Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003901.1 Kokia drynarioides strain JFW-HI SEQ_116961, 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: 11412
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.34
Warning! 144 characters in sequence are not A, C, G, or T
Found at i:1282 original size:48 final size:48
Alignment explanation
Indices: 1206--1297 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
1196 TTGAGCTTCG
** * *
1206 CTTCATTGTTTTGGTCTAGTTCTCTGTATCTCATCAGAAAGATGACTA
1 CTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAGAAAGATGACTA
*
1254 CTTCATTGTTTTGACCCACTTCTTTGTATCTCATCAGAAAGATG
1 CTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAGAAAGATG
1298 GGGTTTGAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (48 bp):
CTTCATTGTTTTGACCCACTTCTCTGTATCTCATCAGAAAGATGACTA
Found at i:1325 original size:123 final size:123
Alignment explanation
Indices: 1145--2043 Score: 1045
Period size: 123 Copynumber: 7.3 Consensus size: 123
1135 ACTTATTTAG
* * * *
1145 CCCACTTCTCTGTATCTCATCAAGAAGATTGGGTTTGAAGTTGAAGTCGCATTGAGCTTCGCTTC
1 CCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTAACTCGCATTGAGCTTCGCTTC
* *
1210 ATTGTTTTGGTCTAGTTCTCTGTATCTCATCAGAAAGATGACTACTTCATTGTTTTGA
66 ATTGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGA
* * * * *
1268 CCCACTTCTTTGTATCTCATCAGAAAGATGGGGTTTGAAGTTGAAGTTGCATTGAGCTTCGCTTC
1 CCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTAACTCGCATTGAGCTTCGCTTC
* * *
1333 ATTGTTTTGGTCTAGTTCTTTGTATCTCATCAGGAAGATGACCACTTCATTGTTTTGA
66 ATTGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGA
* * * ** * *
1391 CCTACTTCTTTGTATCTCATCAGGAAGATGGAGTTTGAAGTTTCCCTCGCATTAAGCTTTGCTTC
1 CCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTAACTCGCATTGAGCTTCGCTTC
* * *
1456 ATTGTTTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGA-TCACTTTATTGTTTTTA
66 ATTGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACT-ACTTCATTGTTTTGA
* * * *
1514 CCCACTTATCTATATCTCATCAGGAAGATGGGGTTTGAAGTTTCAA-TCGCATTGAGTTTTGCTT
1 CCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTT-AACTCGCATTGAGCTTCGCTT
* * *
1578 CATTGTTTTGGTCTACTTCTCTATATCTCATCAGGAAGATGAGC-ACTTTATTATTTTGA
65 CATTGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-CTACTTCATTGTTTTGA
* * * * *
1637 CACACTTTTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTC
1 CCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTAACTCGCATTGAGCTTCGCTTC
* * * * * * **
1702 GTTGATTTGAT-TCACTTCTTTGTATCTTATCAGGAAGATGAATGTTTCATTGTTTTGA
66 ATTGTTTTGGTCT-ACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGA
* * * * * * *
1760 TCTACTTCTCTGAATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTCCCTTC
1 CCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTAACTCGCATTGAGCTTCGCTTC
* * * * * * * * **
1825 GTCGATTAGGTCCACTTTTCTGTATGTCATTAGGAAGATGACCGCTTCATTGTTTTGA
66 ATTGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGA
* * * * *
1883 CCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTTAAAGTTTTACTCACATTGAGCTTTG-TT
1 CCCACTTCTCTGTATCTCATCAGGAAGATGGGG-TTTGAAGTTTAACTCGCATTGAGCTTCGCTT
* * *
1947 TAGTTGATTTGGTCCT-CTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTGTTTTGA
65 CA-TTGTTTTGGT-CTACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGA
** *
2007 CCCTTTTCTTTGTATCTCATCAGGAAGATGGGGTTTG
1 CCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTG
2044 GTCCATTTCT
Statistics
Matches: 666, Mismatches: 99, Indels: 22
0.85 0.13 0.03
Matches are distributed among these distances:
122 2 0.00
123 564 0.85
124 99 0.15
125 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (123 bp):
CCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTAACTCGCATTGAGCTTCGCTTC
ATTGTTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGA
Found at i:1400 original size:48 final size:48
Alignment explanation
Indices: 1329--1420 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
1319 TTGAGCTTCG
** *
1329 CTTCATTGTTTTGGTCTAGTTCTTTGTATCTCATCAGGAAGATGACCA
1 CTTCATTGTTTTGACCTACTTCTTTGTATCTCATCAGGAAGATGACCA
1377 CTTCATTGTTTTGACCTACTTCTTTGTATCTCATCAGGAAGATG
1 CTTCATTGTTTTGACCTACTTCTTTGTATCTCATCAGGAAGATG
1421 GAGTTTGAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (48 bp):
CTTCATTGTTTTGACCTACTTCTTTGTATCTCATCAGGAAGATGACCA
Found at i:2128 original size:57 final size:57
Alignment explanation
Indices: 2040--2150 Score: 186
Period size: 57 Copynumber: 1.9 Consensus size: 57
2030 GAAGATGGGG
* *
2040 TTTGGTCCATTTCTTTGTATCTCATTAGGAAGATGACCACTTTATTACTTTGACGGA
1 TTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGACCACTTTATTACTTTGACGGA
* *
2097 TTTGGTTCACTTCTCTGTATCTCATTAGGAAGATGACCACTTTATTATTTTGAC
1 TTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGACCACTTTATTACTTTGAC
2151 CCACTTCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (57 bp):
TTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGACCACTTTATTACTTTGACGGA
Found at i:2213 original size:143 final size:143
Alignment explanation
Indices: 1952--2236 Score: 417
Period size: 143 Copynumber: 2.0 Consensus size: 143
1942 TTGTTTAGTT
* * * **
1952 GATTTGGTCCTCTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTGTTTTGACCCTTTTCTT
1 GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTTTGACCCACTTCTT
* * * * * *
2017 TGTATCTCATCAGGAAGATGGGGTTTGGTCCATTTCTTTGTATCTCATTAGGAAGATGACCACTT
66 TGTATCTCATCAAGAAGATGAGGTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCACTT
2082 TATTACTTTGACG
131 TATTACTTTGACG
* * * *
2095 GATTTGGTTCACTTCTCTGTATCTCATTAGGAAGATGACCACTTTATTATTTTGACCCACTTCTT
1 GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTTTGACCCACTTCTT
* *
2160 TGTATCTCATCAAGAAGATGAGGTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATCGCTT
66 TGTATCTCATCAAGAAGATGAGGTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCACTT
2225 TATTACTTTGAC
131 TATTACTTTGAC
2237 CCACTTCTCT
Statistics
Matches: 125, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
143 125 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.40
Consensus pattern (143 bp):
GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTTTGACCCACTTCTT
TGTATCTCATCAAGAAGATGAGGTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCACTT
TATTACTTTGACG
Found at i:2242 original size:86 final size:85
Alignment explanation
Indices: 2097--2408 Score: 358
Period size: 86 Copynumber: 3.6 Consensus size: 85
2087 CTTTGACGGA
* * * * * * *
2097 TTTGGTTCACTTCTCTGTATCTCATTAGGAAGATGACCACTTTATTATTTTGACCCACTTCTTTG
1 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATCGCTTTATTACTTTGACCCACTTCTATG
2162 TATCTCATCAAGAAGATGAGG
66 TATCTCAT-AAGAAGATGAGG
*
2183 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATCGCTTTATTACTTTGACCCACTTCTCTG
1 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATCGCTTTATTACTTTGACCCACTTCTATG
2248 TATCTCATAAGGAAGAT-AGGG
66 TATCTCATAA-GAAGATGA-GG
* * * * * * * *
2269 TTTGGTTCTCTTATCTTTATCTCATCAGGAAGATGA-CTGCTTCATTATTTTGGCCCACTTCTAC
1 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATC-GCTTTATTACTTTGACCCACTTCTAT
* * * *
2333 GTATCTTATTAGGAAGACGGGG
65 GTATCTCA-TAAGAAGATGAGG
* * *
2355 TTTGGTCCACTTCTCTATATCTCATCAAGAAGATGATCGATTTATTGCTTTGAC
1 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATCGCTTTATTACTTTGAC
2409 GGATTTGATC
Statistics
Matches: 190, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
85 4 0.02
86 183 0.96
87 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (85 bp):
TTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATCGCTTTATTACTTTGACCCACTTCTATG
TATCTCATAAGAAGATGAGG
Found at i:2318 original size:172 final size:172
Alignment explanation
Indices: 2097--2408 Score: 462
Period size: 172 Copynumber: 1.8 Consensus size: 172
2087 CTTTGACGGA
* * * **
2097 TTTGGTTCACTTCTCTGTATCTCATTAGGAAGATGACCACTTTATTATTTTGACCCACTTCTTTG
1 TTTGGTTCACTTATCTGTATCTCATCAGGAAGATGACCACTTCATTATTTTGACCCACTTCTACG
* * *
2162 TATCTCATCAAGAAGATGAGGTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATCGCTTTA
66 TATCTCATCAAGAAGACGAGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATGATCGATTTA
2227 TTACTTTGACCCACTTCTCTGTATCTCATAAGGAAGATAGGG
131 TTACTTTGACCCACTTCTCTGTATCTCATAAGGAAGATAGGG
* * ** *
2269 TTTGGTTCTCTTATCTTTATCTCATCAGGAAGATGACTGCTTCATTATTTTGGCCCACTTCTACG
1 TTTGGTTCACTTATCTGTATCTCATCAGGAAGATGACCACTTCATTATTTTGACCCACTTCTACG
* * * *
2334 TATCTTATTAGGAAGACGGGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATGATCGATTTA
66 TATCTCATCAAGAAGACGAGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATGATCGATTTA
*
2399 TTGCTTTGAC
131 TTACTTTGAC
2409 GGATTTGATC
Statistics
Matches: 122, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
172 122 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (172 bp):
TTTGGTTCACTTATCTGTATCTCATCAGGAAGATGACCACTTCATTATTTTGACCCACTTCTACG
TATCTCATCAAGAAGACGAGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATGATCGATTTA
TTACTTTGACCCACTTCTCTGTATCTCATAAGGAAGATAGGG
Found at i:2423 original size:229 final size:232
Alignment explanation
Indices: 2183--2646 Score: 583
Period size: 229 Copynumber: 2.0 Consensus size: 232
2173 GAAGATGAGG
* * *
2183 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATGATCGCTTTATTACTTTGACCCACTTCTCTG
1 TTTGATCCACTTCTCTATATATCATCAGGAAGATGACCGCTTTATTACTTTGACCCACTTCTCTG
* * * * * *
2248 TATCTCATAAGGAAGATAGGGTTTGGTTCTCTTATCTTTATCTCATCAGGAAGATGACTGC-TT-
66 TATCTCATAAGGAAGATAGAGTTTGGTCCACTTATCTATATCCCATCAGGAAGATGACCGCTTTG
* * *
2311 CATT-ATTTTGGCCCACTTCTACGTATCTTATTAGGAAGACGGGGTTTGGTCCACTTCTCTATAT
131 CATTGAATTTGGCCCACTTCTACGTATCTTATCAAGAAGACGGGGTTTGGTCCACTTCTCTATAT
*
2375 CTCATCAAGAAGATGATCGATTTATTGCTTTGACGGA
196 CTCATCAAGAAGATGACCGATTTATTGCTTTGACGGA
* * * *
2412 TTTGATCCACTTCTCTGTATATCATTAGGAAGATGACCGTTTTATTTCTTTGACCCACTTCTCTG
1 TTTGATCCACTTCTCTATATATCATCAGGAAGATGACCGCTTTATTACTTTGACCCACTTCTCTG
* * * * *
2477 TATCTCCTCAGTAAGATCGAGTTTGGTCCACTTCTCTATATCCCATCAGGAAGATGACCGCTTTA
66 TATCTCATAAGGAAGATAGAGTTTGGTCCACTTATCTATATCCCATCAGGAAGATGACCGC--T-
* * * * *
2542 TTGCTTTGACGAATTTGGTCCACTTCTATGTATCTTATCAAGAAGATGGGGTTTGGTTCACTTCT
128 TTGCATT---GAATTTGGCCCACTTCTACGTATCTTATCAAGAAGACGGGGTTTGGTCCACTTCT
* * *
2607 TTGTATCTCATCAAGAAGATGACCGTTTTATTGCTTTGAC
190 CTATATCTCATCAAGAAGATGACCGATTTATTGCTTTGAC
2647 CCACTTTTTT
Statistics
Matches: 196, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
229 108 0.55
233 2 0.01
234 3 0.02
238 83 0.42
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (232 bp):
TTTGATCCACTTCTCTATATATCATCAGGAAGATGACCGCTTTATTACTTTGACCCACTTCTCTG
TATCTCATAAGGAAGATAGAGTTTGGTCCACTTATCTATATCCCATCAGGAAGATGACCGCTTTG
CATTGAATTTGGCCCACTTCTACGTATCTTATCAAGAAGACGGGGTTTGGTCCACTTCTCTATAT
CTCATCAAGAAGATGACCGATTTATTGCTTTGACGGA
Found at i:2427 original size:57 final size:57
Alignment explanation
Indices: 2355--2465 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
2345 GAAGACGGGG
* * *
2355 TTTGGTCCACTTCTCTATATCTCATCAAGAAGATGATCGATTTATTGCTTTGACGGA
1 TTTGATCCACTTCTCTATATATCATCAAGAAGATGACCGATTTATTGCTTTGACGGA
* * * * *
2412 TTTGATCCACTTCTCTGTATATCATTAGGAAGATGACCGTTTTATTTCTTTGAC
1 TTTGATCCACTTCTCTATATATCATCAAGAAGATGACCGATTTATTGCTTTGAC
2466 CCACTTCTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.41
Consensus pattern (57 bp):
TTTGATCCACTTCTCTATATATCATCAAGAAGATGACCGATTTATTGCTTTGACGGA
Found at i:2430 original size:315 final size:315
Alignment explanation
Indices: 1954--2713 Score: 873
Period size: 315 Copynumber: 2.4 Consensus size: 315
1944 GTTTAGTTGA
* * ** **
1954 TTTGGTCCTCTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTGTTTTGACCCTTTTCTTTG
1 TTTGGTCCTCTTATCTGTATCTCATCAAGAAGATGACTACTTCATTATTTTGACCCACTTCTACG
* * * * * *
2019 TATCTCATCAGGAAGATGGGGTTTGGTCCATTTCTTTGTATCTCATTAGGAAGATGACCACTTTA
66 TATCTCATCAGGAAGACGGGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCACTTTA
* * *
2084 TTACTTTGACGGATTTGGTTCACTTCTCTGTATCTCATTAGGAAGATGACCACTTTATTAT-TTT
131 TTACTTTGACGGATTTGATCCACTTCTCTGTATATCATTAGGAAGATGACCACTTTATT-TCTTT
* *
2148 GACCCACTTCTTTGTATCTCATCAAG-AAGAT-GAGGTTTGGTCCACTTCTCTATATCTCATCAG
195 GACCCACTTCTCTGTATCTCATC-AGTAAGATCGA-GTTTGGTCCACTTCTCTATATCCCATCAG
*
2211 GAAGATGATCGCTTTATTACTTTGACCCACTTCTCTGTATCTCATAAGGAAGATAGGG
258 GAAGATGACCGCTTTATTACTTTGACCCACTTCTCTGTATCTCATAAGGAAGATAGGG
* * * * *
2269 TTTGGTTCTCTTATCTTTATCTCATCAGGAAGATGACTGCTTCATTATTTTGGCCCACTTCTACG
1 TTTGGTCCTCTTATCTGTATCTCATCAAGAAGATGACTACTTCATTATTTTGACCCACTTCTACG
* * *
2334 TATCTTATTAGGAAGACGGGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATGATCGA-TTT
66 TATCTCATCAGGAAGACGGGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATGA-CCACTTT
* **
2398 ATTGCTTTGACGGATTTGATCCACTTCTCTGTATATCATTAGGAAGATGACCGTTTTATTTCTTT
130 ATTACTTTGACGGATTTGATCCACTTCTCTGTATATCATTAGGAAGATGACCACTTTATTTCTTT
*
2463 GACCCACTTCTCTGTATCTCCTCAGTAAGATCGAGTTTGGTCCACTTCTCTATATCCCATCAGGA
195 GACCCACTTCTCTGTATCTCATCAGTAAGATCGAGTTTGGTCCACTTCTCTATATCCCATCAGGA
* * * *
2528 AGATGACCGCTTTATTGCTTTGACGAATTTGGTCCACTTCTATGTATCTTATCAA-GAAGATGGG
260 AGATGACCGCTTTATTACTTTGAC---------CCACTTCTCTGTATCTCAT-AAGGAAGATAGG
2592 G
315 G
* * * * *** * ** * **
2593 TTTGGTTCACTTCTTTGTATCTCATCAAGAAGATGACCGTTTTATTGCTTTGACCCACTTTTTTG
1 TTTGGTCCTCTTATCTGTATCTCATCAAGAAGATGACTACTTCATTATTTTGACCCACTTCTACG
* * ** * * *
2658 TATCTCATCAAGAAGATGGGGTTTGGTTTACTTCTCTGTATCTCATTAGGAAGATG
66 TATCTCATCAGGAAGACGGGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATG
2714 GGGTTTGAAG
Statistics
Matches: 374, Mismatches: 57, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
314 3 0.01
315 241 0.64
316 4 0.01
324 124 0.33
325 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (315 bp):
TTTGGTCCTCTTATCTGTATCTCATCAAGAAGATGACTACTTCATTATTTTGACCCACTTCTACG
TATCTCATCAGGAAGACGGGGTTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCACTTTA
TTACTTTGACGGATTTGATCCACTTCTCTGTATATCATTAGGAAGATGACCACTTTATTTCTTTG
ACCCACTTCTCTGTATCTCATCAGTAAGATCGAGTTTGGTCCACTTCTCTATATCCCATCAGGAA
GATGACCGCTTTATTACTTTGACCCACTTCTCTGTATCTCATAAGGAAGATAGGG
Found at i:2606 original size:38 final size:38
Alignment explanation
Indices: 2555--2720 Score: 125
Period size: 38 Copynumber: 4.1 Consensus size: 38
2545 CTTTGACGAA
*
2555 TTTGGTCCACTTCTATGTATCTTATCAAGAAGATGGGG
1 TTTGGTCCACTTCTATGTATCTCATCAAGAAGATGGGG
* * *
2593 TTTGGTTCACTTCTTTGTATCTCATCAAGAAGATGACCGTTTTATTGC
1 TTTGGTCCACTTCTATGTATCTCATCAAGAAGATG---G-------GG
** * *
2641 TTTGACCCACTTTTTTGTATCTCATCAAGAAGATGGGG
1 TTTGGTCCACTTCTATGTATCTCATCAAGAAGATGGGG
** * * *
2679 TTTGGTTTACTTCTCTGTATCTCATTAGGAAGATGGGG
1 TTTGGTCCACTTCTATGTATCTCATCAAGAAGATGGGG
2717 TTTG
1 TTTG
2721 AAGTTTCACT
Statistics
Matches: 101, Mismatches: 17, Indels: 20
0.73 0.12 0.14
Matches are distributed among these distances:
38 67 0.66
41 1 0.01
45 1 0.01
48 32 0.32
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (38 bp):
TTTGGTCCACTTCTATGTATCTCATCAAGAAGATGGGG
Found at i:2910 original size:46 final size:46
Alignment explanation
Indices: 2838--3069 Score: 251
Period size: 46 Copynumber: 5.2 Consensus size: 46
2828 TAATAGTTTC
* *
2838 AATCTGCCCCTCTTAACTTAGTGGTAAAAGATTGGATGATGGCTTT
1 AATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGCTTT
* *
2884 AATCTGCCCCTTTTGACTTAGGGGTAAAAGATTGGATGATGGCTTC
1 AATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGCTTT
* *
2930 AATCTGCCTCTCTTGA-TTAGGGGTAAAAGATTAGA--ATGG-TTT
1 AATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGCTTT
* * * * * *
2972 CCACCTGCCTCTCTAGA-TTAGGGGTAAAAGATTGGACGATGACTTT
1 -AATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGCTTT
* ** * * *
3018 -AGCTTTCCCTCTTGACTTAAGGGTAAAAGATTGGATGATGACTTC
1 AATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGCTTT
3063 AATCTGC
1 AATCTGC
3070 TTCTCTACAT
Statistics
Matches: 156, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
42 2 0.01
43 35 0.22
44 10 0.06
45 47 0.30
46 62 0.40
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (46 bp):
AATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGCTTT
Found at i:3058 original size:45 final size:45
Alignment explanation
Indices: 2845--3061 Score: 189
Period size: 45 Copynumber: 4.8 Consensus size: 45
2835 TTCAATCTGC
* * * *
2845 CCCTCTTAACTTAGTGGTAAAAGATTGGATGATGGCTTT-AATCTG
1 CCCTCTTGACTTAGGGGTAAAAGATTGGATGATGACTTTCACT-TG
* * *
2890 CCCCTTTTGACTTAGGGGTAAAAGATTGGATGATGGC-TTCAATCTG
1 -CCCTCTTGACTTAGGGGTAAAAGATTGGATGATGACTTTCACT-TG
* * *
2936 CCTCTCTTGA-TTAGGGGTAAAAGATTAGA--ATG-GTTTCCACCTG
1 CC-CTCTTGACTTAGGGGTAAAAGATTGGATGATGACTTT-CACTTG
* * *
2979 CCTCTCTAGA-TTAGGGGTAAAAGATTGGACGATGACTTT-AGCTTT
1 CC-CTCTTGACTTAGGGGTAAAAGATTGGATGATGACTTTCA-CTTG
*
3024 CCCTCTTGACTTAAGGGTAAAAGATTGGATGATGACTT
1 CCCTCTTGACTTAGGGGTAAAAGATTGGATGATGACTT
3062 CAATCTGCTT
Statistics
Matches: 146, Mismatches: 16, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
43 34 0.23
44 9 0.06
45 55 0.38
46 48 0.33
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
CCCTCTTGACTTAGGGGTAAAAGATTGGATGATGACTTTCACTTG
Found at i:4039 original size:5 final size:5
Alignment explanation
Indices: 4025--4069 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
4015 ACCTCTCCTT
*
4025 TTTTC TTTT- TCTT- TTTTC TGTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC TTTTC T
4070 CTCTTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 6 0.17
5 25 0.69
6 5 0.14
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:4074 original size:24 final size:24
Alignment explanation
Indices: 4025--4076 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4015 ACCTCTCCTT
* *
4025 TTTTCTTTTTCTTTTTTCTGTTTC
1 TTTTCTTTTTCTTTTTTCTCTCTC
*
4049 TTTTC-TTTTCTTTTCTTTTCTCTC
1 TTTTCTTTTTCTTTT-TTCTCTCTC
4073 TTTT
1 TTTT
4077 TTAGGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (24 bp):
TTTTCTTTTTCTTTTTTCTCTCTC
Found at i:4077 original size:15 final size:14
Alignment explanation
Indices: 4022--4077 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 14
4012 TTGACCTCTC
4022 CTTTT-TTCTTTTT
1 CTTTTCTTCTTTTT
*
4035 CTTTT-TTCTGTTT
1 CTTTTCTTCTTTTT
*
4048 CTTTTCTTTTCTTTT
1 CTTTTCTTCT-TTTT
4063 CTTTTCTCTCTTTTT
1 CTTTTCT-TCTTTTT
4078 TAGGTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 17 0.47
14 3 0.08
15 14 0.39
16 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (14 bp):
CTTTTCTTCTTTTT
Found at i:10169 original size:17 final size:17
Alignment explanation
Indices: 10149--10239 Score: 78
Period size: 17 Copynumber: 5.3 Consensus size: 17
10139 TATTTTAAGA
* *
10149 TTAAATTGATTTTGAAT
1 TTAAATTGAATTTAAAT
*
10166 TTAAATTTAATTTAAAT
1 TTAAATTGAATTTAAAT
*
10183 TTAAATTTG-TTTTAAAAT
1 TTAAA-TTGAATTT-AAAT
*
10201 TT-AATTTAATTTAAAT
1 TTAAATTGAATTTAAAT
* *
10217 TTAGATTTATATTTAAAT
1 TTAAATTGA-ATTTAAAT
10235 TTAAA
1 TTAAA
10240 ACTTATTATA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
16 8 0.13
17 32 0.53
18 20 0.33
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAAATTGAATTTAAAT
Found at i:10172 original size:6 final size:6
Alignment explanation
Indices: 10163--10239 Score: 81
Period size: 6 Copynumber: 13.3 Consensus size: 6
10153 ATTGATTTTG
**
10163 AATTTA AATTT- AATTTA AATTTA AATTT- GTTTTAA AATTT- AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* *
10208 AATTTA AATTTA GATTTA TATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA
10240 ACTTATTATA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
5 18 0.30
6 39 0.65
7 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:10174 original size:34 final size:33
Alignment explanation
Indices: 10130--10239 Score: 87
Period size: 34 Copynumber: 3.2 Consensus size: 33
10120 TTAAACCCAT
* * *
10130 TTTAAGATTTATTTTAAGATTAAATTGATTTTGAA
1 TTTAA-ATTTATTTTAA-ATTAAATTTAATTTAAA
* **
10165 TTTAAATTTAATTTAAATTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAA-TTAAATTTAATTT-AAA
* *
10200 TTT-AATTTAATTTAAATTTAGATTTATATTTAAA
1 TTTAAATTTATTTTAAA-TTAAATTTA-ATTTAAA
10234 TTTAAA
1 TTTAAA
10240 ACTTATTATA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
33 1 0.02
34 48 0.75
35 15 0.23
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (33 bp):
TTTAAATTTATTTTAAATTAAATTTAATTTAAA
Done.