Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010973.1 Kokia drynarioides strain JFW-HI SEQ_125942, 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: 20915
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:1504 original size:85 final size:85
Alignment explanation
Indices: 1360--1519 Score: 234
Period size: 85 Copynumber: 1.9 Consensus size: 85
1350 AACTTCATCT
* *
1360 TTTGGTCCACTTCTTTGTATCTTATCAGGAAGATGACCACTTCATTGTTTTGATCCACTTCTCTA
1 TTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTCATTGCTTTGATCCACTTCTCTA
1425 TATCTCATCAAGCAGACAGA
66 TATCTCATCAAGCAGACAGA
* * *
1445 TTTGGTCCACTT-TTCTGTGTCTCATCAGGAAGATGACCTCTTTATTGCTTTGA-CTCACTTCTC
1 TTTGGTCCACTTCTT-TGTATCTCATCAGGAAGATGACCACTTCATTGCTTTGATC-CACTTCTC
*
1508 TGTATCTCATCA
64 TATATCTCATCA
1520 CGAATATAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
84 3 0.04
85 64 0.96
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.40
Consensus pattern (85 bp):
TTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTCATTGCTTTGATCCACTTCTCTA
TATCTCATCAAGCAGACAGA
Found at i:1682 original size:85 final size:85
Alignment explanation
Indices: 1567--1733 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
1557 TTGCTTCATT
* * * *
1567 GATTTGATCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
1 GATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAACGCTTCATTGATTTAACCCACTTCTC
*
1632 TGTATCTCATCAGGAAGGTG
66 TGTATCTCATCAAGAAGGTG
* * * * *
1652 GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGAACGCTTTATTGCTTTGACCCACTTCTT
1 GATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAACGCTTCATTGATTTAACCCACTTCTC
*
1717 TGTATCTTATCAAGAAG
66 TGTATCTCATCAAGAAG
1734 ACGGGGGTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (85 bp):
GATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAACGCTTCATTGATTTAACCCACTTCTC
TGTATCTCATCAAGAAGGTG
Found at i:1747 original size:209 final size:209
Alignment explanation
Indices: 1360--2095 Score: 1080
Period size: 209 Copynumber: 3.5 Consensus size: 209
1350 AACTTCATCT
* * * * * * *
1360 TTTGGTCCACTTCTTTGTATCTTATCAGGAAGATGACCACTTCATTGTTTTGATCCACTTCTCTA
1 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTG
* * * * * * *
1425 TATCTCATCAAGCAGACAGATTTGGTCCACTTTTCTGTGTCTCATCAGGAAGATGACCTCTTTAT
66 TATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAACGCTTTAT
* * * ** * *
1490 TGCTTTGACTCACTTCTCTGTATCTCATCACGAATATAGGGATTTGAAGTTTCATTCACATTAAG
131 TGCTTTGACCCACTTCTCTGTATCTCATCAAGAAAACGGGGGTTTGAAGTTTCACTCACATTAAG
1555 CTTTGCTTCATTGA
196 CTTTGCTTCATTGA
*
1569 TTTGATCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTG
1 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTG
* * *
1634 TATCTCATCAGGAAGGTGGATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGAACGCTTTAT
66 TATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAACGCTTTAT
* * *
1699 TGCTTTGACCCACTTCTTTGTATCTTATCAAGAAGACGGGGGTTTGAAGTTTCACTCACATTAAG
131 TGCTTTGACCCACTTCTCTGTATCTCATCAAGAAAACGGGGGTTTGAAGTTTCACTCACATTAAG
1764 CTTTGCTTCATTGA
196 CTTTGCTTCATTGA
*
1778 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGATTTAATCCACTTCTCTG
1 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTG
*
1843 TATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCACCAGGAAGATG-ACTGCTTTA
66 TATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAAC-GCTTTA
* **
1907 TTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAAATGGGGGGGTTTGAAGTTTCACTCTGATT
130 TTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAAA--CGGGGGTTTGAAGTTTCACTCACATT
*
1972 GAGCTTTGCTTCATTGA
193 AAGCTTTGCTTCATTGA
* *
1989 TTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCG-TCTCATTGATTTAATCCACTTCTTT
1 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCT-TCATTGATTTAATCCACTTCTCT
* *
2053 GTATCTAATCAAGAAGGTGGATTTGGTCCACTTCTCTGTATCT
65 GTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCT
2096 AATAAAAAAG
Statistics
Matches: 478, Mismatches: 45, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
208 2 0.00
209 336 0.70
210 1 0.00
211 139 0.29
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (209 bp):
TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTG
TATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAACGCTTTAT
TGCTTTGACCCACTTCTCTGTATCTCATCAAGAAAACGGGGGTTTGAAGTTTCACTCACATTAAG
CTTTGCTTCATTGA
Found at i:1838 original size:48 final size:48
Alignment explanation
Indices: 1767--1937 Score: 184
Period size: 48 Copynumber: 3.8 Consensus size: 48
1757 CATTAAGCTT
* *
1767 TGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGAC
1 TGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
* *
1815 TGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAG--G-C
1 TGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
* *
1860 -G-------GATTTGGTCCACTTCTCTGTATCTCACCAGGAAGATGAC
1 TGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
* * *
1900 TGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCA
1 TGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCA
1938 AGAAAATGGG
Statistics
Matches: 100, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
37 30 0.30
39 1 0.01
40 1 0.01
41 1 0.01
44 1 0.01
45 1 0.01
46 1 0.01
48 64 0.64
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (48 bp):
TGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
Found at i:1921 original size:85 final size:85
Alignment explanation
Indices: 1776--1941 Score: 278
Period size: 85 Copynumber: 2.0 Consensus size: 85
1766 TTGCTTCATT
* * *
1776 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGATTTAATCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCACCAGGAAGATGACTGCTTCATTGATTTAACCCACTTCTC
1841 TGTATCTCATCAAGAAGGCG
66 TGTATCTCATCAAGAAGGCG
* * *
1861 GATTTGGTCCACTTCTCTGTATCTCACCAGGAAGATGACTGCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCACCAGGAAGATGACTGCTTCATTGATTTAACCCACTTCTC
1926 TGTATCTCATCAAGAA
66 TGTATCTCATCAAGAA
1942 AATGGGGGGG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTGTATCTCACCAGGAAGATGACTGCTTCATTGATTTAACCCACTTCTC
TGTATCTCATCAAGAAGGCG
Found at i:2154 original size:162 final size:163
Alignment explanation
Indices: 1917--2263 Score: 518
Period size: 162 Copynumber: 2.1 Consensus size: 163
1907 TTGCTTTGAC
* * **
1917 CCACTTCTCTGTATCTCATCAAGAAAATGGGGGGGTTTGAAGTTTCACTCTGATTGAGCTTTGCT
1 CCACTTCTCTGTATCTAATCAAAAAAATGGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCT
* *
1982 TCATTGATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCGTCTCATTGATTTAATCCAC
66 TCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCAC
* ***
2047 TTCTTTGTATCTAATCAAGAAGGTGGATTTGGT
131 TTCTCTGTATCTAATCAAGAAGACAGATTTGGT
*
2080 CCACTTCTCTGTATCTAAT-AAAAAAGAT-GGGGGGTTTGAAGTTTCACTCACATTGAGCTTTTC
1 CCACTTCTCTGTATCTAATCAAAAAA-ATGGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGC
** *
2143 TTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATTGCCTCATTGATTTAATTCA
65 TTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCA
* *
2208 GTTCTCTGTATCTAATCAGGAAGACAGATTTGGT
130 CTTCTCTGTATCTAATCAAGAAGACAGATTTGGT
*
2242 CCACTTCTCTGTATCTTATCAA
1 CCACTTCTCTGTATCTAATCAA
2264 GAAGATGACC
Statistics
Matches: 165, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
162 143 0.87
163 22 0.13
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (163 bp):
CCACTTCTCTGTATCTAATCAAAAAAATGGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCT
TCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCAC
TTCTCTGTATCTAATCAAGAAGACAGATTTGGT
Found at i:2161 original size:373 final size:370
Alignment explanation
Indices: 1708--2466 Score: 1144
Period size: 373 Copynumber: 2.0 Consensus size: 370
1698 TTGCTTTGAC
* * * *
1708 CCACTTCTTTGTATCTTATCAAGAAGACGGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTC
1 CCACTTCTCTGTATCTAATAAAAAAGACGGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTC
*
1773 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGATTTAATCCACTT
66 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCATTGATTTAATCCACTT
* * * * * *
1838 CTCTGTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCACCAGGAAGATGACTGC
131 CTCTGTATCTAATCAAGAAGACAGATTTGGTCCACTTCTCTGTATCTCACCAAGAAGATGACCGA
* * *
1903 TTTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAAATGGGGGGGTTTGAAGTTTCACTCT
196 TTTATTGCTTTGACCCACTTCTATATATCTCATCAAGAAAAT--GGGGGTTTGAAGTTTCACTCA
* * * * *
1968 GATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGA-C-CGTCT
259 CATTGAACTTTGCTTCATTGATTTGATCTACTTCTCTATATCTCATCAGGAAGATGATCAC-T-T
* *
2031 CATTGATTTAATCCACTTCTTTGTATCTAATCAAGAAGGTGGATTTGGT
322 CATTGATTTAATCCACTTCTCTGTATCTAATCAAGAAGGCGGATTTGGT
* * *
2080 CCACTTCTCTGTATCTAATAAAAAAGATGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTTCTT
1 CCACTTCTCTGTATCTAATAAAAAAGA-CGGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTT
* * *
2145 CATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATTGCCTCATTGATTTAATTCAGT
65 CATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCATTGATTTAATCCACT
* * *
2210 TCTCTGTATCTAATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTTATCAAGAAGATGACCG
130 TCTCTGTATCTAATCAAGAAGACAGATTTGGTCCACTTCTCTGTATCTCACCAAGAAGATGACCG
* *
2275 ATTTATTGCTTTGACCCACTTCTATATATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCAC
195 ATTTATTGCTTTGACCCACTTCTATATATCTCATCAAGAAAATGGGGGTTTGAAGTTTCACTCAC
2340 ATTGAACTTTGCTTCATTGATTTGATCTACTTCTCTATATCTCATCAGGAAGATGATCACTTCAT
260 ATTGAACTTTGCTTCATTGATTTGATCTACTTCTCTATATCTCATCAGGAAGATGATCACTTCAT
* *
2405 TGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTGGT
325 TGATTTAATCCACTTCTCTGTATCTAATCAAGAAGGCGGATTTGGT
*
2451 CCACTTCTCTATATCT
1 CCACTTCTCTGTATCT
2467 CATCAGAAAG
Statistics
Matches: 349, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
371 133 0.38
372 25 0.07
373 191 0.55
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (370 bp):
CCACTTCTCTGTATCTAATAAAAAAGACGGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTC
ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCATTGATTTAATCCACTT
CTCTGTATCTAATCAAGAAGACAGATTTGGTCCACTTCTCTGTATCTCACCAAGAAGATGACCGA
TTTATTGCTTTGACCCACTTCTATATATCTCATCAAGAAAATGGGGGTTTGAAGTTTCACTCACA
TTGAACTTTGCTTCATTGATTTGATCTACTTCTCTATATCTCATCAGGAAGATGATCACTTCATT
GATTTAATCCACTTCTCTGTATCTAATCAAGAAGGCGGATTTGGT
Found at i:2371 original size:209 final size:209
Alignment explanation
Indices: 2080--3066 Score: 1408
Period size: 209 Copynumber: 4.7 Consensus size: 209
2070 TGGATTTGGT
* * * ** *
2080 CCACTTCTCTGTATCTAATAAAAAAGATGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTTCTT
1 CCACTTCTCTATATCTCATCAGGAAGAT-GGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTT
* * * *
2145 CATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATTGCCTCATTGATTTAATTCAGT
65 CATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACT
* * * *
2210 TCTCTGTATCTAATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTTATCA-AGAAGATGACC
130 TCTCTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGA-AAGATGACC
2274 GA-TTTATTGCTTTGAC
194 -ACTTTATTGCTTTGAC
* *
2290 CCACTTCTATATATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAACTTTGCTTC
1 CCACTTCTCTATATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
* * *
2355 ATTGATTTGATCTACTTCTCTATATCTCATCAGGAAGATGATCACTTCATTGATTTAATCCACTT
66 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTT
* *
2420 CTCTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTATATCTCATCAGAAAGATGATCGA
131 CTCTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGA-CCA
*
2485 -TTTATTGCTTTAAC
195 CTTTATTGCTTTGAC
* *
2499 CCACTTCTCTATATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTC
1 CCACTTCTCTATATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
* * * *
2564 ATTGATTTGATCTACTTCTCTATATCTCATTAGGAAGATG-TCTGCTTCATTGATTTAGTCCACT
66 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATC-GCTTCATTGATTTAATCCACT
* *
2628 TCTCTATATCTCATCAGGAAGGCGGATTTGGTCCACTTTTCTGTATCTCATCAGAAAGATGACCA
130 TCTCTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCA
2693 CTTTATTGCTTTGAC
195 CTTTATTGCTTTGAC
* * *
2708 CCACTTCTCTATATCTCATCAGGAAGATGGGGGTTTGAAGTTTTACTCATATTGAGCTTTCCTTC
1 CCACTTCTCTATATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
* ** * *
2773 ATTGATTTGGTCTACTTCTCTGTATCTCATAAAAAAGATGACCGTTTCATTGATTTAATCCACTT
66 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTT
* * *
2838 CTCTGTATCTTATCAGGAAGGCGGATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCAC
131 CTCTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCAC
2903 TTTATTGCTTTGAC
196 TTTATTGCTTTGAC
* * **
2917 CCACTTCT-TCGTATCTCATTAGGAAGATGGGTTTTTGAAGTTTCACTCACATTGAGCTTTGCTT
1 CCACTTCTCT-ATATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTT
* * * * * * *
2981 CATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCTCTTTATTGCTTTGACCCACT
65 CATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACT
*
3046 TCTCTATATCTCATCAGGAAG
130 TCTCTGTATCTCATCAGGAAG
3067 ATGGGGTTTG
Statistics
Matches: 702, Mismatches: 69, Indels: 13
0.90 0.09 0.02
Matches are distributed among these distances:
208 5 0.01
209 672 0.96
210 25 0.04
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (209 bp):
CCACTTCTCTATATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTT
CTCTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCAC
TTTATTGCTTTGAC
Found at i:2503 original size:85 final size:85
Alignment explanation
Indices: 2358--2524 Score: 255
Period size: 85 Copynumber: 2.0 Consensus size: 85
2348 TTGCTTCATT
* * *
2358 GATTTGATCTACTTCTCTATATCTCATCAGGAAGATGATCACTTCATTGATTTAATCCACTTCTC
1 GATTTGATCCACTTCTCTATATCTCATCAGAAAGATGATCACTTCATTGATTTAACCCACTTCTC
*
2423 TGTATCTCATCAGGAAGGCG
66 TATATCTCATCAGGAAGGCG
* * *
2443 GATTTGGTCCACTTCTCTATATCTCATCAGAAAGATGATCGA-TTTATTGCTTTAACCCACTTCT
1 GATTTGATCCACTTCTCTATATCTCATCAGAAAGATGATC-ACTTCATTGATTTAACCCACTTCT
2507 CTATATCTCATCAGGAAG
65 CTATATCTCATCAGGAAG
2525 ATAGGGGTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
85 73 0.99
86 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (85 bp):
GATTTGATCCACTTCTCTATATCTCATCAGAAAGATGATCACTTCATTGATTTAACCCACTTCTC
TATATCTCATCAGGAAGGCG
Found at i:2921 original size:85 final size:85
Alignment explanation
Indices: 2776--2942 Score: 203
Period size: 85 Copynumber: 2.0 Consensus size: 85
2766 TTCCTTCATT
* * *
2776 GATTTGGTCTACTTCTCTGTATCTCATAAAAAAGATGACCGTTTCATTGATTTAATCCACTTC-T
1 GATTTGGTCCACTTCTCTGTATCTCATAAAAAAGATGACCCTTTCATTGATTTAACCCACTTCTT
*
2840 CTGTATCTTATCAGGAAGGCG
66 C-GTATCTCATCAGGAAGGCG
* * ** * *
2861 GATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTT-ATTGCTTTGACCCACTTCT
1 GATTTGGTCCACTTCTCTGTATCTCATAAAAAAGATGACC-CTTTCATTGATTTAACCCACTTCT
*
2925 TCGTATCTCATTAGGAAG
65 TCGTATCTCATCAGGAAG
2943 ATGGGTTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
85 64 0.93
86 5 0.07
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTGTATCTCATAAAAAAGATGACCCTTTCATTGATTTAACCCACTTCTT
CGTATCTCATCAGGAAGGCG
Found at i:3122 original size:124 final size:124
Alignment explanation
Indices: 2861--3147 Score: 436
Period size: 124 Copynumber: 2.3 Consensus size: 124
2851 CAGGAAGGCG
* * *
2861 GATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTT
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGCTTTGACCCACTTCTT
* * *
2926 CGTATCTCATTAGGAAGATGGGTTTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATT
66 CATATCTCATCAGGAAGATGGGTGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATT
*
2985 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCTCTTTATTGCTTTGACCCACTTC-T
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGCTTTGACCCACTTCTT
* *
3049 CTATATCTCATCAGGAAGATGGG-GTTTGAAGTTTCACTCACATTGAGTTTTGTTTCATT
66 C-ATATCTCATCAGGAAGATGGGTGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATT
*
3108 GATTTGGTCTTACTTCTCTGTATCTC-TTAAGGAAGATGAC
1 GATTTGGTC-TACTTCTCTGTATCTCATCAA-GAAGATGAC
3148 AGCTTCATTT
Statistics
Matches: 150, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
123 47 0.31
124 103 0.69
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (124 bp):
GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGCTTTGACCCACTTCTT
CATATCTCATCAGGAAGATGGGTGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATT
Found at i:10154 original size:61 final size:61
Alignment explanation
Indices: 10027--10205 Score: 263
Period size: 61 Copynumber: 3.0 Consensus size: 61
10017 GTTTTACTCA
* * * * * * * *
10027 CATTTATTACTCACGATGACACAAAGTCTTCGGACC-CTTGTT-CGCATTGGAATTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGAACCTCTTGTTCCGTATAGGAACTCATTT
10086 CATTTAATACTCACGATGACATATAGTCATCGAACCTCTTGTTCCGTATAGGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGAACCTCTTGTTCCGTATAGGAACTCATTT
*
10147 CATTTAATACTCACGATGACATATAGTCATCGAACCTGTTGTTCCGTATAGGAACTCAT
1 CATTTAATACTCACGATGACATATAGTCATCGAACCTCTTGTTCCGTATAGGAACTCAT
10206 ATACTCACGA
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
59 31 0.28
60 6 0.06
61 72 0.66
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (61 bp):
CATTTAATACTCACGATGACATATAGTCATCGAACCTCTTGTTCCGTATAGGAACTCATTT
Found at i:10279 original size:51 final size:50
Alignment explanation
Indices: 10154--10341 Score: 216
Period size: 51 Copynumber: 3.6 Consensus size: 50
10144 TTTCATTTAA
* ** * *
10154 TACTCACGATGACA-TATAGTCATCGAACCTGTTGTTCCGTATAGGAACTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTAT-GG-ATTCATT
** *
10207 TACTCACGATGACACGGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGT-ATGGATTCATT
*
10258 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGT-ATGGATTCATT
*
10309 TACTTACGATGACACTTAGTCATCGGATCCTTT
1 TACTCACGATGACACTTAGTCATCGGA-CCTTT
10342 CGTTTATAAC
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
51 77 0.65
52 13 0.11
53 28 0.24
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (50 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATGGATTCATT
Found at i:17270 original size:30 final size:29
Alignment explanation
Indices: 17229--17414 Score: 196
Period size: 30 Copynumber: 6.3 Consensus size: 29
17219 NNNNNNNNNN
17229 GGGTCAAAATGTAATTTTAGGAAAGTTTAA
1 GGGTCAAAATGTAATTTT-GGAAAGTTTAA
* * * * **
17259 GGGTTAAAATGTGATTTTGGGATGTTTGT
1 GGGTCAAAATGTAATTTTGGAAAGTTTAA
*
17288 GGGTCAAAATGTATTTTTGGAAAGTTT-A
1 GGGTCAAAATGTAATTTTGGAAAGTTTAA
* *
17316 GTGGTCAAAATGCAATTTTAGAAAAG-TTAGA
1 G-GGTCAAAATGTAATTTT-GGAAAGTTTA-A
*
17347 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGG-AAAGTTTAA
*
17377 GGGTCAAAAAGTAATTTTGGAAAAGTTTAA
1 GGGTCAAAATGTAATTTTGG-AAAGTTTAA
*
17407 GAGTCAAA
1 GGGTCAAA
17415 TTTTGATTTT
Statistics
Matches: 129, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
28 1 0.01
29 47 0.36
30 76 0.59
31 5 0.04
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAGTTTAA
Found at i:17352 original size:59 final size:57
Alignment explanation
Indices: 17229--17403 Score: 188
Period size: 59 Copynumber: 2.9 Consensus size: 57
17219 NNNNNNNNNN
* * * ** * * *
17229 GGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTGATTTTGGGATGTTTGT
1 GGGTCAAAATGT-ATTTTTGGAAAGTTT-AGGGTCAAAATGTAATTTTGAAAAGTTAGA
*
17288 GGGTCAAAATGTATTTTTGGAAAGTTTAGTGGTCAAAATGCAATTTTAGAAAAGTTAGA
1 GGGTCAAAATGTATTTTTGGAAAGTTTAG-GGTCAAAATGTAATTTT-GAAAAGTTAGA
* *
17347 GGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAAAGTAATTTTGGAAAAGTT
1 GGGTCAAAATGTATTTTTGG-AAAGTTTA-GGGTCAAAATGTAATTTT-GAAAAGTT
17404 TAAGAGTCAA
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
57 2 0.02
58 28 0.28
59 37 0.37
60 31 0.31
61 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (57 bp):
GGGTCAAAATGTATTTTTGGAAAGTTTAGGGTCAAAATGTAATTTTGAAAAGTTAGA
Done.