGGTA
* * *
1746 AAAATGAAATTTTTGGGAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCG-GGGTA
*
1776 AAAAT-GAGAGTTTTGGAAGTTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTCG-GGGTA
* * *
1805 AAAACGGATTTTTTGGAAGTTTCGAGGTCAA
1 AAAATGGAATTTTTGGAAG-TTCGGGGT--A
** * *
1836 AAAATGGGGTTTTTTGAAGTTCGGGGTG
1 AAAATGGAATTTTTGGAAGTTCGGGGTA
*
1864 AAAACGGAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGA-AGTT
1886 TAGGGACCTC
Statistics
Matches: 323, Mismatches: 61, Indels: 41
0.76 0.14 0.10
Matches are distributed among these distances:
28 22 0.07
29 177 0.55
30 99 0.31
31 25 0.08
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTA
Found at i:2864 original size:3 final size:3
Alignment explanation
Indices: 2845--2885 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
2835 TTAAAAGAAA
* *
2845 ATT AAT ATT AAT ATT ATT ATT ATT ATT ATT AATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A
2886 ATGGGGCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:2922 original size:17 final size:19
Alignment explanation
Indices: 2896--2939 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
2886 ATGGGGCAGT
*
2896 TATTAATATTAACAC-ATC
1 TATTATTATTAACACTATC
*
2914 -ATTATTATTACCACTATC
1 TATTATTATTAACACTATC
2932 TATTATTA
1 TATTATTA
2940 CTACTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 12 0.55
18 3 0.14
19 7 0.32
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTATTATTAACACTATC
Found at i:2937 original size:16 final size:16
Alignment explanation
Indices: 2916--2946 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2906 AACACATCAT
2916 TATTATTACCACTATC
1 TATTATTACCACTATC
*
2932 TATTATTACTACTAT
1 TATTATTACCACTAT
2947 TAATATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTATTACCACTATC
Found at i:3647 original size:17 final size:17
Alignment explanation
Indices: 3627--3673 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
3617 AAATGAATTT
3627 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
3644 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
3661 TAAATTTAAATTT
1 TAAATTTAAATTT
3674 GTTGGGCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:4595 original size:201 final size:202
Alignment explanation
Indices: 4233--4715 Score: 702
Period size: 201 Copynumber: 2.4 Consensus size: 202
4223 AGGAAGCTAT
* * * **
4233 CTGTTTTTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGTTCACACCATGGATTTGGCTT
1 CTGTTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACACCGTGGATTTGATTT
* * ** * *
4298 GGTCTTCTTCTTAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTTAATTTGCTTCTCTGTA
66 GGTCTTCTTCTCAATATCTCATCAAGAAGATGACAACGTCGTTTGTTTCAATTCGCTTCTCTGTA
4363 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCG-CCAAGAAGCTAACC-TTTTATT
131 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCGTCC-AGAAGCTAACCGTTTTATT
*
4426 GCTTCGAC
195 ACTTCGAC
* * *
4434 CTGTTTCTCAGTGTCTCATCAGGAAGTTAGGGTTCGAAGATTTGTTCACACCGTGGATTTGATTT
1 CTGTTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACACCGTGGATTTGATTT
*
4499 GGTCTTCTTCTCAATATCTCAT-AAGGAAGATGACAATGTCGTTTGTTTCAATTCGCTTCTCTGT
66 GGTCTTCTTCTCAATATCTCATCAA-GAAGATGACAACGTCGTTTGTTTCAATTCGCTTCTCTGT
* * * *
4563 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTTGTCCGGAAGCTAACCGTTTTATT
130 ATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCGTCCAGAAGCTAACCGTTTTATT
4628 ACTTCGAC
195 ACTTCGAC
* * *
4636 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATCACGTGTGGGTTTGAT
1 CTGTTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCA-CAC-CGTGGATTTGAT
4701 TTGGTCTTCTTCTCA
64 TTGGTCTTCTTCTCA
4716 TCAGGAAGAT
Statistics
Matches: 251, Mismatches: 26, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
200 2 0.01
201 161 0.64
202 60 0.24
203 3 0.01
204 25 0.10
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (202 bp):
CTGTTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACACCGTGGATTTGATTT
GGTCTTCTTCTCAATATCTCATCAAGAAGATGACAACGTCGTTTGTTTCAATTCGCTTCTCTGTA
TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCGTCCAGAAGCTAACCGTTTTATTA
CTTCGAC
Found at i:4879 original size:158 final size:159
Alignment explanation
Indices: 4587--4930 Score: 532
Period size: 158 Copynumber: 2.2 Consensus size: 159
4577 ACGAATTTGG
** *
4587 TTCACTTCTC-AGTATCTTGTCCGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATC
1 TTCACTTCTCTA-TATCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATC
* * *
4651 TCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATCACGTGTGGGTTTGATTTGGTCTTCTTCTCA
65 TCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATCACGCGTGGGTTTGATTTGATCTTCTTCCCA
4716 TCAGGAAGATGACCACGTCATTTGTTTCAA
130 TCAGGAAGATGACCACGTCATTTGTTTCAA
* *
4746 -TCAACTTCTCTATATCTCATCAGGAAGCTAGCTGTTTTATTACTTCGACCTGCTT-TCAGTATC
1 TTC-ACTTCTCTATATCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATC
* *
4809 TCATCAGGAAGCTGGGGTTTGAAGATTTGTTCGTCACGCGTGGGTTTGATTTGATCTTCTTCCCA
65 TCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATCACGCGTGGGTTTGATTTGATCTTCTTCCCA
4874 TCAGGAAGATGACCACGTCATTTGTTTCAA
130 TCAGGAAGATGACCACGTCATTTGTTTCAA
* * *
4904 TTCGCTTCTCTGTATCTCATTAGGAAG
1 TTCACTTCTCTATATCTCATCAGGAAG
4931 ACGAATTTGG
Statistics
Matches: 169, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
158 121 0.72
159 47 0.28
160 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (159 bp):
TTCACTTCTCTATATCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCT
CATCAGGAAGCTGGGGTTCGAAGATTTGTTCATCACGCGTGGGTTTGATTTGATCTTCTTCCCAT
CAGGAAGATGACCACGTCATTTGTTTCAA
Found at i:4931 original size:354 final size:358
Alignment explanation
Indices: 4419--5068 Score: 900
Period size: 354 Copynumber: 1.8 Consensus size: 358
4409 GAAGCTAACC
* * * *
4419 TTTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCAGGAAGTTAGGGTTCGAAGATTTGTTCACA
1 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGTTCACA
* * *
4484 CCGTGGATTTGATTTGGTCTTCTTCTCAATATCTCATAAGGAAGATGACAATGTCGTTTGTTTCA
66 CCGTGGATTTGATTTGATCTTCTTCTC---A-CTCATAAGGAAGATGACAACGTCATTTGTTTCA
* * ** *
4549 ATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTTGTCCGGAAG
127 ATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAG
*
4614 CTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
192 CTAACCG-TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTT
* * *
4679 G-T-TCATCACGTGTGGGTTTGATTTGGTCTTCTTCTCATCAGGAAGATGACCACGTCATTTGTT
256 GCTCACATCAAGCGTGGGTTTGATTTGGTCTTCTTCTCATCAGGAAGATGACCACGTCATTTGTT
4742 TCAATCAACTTCTCTATATCTCATCAGGAAGCTAGCTG
321 TCAATCAACTTCTCTATATCTCATCAGGAAGCTAGCTG
* * *
4780 TTTTATTACTTCGACCTGCTT-TCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGTTCGTC
1 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGTTC-AC
* * *
4844 ACGCGTGGGTTTGATTTGATCTTC-T-TC-C-CATCAGGAAGATGACCACGTCATTTGTTTCAAT
65 AC-CGTGGATTTGATTTGATCTTCTTCTCACTCATAAGGAAGATGACAACGTCATTTGTTTCAAT
* * *
4905 TCGCTTCTCTGTATCTCATTAGGAAGACGAATTTGGTCCACCTCTTAGTATCTCATCAGGAAGTT
129 TCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCT
** * * *
4970 AACCGTTTATTACTTCGATTTGCTTCTCGGTGTCTCATCAGGAAGCTGGGATTTGAAGATTTGCT
194 AACCGTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCT
* *
5035 CACATCAAGCGTGGGTTTTATTTGGTCTTTTTCT
259 CACATCAAGCGTGGGTTTGATTTGGTCTTCTTCT
5069 TAGTATCTCA
Statistics
Matches: 253, Mismatches: 32, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
353 52 0.21
354 92 0.36
355 29 0.11
360 38 0.15
361 23 0.09
362 19 0.08
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (358 bp):
TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGTTCACA
CCGTGGATTTGATTTGATCTTCTTCTCACTCATAAGGAAGATGACAACGTCATTTGTTTCAATTC
GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAA
CCGTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCA
CATCAAGCGTGGGTTTGATTTGGTCTTCTTCTCATCAGGAAGATGACCACGTCATTTGTTTCAAT
CAACTTCTCTATATCTCATCAGGAAGCTAGCTG
Done.