Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014442.1 Kokia drynarioides strain JFW-HI SEQ_129481, 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: 4548
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.32
Warning! 251 characters in sequence are not A, C, G, or T
Found at i:392 original size:221 final size:220
Alignment explanation
Indices: 1--518 Score: 858
Period size: 221 Copynumber: 2.3 Consensus size: 220
* * *
1 ACTGATGTGGCGTAAAACCAATAGAAAAGGGACACAAAATGACGTGGTGTCACTGTTTCATTCAA
1 ACTGATATGGCGTAAAACTATTAGAAAAGGGACAC--AATGACGTGGTGTCACTGTTTCATTCAA
* *
66 -TCATTTTCCATTGAAGAAGTGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTT
64 TTC-TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTT
* *
130 TTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTTAGGA
128 TTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGA
195 TGAAAATGATGAAATTAAGAATGAAAAT
193 TGAAAATGATGAAATTAAGAATGAAAAT
* *
223 ACTGATCTGGCGTAAAACTATTAGAAAAGGGACACAGATGACGTCGTGTCACTGTTTCATTCAAT
1 ACTGATATGGCGTAAAACTATTAGAAAAGGGACACA-ATGACGTGGTGTCACTGTTTCATTCAAT
*
288 TCTTTTCCGTTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTT
65 TCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTT
* *
353 ATGTCACACCAACAATTTCATCCTGCATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATG
130 ATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATG
* *
418 GAAATGTTGAAATTAAGAATGAAAAT
195 AAAATGATGAAATTAAGAATGAAAAT
444 ACTGATATGGCGTAAAACTATTAGAAAAGGGACACAACTGACGTGGTGTCACTGTTTCATTCAAT
1 ACTGATATGGCGTAAAACTATTAGAAAAGGGACACAA-TGACGTGGTGTCACTGTTTCATTCAAT
509 TCTTTTCCAT
65 TCTTTTCCAT
519 NNNNNNNNNN
Statistics
Matches: 277, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
220 2 0.01
221 241 0.87
222 34 0.12
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (220 bp):
ACTGATATGGCGTAAAACTATTAGAAAAGGGACACAATGACGTGGTGTCACTGTTTCATTCAATT
CTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTA
TGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGA
AAATGATGAAATTAAGAATGAAAAT
Found at i:994 original size:221 final size:221
Alignment explanation
Indices: 608--1317 Score: 1086
Period size: 221 Copynumber: 3.2 Consensus size: 221
598 NNNNNNNNNN
*
608 ACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCC
1 ACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCC
* * ** ** * *
673 CTTTCCAATTGTTTTATGCTACTTCAACAATTTCATTTTGAATTTCAGGATTTTAATTTTAATTT
66 CTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTTAATTT
* * *
738 -TAATTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTAAAG
131 GT-TTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATAG
802 GAAAAGGGACACAAATGACGTGGTGTC
195 GAAAAGGGACACAAATGACGTGGTGTC
* *
829 ACGGTTTCATTCAATTCA-TTTCCATTGAAGAGGAGAAAGGATTGTATAAAACAGGGATATTATC
1 ACTGTTTCATTCAA-TCATTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATC
* *
893 CCTTTCCAAAAGTTTTGTGCCACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTTAATT
65 CCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTTAATT
* * ** *
958 TGTTTTTTTCAGGATGAAAACGTT-ATAATTAAGAATGAAAATACTAATAAGGTGTAAAACTATT
130 TGTTTTTTTCAGGATGAAAATGTTGA-AATTAAGAATGAAAATACTGATGTGGCGTAAAACTA-T
*
1022 A-GAAAAGGGACACAAAAGACGTGGTGTC
193 AGGAAAAGGGACACAAATGACGTGGTGTC
*
1050 ACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCC
1 ACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCC
*
1115 CTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCGGGATTTTGATTTTAATTT
66 CTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTTAATTT
* * * *
1180 GATTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGC
131 GTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATAGG
* *
1245 AAAAGGGACGCAAATGACGTTGTGTC
196 AAAAGGGACACAAATGACGTGGTGTC
1271 ACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAT
1 ACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAT
1318 NNNNNNNNNN
Statistics
Matches: 441, Mismatches: 41, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
220 4 0.01
221 431 0.98
222 6 0.01
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (221 bp):
ACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCC
CTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTTAATTT
GTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATAGG
AAAAGGGACACAAATGACGTGGTGTC
Found at i:1868 original size:221 final size:221
Alignment explanation
Indices: 1480--3442 Score: 3080
Period size: 221 Copynumber: 8.9 Consensus size: 221
1470 NNNNNNNNNN
* *
1480 TTTTCCATTGAAGAGGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCTAATAGTTTTAT
1 TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
* * * *
1545 GCCACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTTAATTTTATTTTCTCAGGATGAA
66 GCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGAA
* *
1610 AATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACACAACTGG
131 AATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACACAAATGA
*
1675 TGTGGTGTCACTGTTTCATTCAATTC
196 CGTGGTGTCACTGTTTCATTCAATTC
*
1701 TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTGTCCAATAGTTTTAT
1 TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
*
1766 GCCACATCAACAATTTCATCCTAAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGAA
66 GCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGAA
* * * *
1831 AATGTTGACATTAAGAATGAAAATACTGATGTGGCGTAAAACCAATAGAAAAGGGACACAAAATG
131 AATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACAC-AAATG
*
1896 ACGTGGTGTCACTATTTCATTCAA-TC
195 ACGTGGTGTCACTGTTTCATTCAATTC
* *
1922 ATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAAGGATATTATCCCTTTCCAATAGTTTTA
1 -TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTA
* * * *
1987 TGCCACATCAACAATTTCATCCTGAATTTCCGGATTTTAATTTTAATTT-ATTTTTTTAGGTTGA
65 TGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGA
* * *
2051 AAATGATGAAATTAAGAATGAAAATACTGATCTGGCGTAAAACTATTAGAAAAGGGACACAGATG
130 AAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACACAAATG
*
2116 ACGTCGTGTCACTGTTTCATTCAATTC
195 ACGTGGTGTCACTGTTTCATTCAATTC
*
2143 TTTTCCGTTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
1 TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
* * * * * *
2208 GTCACACCAACAATTTCATCCTGTATTTTAGGATTTTAATTTTAATTTGATTTTTTCAGGATGGA
66 GCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGAA
* * *
2273 AATGTTGAAATTAATAATGAAAATATTGATATGGCGTAAAACTATTAGAAAAGGGACACAACTGA
131 AATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACACAAATGA
2338 CGTGGTGTCACTGTTTCATTCAATTC
196 CGTGGTGTCACTGTTTCATTCAATTC
*
2364 TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTGTCCAATAGTTTTAT
1 TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
*
2429 GCCACATCAACAATTTCATCCTAAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGAA
66 GCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGAA
* * * *
2494 AATGTTGACATTAAGAATGAAAATACTGATGTGGCGTAAAACCAATAGAAAAGGGACACAAAATG
131 AATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACAC-AAATG
2559 ACGTGGTGTCACTGTTTCATTCAA-TC
195 ACGTGGTGTCACTGTTTCATTCAATTC
* * *
2585 ATTTTCCGTTGAAGAAGAGAAAGGATTGTATGAAATAGGGATATTATCCCTTTCCAATAGTTTTA
1 -TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTA
*
2650 TGCCACATCAACAATTTCATCCTG-ATTTCAGGATTTTAATTTTAATTTGATTTT-TTAGGATGA
65 TGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGA
* * * * *
2713 AAATGATGAAATTAAGAATGAAAATATTGATCTGGCGTAAAACTATTAGAAAAGGGACATAGATG
130 AAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACACAAATG
*
2778 ACGTCGTGTCACTGTTTCATTCAATTC
195 ACGTGGTGTCACTGTTTCATTCAATTC
* *
2805 TTTTCCGTTGAAGAAGATAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
1 TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
* * * * *
2870 GCCACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTTAATAT-ATTTTTTTCAGGATGA
66 GCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGA-TTTTCTCAGGATGA
*
2934 AAATGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAAACTATT-GTAAAAGGGACACAAAT
130 AAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAG-AAAAGGGACACAAAT
*
2998 GACGTGGTGTCACTGTTTCATTCAATCC
194 GACGTGGTGTCACTGTTTCATTCAATTC
* *
3026 TTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCATTAGTTTTAT
1 TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
*
3091 GCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGTTTTTCTCAGGATGAA
66 GCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGAA
* * * * *
3156 AATGTTGACATTAAGAATGAAAATACTGATTTGGCGTAAAACCAATAGAAAAGGTACACAAATGA
131 AATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACACAAATGA
3221 CGTGGTGTCACTGTTTCATTCAA-TC
196 CGTGGTGTCACTGTTTCATTCAATTC
* *
3246 ATTTTCCATTGAAGAAGAGAAAGGATTGTA-AGAAACAGGGATATTATCCCTTCCCGATAGTTTT
1 -TTTTCCATTGAAGAAGAGAAAGGATTGTATA-AAACAGGGATATTATCCCTTTCCAATAGTTTT
* * * *
3310 ATGCCACATCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATG
64 ATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATG
* * * *
3375 AAAATGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAACTATTAGAAAAGGGACACAGAT
129 AAAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACACAAAT
3440 GAC
194 GAC
3443 ACATCAACAA
Statistics
Matches: 1598, Mismatches: 129, Indels: 30
0.91 0.07 0.02
Matches are distributed among these distances:
219 112 0.07
220 222 0.14
221 1019 0.64
222 245 0.15
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (221 bp):
TTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAT
GCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAGGATGAA
AATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAAAGGGACACAAATGA
CGTGGTGTCACTGTTTCATTCAATTC
Found at i:3542 original size:128 final size:128
Alignment explanation
Indices: 3314--3570 Score: 406
Period size: 128 Copynumber: 2.0 Consensus size: 128
3304 AGTTTTATGC
3314 CACATCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATGAAAA
1 CACATCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATGAAAA
* *
3379 TGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAACTATTAGAAAAGGGACACAGATGA
66 TGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAACTAATAGAAAAGGGACACAAATGA
* ** * * * *
3442 CACATCAACAATTTCATTTTGAATTTTAGGATTTTAATTTTAATTTTATTTTTTCAGGATGAAAA
1 CACATCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATGAAAA
* * *
3507 TGTTGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGA
66 TGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAACTAATAGAAAAGGGACACAAATGA
3570 C
1 C
3571 GTGGTGTCAC
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 117 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33
Consensus pattern (128 bp):
CACATCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATGAAAA
TGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAACTAATAGAAAAGGGACACAAATGA
Found at i:3737 original size:349 final size:349
Alignment explanation
Indices: 3093--3791 Score: 1107
Period size: 349 Copynumber: 2.0 Consensus size: 349
3083 AGTTTTATGC
3093 CACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGTTTTTCTCAGGATGAAAA
1 CACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGTTTTTCTCAGGATGAAAA
* * *
3158 TGTTGACATTAAGAATGAAAATACTGATTTGGCGTAAAACCAATAGAAAAGGTACACAAATGACG
66 TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACCAATAGAAAAGGGACACAAATGACG
*
3223 TGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAAGAAACAGGGAT
131 TGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAAGAAACAAGGAT
* * *
3288 ATTATCCCTTCCCGATAGTTTTATGCCACATCAACAATATCATCCTGAATTTCAAGATTTTAATT
196 ATTATCCCTTCCCAATAGTTTTATGCCACACCAACAATATCATCATGAATTTCAAGATTTTAATT
*
3353 TTAATTTGATTTTTTCAAGATGAAAATGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAA
261 TTAATTTGATTTTCTCAAGATGAAAATGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAA
*
3418 CTATTAG-AAAAGGGACACAGATGA
326 CTATT-GCAAAAGGGACACAAATGA
** * *
3442 CACATCAACAATTTCATTTTGAATTTTAGGATTTTAATTTTAATTT-TATTTTTTCAGGATGAAA
1 CACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGT-TTTTCTCAGGATGAAA
* * *
3506 ATGTTGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGAC
65 ATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACCAATAGAAAAGGGACACAAATGAC
*
3571 GTGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATA-AAACAAGG
130 GTGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTA-AGAAACAAGG
* * * * * *
3635 ATATTATCCGTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGTATTTCAGGATTTTGA
194 ATATTATCCCTTCCCAATAGTTTTATGCCACACCAACAATATCATCATGAATTTCAAGATTTTAA
* * * *
3700 TTTTAATTTGATTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGTGTAA
259 TTTTAATTTGATTTTCTCAAGATGAAAATGATGAAATTAAGAATGAAAATAATGATGTGGCGTAA
3765 AACTATTGCAAAAGGGACACAAATGA
324 AACTATTGCAAAAGGGACACAAATGA
3791 C
1 C
3792 GTTGTGTCAC
Statistics
Matches: 320, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
348 2 0.01
349 317 0.99
350 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (349 bp):
CACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGTTTTTCTCAGGATGAAAA
TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACCAATAGAAAAGGGACACAAATGACG
TGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAAGAAACAAGGAT
ATTATCCCTTCCCAATAGTTTTATGCCACACCAACAATATCATCATGAATTTCAAGATTTTAATT
TTAATTTGATTTTCTCAAGATGAAAATGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAA
CTATTGCAAAAGGGACACAAATGA
Found at i:3830 original size:221 final size:221
Alignment explanation
Indices: 3442--4548 Score: 1651
Period size: 221 Copynumber: 5.0 Consensus size: 221
3432 ACACAGATGA
* ** * *
3442 CACATCAACAATTTCATTTTGAATTTTAGGATTTTAATTTTAATTTTATTTTTTCAGGATGAAAA
1 CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAA
* *
3507 TGTTGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACG
66 TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACG
*
3572 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGAT
131 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGAT
*
3637 ATTATCCGTTTCCAATAGTTTTATGC
196 ATTATCCCTTTCCAATAGTTTTATGC
* * * *
3663 CACACCAACAATTTCATCATGTATTTCAGGATTTTGATTTTAATTTGATTTTCTCAGGATGAAAA
1 CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAA
* *
3728 TGTTGAAATTAAGAATGAAAATACTGATGTGGTGTAAAACTATTGCAAAAGGGACACAAATGACG
66 TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACG
* * *
3793 TTGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGAT
131 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGAT
* * *
3858 ATTATCCCTTTTCAATTGGTTTATGC
196 ATTATCCCTTTCCAATAGTTTTATGC
* * ** *
3884 CGCATCAACAATTTCATTTTGAATTTCAGGATTTTAATTTTAATTTTATTTTTTCAGGATGAAAA
1 CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAA
* * * * *
3949 TGTTAAAATTAAGAATGGAAATACTGATGTGGCATAAAACTAATGGAAAAGCGACACAAATGACG
66 TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACG
* * *
4014 TGGTGTCACGGTTTCATTCAATTCTTTTCCATTGAAGAGGAGAAAGGATTGTATAAAACAGGGAT
131 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGAT
* *
4079 ATTATCCCTTTCCAGTAGTTTTGTGC
196 ATTATCCCTTTCCAATAGTTTTATGC
* *
4105 CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAAGTTGAAAA
1 CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAA
* * * * *
4170 TGTTAAAATTGAGAATGAAAATACTGATGTGGCATAAAACTATTAGAAAAGGGACACATATGACG
66 TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACG
* *
4235 TCGTGTCACTGTTTC--TCAATCCTTTTCCATTGAAGAAGAGAAAGGATTTTATAAAACAGGGAT
131 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGAT
* *
4298 GTTATCCCTTTCCAGTAGTTTTATGC
196 ATTATCCCTTTCCAATAGTTTTATGC
* *
4324 CACACCAACAATTTCATCCTGTATTTCAGGATTTTAATTTTAATTTGTTTTTTTCAGGATGAAAA
1 CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAA
* * **
4389 TGTTGAAATTAAGAATGAAAATACTGATATGGTGTAAAACTATTAAAAAAGGGACACAAATGACG
66 TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACG
* * * * **
4454 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTAAAGAAGAGAAAGGGTGGTATGAAGTAGGGAT
131 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGAT
* *
4519 ATTATCCCTTTCCGATAGTTTTTTGC
196 ATTATCCCTTTCCAATAGTTTTATGC
4545 CACA
1 CACA
Statistics
Matches: 795, Mismatches: 89, Indels: 4
0.90 0.10 0.00
Matches are distributed among these distances:
219 202 0.25
221 593 0.75
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (221 bp):
CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAA
TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACG
TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGAT
ATTATCCCTTTCCAATAGTTTTATGC
Found at i:3960 original size:570 final size:570
Alignment explanation
Indices: 2872--4012 Score: 1809
Period size: 570 Copynumber: 2.0 Consensus size: 570
2862 AGTTTTATGC
* *
2872 CACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTTAATATATTTTTTTCAGGATGAAAA
1 CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATATATTTTTTTCAGGATGAAAA
* *
2937 TGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAAACTATTGTAAAAGGGACACAAATGACG
66 TGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAAACTAATGGAAAAGGGACACAAATGACG
* *
3002 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGAT
131 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGAT
* * *
3067 ATTATCCCTTTCCATTAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATT
196 ATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGAATTTCAGGATTTTAATT
* * *
3132 TTAATTTGTTTTTCTCAGGATGAAAATGTTGACATTAAGAATGAAAATACTGATTTGGCGTAAAA
261 TTAATTTGATTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAA
*
3197 CCAATAGAAAAGGTACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAA
326 CCAATAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAA
* *
3262 GAGAAAGGATTGTAAGAAACAGGGATATTATCCCTTCCCGATAGTTTTATGCCACATCAACAATA
391 GAGAAAGGATTGTAAGAAACAGGGATATTATCCCTTCCCAATAGGTTTATGCCACATCAACAATA
*
3327 TCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATGAAAATGATGAAATTAAG
456 TCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATGAAAATGATAAAATTAAG
* * * *
3392 AATGAAAATAATGATGTGGCGTAAAACTATTAGAAAAGGGACACAGATGA
521 AATGAAAATAATGATGTGGCATAAAACTAATAGAAAAGCGACACAAATGA
* ** * *
3442 CACATCAACAATTTCATTTTGAATTTTAGGATTTTAATTTTAAT-TTTATTTTTTCAGGATGAAA
1 CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATATAT-TTTTTTCAGGATGAAA
* *
3506 ATGTTGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGAC
65 ATGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAAACTAATGGAAAAGGGACACAAATGAC
3571 GTGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGA
130 GTGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGA
* * *
3636 TATTATCCGTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGTATTTCAGGATTTTGAT
195 TATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGAATTTCAGGATTTTAAT
*
3701 TTTAATTTGATTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGTGTAAA
260 TTTAATTTGATTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAA
* * *
3766 A-CTATTGCAAAAGGGACACAAATGACGTTGTGTCACTGTTTCATTCAATCATTTTCCATTGAAG
325 ACCAATAG-AAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAG
* ** * *
3830 AAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTTCAATTGGTTTATGCCGCATCAACAA
389 AAGAGAAAGGATTGTAAGAAACAGGGATATTATCCCTTCCCAATAGGTTTATGCCACATCAACAA
* ** * * * *
3895 TTTCATTTTGAATTTCAGGATTTTAATTTTAATTTTATTTTTTCAGGATGAAAATGTTAAAATTA
454 TATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATGAAAATGATAAAATTA
* * *
3960 AGAATGGAAATACTGATGTGGCATAAAACTAATGGAAAAGCGACACAAATGA
519 AGAATGAAAATAATGATGTGGCATAAAACTAATAGAAAAGCGACACAAATGA
4012 C
1 C
4013 GTGGTGTCAC
Statistics
Matches: 520, Mismatches: 49, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
569 6 0.01
570 514 0.99
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (570 bp):
CACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATATATTTTTTTCAGGATGAAAA
TGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAAACTAATGGAAAAGGGACACAAATGACG
TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGAT
ATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGAATTTCAGGATTTTAATT
TTAATTTGATTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAA
CCAATAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAA
GAGAAAGGATTGTAAGAAACAGGGATATTATCCCTTCCCAATAGGTTTATGCCACATCAACAATA
TCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAAGATGAAAATGATAAAATTAAG
AATGAAAATAATGATGTGGCATAAAACTAATAGAAAAGCGACACAAATGA
Found at i:4227 original size:791 final size:789
Alignment explanation
Indices: 2653--4233 Score: 2564
Period size: 791 Copynumber: 2.0 Consensus size: 789
2643 AGTTTTATGC
2653 CACATCAACAATTTCATCCTGATTTCAGGATTTTAATTTTAATTTGATTTTTTAGGATGAAAATG
1 CACATCAACAATTTCATCCTGATTTCAGGATTTTAATTTTAATTTGATTTTTTAGGATGAAAATG
* * *
2718 ATGAAATTAAGAATGAAAATATTGATCTGGCGTAAAACTATTAGAAAAGGGACATAGATGACGTC
66 ATGAAATTAAGAATGAAAATATTGATCTGGCGTAAAACTAATAGAAAAGGGACACAAATGACGTC
* * * *
2783 GTGTCACTGTTTCATTCAATTCTTTTCCGTTGAAGAAGATAAAGGATTGTATAAAACAGGGATAT
131 GTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGATAT
*
2848 TATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCAGGATTTTGATTTT
196 TATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGTATTTCAGGATTTTGATTTT
*
2913 AATATATTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAAACT
261 AATATATTTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAAACT
* *
2978 ATTGTAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGA
326 ATTGCAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAAGA
* *
3043 GAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCATTAGTTTTATGCCACATCAACAATTTC
391 GAAAGGATTGTATGAAACAGGGATATTATCCCTTTCAATTAGGTTTATGCCACATCAACAATTTC
* *
3108 ATCCTGAATTTCAGGATTTTAATTTTAATTTGTTTTTCTCAGGATGAAAATGTTGACATTAAGAA
456 ATCCTGAATTTCAGGATTTTAATTTTAATTTGTTTTTCTCAGGATGAAAATGTTAAAATTAAGAA
* * *
3173 TGAAAATACTGATTTGGCGTAAAACCAATAGAAAAGGTACACAAATGACGTGGTGTCACTGTTTC
521 TGAAAATACTGATGTGGCATAAAACCAATAGAAAAGGTACACAAATGACGTGGTGTCACGGTTTC
*
3238 ATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAAGAAACAGGGATATTATCCCTTCCCGA
586 ATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAAGAAACAGGGATATTATCCCTTCCAGA
*
3303 TAGTTTTATGCCACATCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTT
651 TAGTTTTATGCCACACCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTT
* *
3368 CAAGATGAAAATGATGAAATTAAGAATGAAAATAATGATGTGGCGTAAAACTATTAGAAAAGGGA
716 CAAGATGAAAATGATAAAATTAAGAATGAAAATAATGATGTGGCATAAAACTATTAGAAAAGGGA
3433 CACAGATGA
781 CACAGATGA
** * *
3442 CACATCAACAATTTCATTTTGAATTTTAGGATTTTAATTTTAATTTTATTTTTTCAGGATGAAAA
1 CACATCAACAATTTCATCCTG-ATTTCAGGATTTTAATTTTAATTTGATTTTTT-AGGATGAAAA
* * *
3507 TGTTGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACG
64 TGATGAAATTAAGAATGAAAATATTGATCTGGCGTAAAACTAATAGAAAAGGGACACAAATGACG
*
3572 TGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGAT
129 TCGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGAT
*
3637 ATTATCCGTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGTATTTCAGGATTTTGATT
194 ATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGTATTTCAGGATTTTGATT
* * * *
3702 TTAATTTGA-TTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGTGTAAA
259 TTAATAT-ATTTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAA
*
3766 ACTATTGCAAAAGGGACACAAATGACGTTGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGA
323 ACTATTGCAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGA
*
3831 AGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTTCAATT-GGTTTATGCCGCATCAACAA
388 AGAGAAAGGATTGTATGAAACAGGGATATTATCCC-TTTCAATTAGGTTTATGCCACATCAACAA
** *
3895 TTTCATTTTGAATTTCAGGATTTTAATTTTAATTT-TATTTTTTCAGGATGAAAATGTTAAAATT
452 TTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGT-TTTTCTCAGGATGAAAATGTTAAAATT
* * *
3959 AAGAATGGAAATACTGATGTGGCATAAAACTAATGGAAAAGCG-ACACAAATGACGTGGTGTCAC
516 AAGAATGAAAATACTGATGTGGCATAAAACCAATAGAAAAG-GTACACAAATGACGTGGTGTCAC
*
4023 GGTTTCATTCAATTC-TTTTCCATTGAAGAGGAGAAAGGATTGTATA-AAACAGGGATATTATCC
580 GGTTTCATTCAA-TCATTTTCCATTGAAGAAGAGAAAGGATTGTA-AGAAACAGGGATATTATCC
* * *
4086 CTTTCCAG-TAGTTTTGTGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATT
643 C-TTCCAGATAGTTTTATGCCACACCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATT
* * * *
4150 TGATTTTTTCAAGTTGAAAATGTTAAAATTGAGAATGAAAATACTGATGTGGCATAAAACTATTA
707 TGATTTTTTCAAGATGAAAATGATAAAATTAAGAATGAAAATAATGATGTGGCATAAAACTATTA
*
4215 GAAAAGGGACACATATGA
772 GAAAAGGGACACAGATGA
4233 C
1 C
4234 GTCGTGTCAC
Statistics
Matches: 731, Mismatches: 52, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
789 19 0.03
790 31 0.04
791 664 0.91
792 17 0.02
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (789 bp):
CACATCAACAATTTCATCCTGATTTCAGGATTTTAATTTTAATTTGATTTTTTAGGATGAAAATG
ATGAAATTAAGAATGAAAATATTGATCTGGCGTAAAACTAATAGAAAAGGGACACAAATGACGTC
GTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAAGGATAT
TATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCATGTATTTCAGGATTTTGATTTT
AATATATTTTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATAATGATATGGCGTAAAACT
ATTGCAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCATTGAAGAAGA
GAAAGGATTGTATGAAACAGGGATATTATCCCTTTCAATTAGGTTTATGCCACATCAACAATTTC
ATCCTGAATTTCAGGATTTTAATTTTAATTTGTTTTTCTCAGGATGAAAATGTTAAAATTAAGAA
TGAAAATACTGATGTGGCATAAAACCAATAGAAAAGGTACACAAATGACGTGGTGTCACGGTTTC
ATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAAGAAACAGGGATATTATCCCTTCCAGA
TAGTTTTATGCCACACCAACAATATCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTT
CAAGATGAAAATGATAAAATTAAGAATGAAAATAATGATGTGGCATAAAACTATTAGAAAAGGGA
CACAGATGA
Done.