Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_76 ID=scaffold_76-JGI_221_v2.0
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: 16911
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.28
Warning! 478 characters in sequence are not A, C, G, or T
Found at i:1232 original size:339 final size:339
Alignment explanation
Indices: 613--1648 Score: 1487
Period size: 339 Copynumber: 3.1 Consensus size: 339
603 AATCGGTCAA
* * * * * * * *
613 GGGTCAATTCCAAGCGAGCTTACTTG-GTTCCGACCCTATCGGCGAAATTTCCATTTTGACCCGA
1 GGGTCAATTCCAAGCGAGCTTACTTGAATT-CGGCCCGATCAGCGAACTTTCGATTTTGACGCTA
* * * *
677 AACATTTAGTCCATGTTA-TCCGTGTCGATTTTTCTCGATTTGGGACGGAGAAAAATA-TTCGAG
65 AAAATTTAGTCCATGTAACTCC-TGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAG
* * *
740 ATTTCAGTCGCATCCTACGTTGCTGGAA-GCGTAGAATCGATACCGCACGGTCCCGAC-TCTCGG
129 ATTTCAGTCGCATCCTACGTAG-TCGAAGGCGTAGAATCGATTCCGCACGGTCCCGACAT-TCGG
* *
803 GGAGGCTTCCTGAGCCGAGAAACAGTAAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTT
192 CGAGGCTTCCTGAGCTGAGAAACAGTAAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTT
868 GACTCTTTCTCTAGAGCGTTTTCAGCGGCTAGCTCGAAGCAAGGGATTTGCGGAGCTATTTCGAC
257 GACTCTTTCTCTAGAGCGTTTTCAGCGGCTAGCTCGAAGCAAGGGATTTGCGGAGCTATTTCGAC
933 TGAAAAATTGCACTCGGC
322 TGAAAAATTGCACTCGGC
*
951 GGGTCAATTCCAAGCGAGCTTACTTGAATTCGGCCCGATCAGCGAACTTTAGATTTTGACGCTAA
1 GGGTCAATTCCAAGCGAGCTTACTTGAATTCGGCCCGATCAGCGAACTTTCGATTTTGACGCTAA
1016 AAATTTAGTCCATGTAACTCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGAT
66 AAATTTAGTCCATGTAACTCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGAT
* * * *
1081 TTCAGTCGCATCCTACGTAGTTGAAGGCGAAGAATCGATTCCGCACGGTCCCCACATTTGGCGAG
131 TTCAGTCGCATCCTACGTAGTCGAAGGCGTAGAATCGATTCCGCACGGTCCCGACATTCGGCGAG
*
1146 GCTTCCTGAGCTAAGAAACAGTAAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGACT
196 GCTTCCTGAGCTGAGAAACAGTAAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGACT
1211 CTTTCTCTAGAGCGTTTTCAGCGGCTAGCTCGAAGCAAGGGATTTGCGGAGCTATTTCGACTGAA
261 CTTTCTCTAGAGCGTTTTCAGCGGCTAGCTCGAAGCAAGGGATTTGCGGAGCTATTTCGACTGAA
1276 AAATTGCACTCGGC
326 AAATTGCACTCGGC
* *
1290 GGGTCAATTCCACGCGAGCTTACTTGAATTCGGCCCGATCAGCGAACTATCGATTTTGACGCTAA
1 GGGTCAATTCCAAGCGAGCTTACTTGAATTCGGCCCGATCAGCGAACTTTCGATTTTGACGCTAA
* * *
1355 TAATTTAGTCCATGTAACCCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCAAGAT
66 AAATTTAGTCCATGTAACTCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGAT
** ** * * *
1420 TTCAGTCGCATCCTATATAGTCGGTGGCGTAGAATCGGTTCCGCACGCTCCCGACACTCGGCGAG
131 TTCAGTCGCATCCTACGTAGTCGAAGGCGTAGAATCGATTCCGCACGGTCCCGACATTCGGCGAG
* * *
1485 GCTTCCTGAG-TCGAGAAACAGTCAA-AAGCTGGTCAAAAAGGAGCTTTTCTGACCACTTTTTGC
196 GCTTCCTGAGCT-GAGAAACAGT-AAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGA
* * * * * * *
1548 CTGTTTCTCTGGAGCGTTTTCAGCGGATAGCTCGAAGCTAGGGACTCGCGGAGCT-TTTCCAACT
259 CTCTTTCTCTAGAGCGTTTTCAGCGGCTAGCTCGAAGCAAGGGATTTGCGGAGCTATTT-CGACT
* * * *
1612 CG-AAAATCGAACACAGC
323 -GAAAAATTGCACTCGGC
*
1629 GGGTCAATTCCATGCGAGCT
1 GGGTCAATTCCAAGCGAGCT
1649 CAGATCCAAA
Statistics
Matches: 634, Mismatches: 55, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
338 109 0.17
339 521 0.82
340 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (339 bp):
GGGTCAATTCCAAGCGAGCTTACTTGAATTCGGCCCGATCAGCGAACTTTCGATTTTGACGCTAA
AAATTTAGTCCATGTAACTCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGAT
TTCAGTCGCATCCTACGTAGTCGAAGGCGTAGAATCGATTCCGCACGGTCCCGACATTCGGCGAG
GCTTCCTGAGCTGAGAAACAGTAAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGACT
CTTTCTCTAGAGCGTTTTCAGCGGCTAGCTCGAAGCAAGGGATTTGCGGAGCTATTTCGACTGAA
AAATTGCACTCGGC
Found at i:4033 original size:197 final size:197
Alignment explanation
Indices: 3678--4041 Score: 419
Period size: 197 Copynumber: 1.8 Consensus size: 197
3668 GAAACTGGTC
* * **
3678 AAAACGAGCATTTCTGACTCCTTTTTGAATCTTTCTCTGGAGCGTTTTCAGCGGATAGCTTTAAG
1 AAAACGAGCATTTCTGACTCCTTTTTGAACCTTTCTCTGGAGCGTTTTCAGCAGATAGCTCGAAG
* * * ** **
3743 CGAGGGAGTCGCGAACCTTTACCGACTCGAAAATCGCACTCGGCGGGTCAATTCCAAGTTACCTT
66 CAAGGGACTCACGAACCTTTACCGACTCGAAAATCGCACTCAACGGGTCAATTCCAAGGGACCTT
** * * * ** *
3808 ACTTGGTGCCGGTCCGATTGGCGAACTTTTGATTTTGTCAAGCCGAGAACCAGTCAAAAACAGGG
131 ACCCGGTGCCAGCCCGATCGAAGAACTTTCGATTTTGTCAAGCCGAGAACCAGTCAAAAACAGGG
3873 GA
196 GA
*
3875 AAAACGAGCATTTCTGAC-CACTTTTTGACCCTTTCTCTGGAGCGTTTTCAGCAGATAGCTCGAA
1 AAAACGAGCATTTCTGACTC-CTTTTTGAACCTTTCTCTGGAGCGTTTTCAGCAGATAGCTCGAA
* * * * * *
3939 GCAAGGGACTTACGGAGCTATT-CCGACTGGAAAATTGCACTCAACGGGTCATTTCCAAGGGGA-
65 GCAAGGGACTCACGAACCT-TTACCGACTCGAAAATCGCACTCAACGGGTCAATTCCAA-GGGAC
* **
4002 CTTGCCCGGTTTCAGCCCGATCGAAGAACTTTCGATTTTG
128 CTTACCCGGTGCCAGCCCGATCGAAGAACTTTCGATTTTG
4042 ACCCCGAAAT
Statistics
Matches: 135, Mismatches: 29, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
196 1 0.01
197 130 0.96
198 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (197 bp):
AAAACGAGCATTTCTGACTCCTTTTTGAACCTTTCTCTGGAGCGTTTTCAGCAGATAGCTCGAAG
CAAGGGACTCACGAACCTTTACCGACTCGAAAATCGCACTCAACGGGTCAATTCCAAGGGACCTT
ACCCGGTGCCAGCCCGATCGAAGAACTTTCGATTTTGTCAAGCCGAGAACCAGTCAAAAACAGGG
GA
Found at i:5187 original size:318 final size:321
Alignment explanation
Indices: 4540--5384 Score: 907
Period size: 318 Copynumber: 2.6 Consensus size: 321
4530 TCAGAAACTG
* * * * *
4540 GTCAAAAACGAGCATTTCCGACCACTTTTTGACTCTTTTTCTGGAGCATTTTCAGCAGATAGCTG
1 GTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTC-AGAGCGTTTTCAGCAGATAGCTC
* *
4605 TAAGCGAGGGACTTGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCAAAGCGA
65 TAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCAAGCGA
* * ** * * *
4670 GCTTACTTGGTTTTTGCCCGATGGGCGAACTTTCGATTTCGACCCGAAAAATTTAGTCCATGTAA
130 GCTAACTTGCTTTCGGCCCGATCGGCGAACTATCGATTTAGACCCGAAAAATTTAGTCCATGT-A
* ** *
4735 CCCATGTCAGTTTTTCTCCAGTTTGGACTGAGAAAAAACGTTTGAAATTTCAGTTGCATCCTACG
194 --CA--T-AGTTTTTCTCCAGTTTGGACTGAAAAAAAAAATTCGAAATTTCAGTTGCATCCTACG
* * *
4800 TAGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACTCTCTGCGAGACTTCCTGAGCCGAGAA
254 CAGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAAAA
4865 ACA
319 ACA
* *
4868 GTCAAAAACGAGCATTTCTGAACACTTTTTGACTCTTTCTCCGTAGCGTTTTCAGCAGATAGCTC
1 GTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCAG-AGCGTTTTCAGCAGATAGCTC
*
4933 TAAGCGAGGGACTCGCGGAGC-TTTCGGACTCGAAAATCGCACTCAGCGGGTCAATTCCAAGCG-
65 TAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCAAGCGA
* * * *
4996 GCCTAACTTGCTTTCGGCTCGATCGGCGAACTATCGATTTAGACGCTAAAAGTTTAGTCCATGT-
130 G-CTAACTTGCTTTCGGCCCGATCGGCGAACTATCGATTTAGACCCGAAAAATTTAGTCCATGTA
* *
5060 CA-A-TTTTTCTCGA-TTTGGGACTGAAAAAAAAAATTCGAGATTTCAGTCT-CATCCTACGCAG
194 CATAGTTTTTCTCCAGTTT-GGACTGAAAAAAAAAATTCGAAATTTCAGT-TGCATCCTACGCAG
*** * * * *
5121 TTGGAGGCGTAGAATCGATTCCGCACGGTGTTGGCGCTGTGCGAGGCTTCCTTAGCCGAAAAACA
257 TTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAAAAACA
*
5186 GTCAAAAACAGGTCAGAAACGAGCTTTTCTGACCAATTTTTGACTCTTTGGCT-AGAGCGTTTTC
1 GTCAAAAAC--G--AG---C-A---TTTCTGACCACTTTTTGACTCTTT--CTCAGAGCGTTTTC
* * * * * * * * *
5250 AGCGGACAGCCCGAAGCGAGGGACTCGCGGAGCTTTTCAGACTGGAGAATCGCACTTAGCGTGTC
53 AGCAGATAGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTC
** * * * * * *
5315 AATTCCAAGCGAGCTTCCTCGGTTTCAGCCTGATCGGCGAACTTTCGATTTCGACCCCG-AAAAT
118 AATTCCAAGCGAGCTAACTTGCTTTCGGCCCGATCGGCGAACTATCGATTTAGA-CCCGAAAAAT
5379 TTAGTC
182 TTAGTC
5385 GATTAAAGAA
Statistics
Matches: 437, Mismatches: 60, Indels: 38
0.82 0.11 0.07
Matches are distributed among these distances:
317 3 0.01
318 110 0.25
319 2 0.00
320 1 0.00
322 2 0.00
323 2 0.00
325 1 0.00
326 2 0.00
327 92 0.21
328 77 0.18
329 60 0.14
330 80 0.18
331 5 0.01
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (321 bp):
GTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCAGAGCGTTTTCAGCAGATAGCTCT
AAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCAAGCGAG
CTAACTTGCTTTCGGCCCGATCGGCGAACTATCGATTTAGACCCGAAAAATTTAGTCCATGTACA
TAGTTTTTCTCCAGTTTGGACTGAAAAAAAAAATTCGAAATTTCAGTTGCATCCTACGCAGTTGG
AGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAAAAACA
Found at i:9801 original size:339 final size:337
Alignment explanation
Indices: 9182--10217 Score: 1329
Period size: 339 Copynumber: 3.1 Consensus size: 337
9172 AATCGGTCAA
* * * * *
9182 GGGTCAATTCCAAGCGAGCTTACTTGGTTCCGACCCTATCGGCGAAATTTCCATTTTGACCCGAA
1 GGGTCAATTCCAAGCGAGCTTACTTGGTTCCGACCCGATCGGCGAACTTTCGATTTTGACGCTAA
* * *
9247 AAATTTAGTCCATGTTA-TCCGTGTCGATTTTTCTCGATTTGGGACGGAGAAAAATA-TTCGAGA
66 AAATTTAGTCCATGTAACTCC-TGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGA
* * * *
9310 TTTCAGTCGCATCCTACGTTGCTGGAA-GCGTAGAATCGATACCGCACGGTCCCGAC-TCTCGGG
130 TTTCAGTCGCATCCTACGTAG-TCGAAGGCGTAGAATCGATTCCGCACGGTCCCGACAT-TCGGC
*
9373 GAGGCTTCCTGAGCCGAGAAACAGT-AAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTT
193 GAGGCTTCCTGAGCTGAGAAACAGTCAA-AAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTT
* * * * *
9437 GACTC-TTTCTCTAGAGCGTTTTCAGCGGCTAGCTCGAAGCAAGGGATTTGCGGAGCTATTTCGA
257 G-CTCTTTTCTCTGGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCT-TTTCGA
* *
9501 CTGAAAAATTGCACTCGGC
320 CTG-AAAATCGCACTCAGC
* * * *
9520 GGGTCAATTCCAAGCGAGCTTACTTGAATT-CGGCCCGATCAGCGAACTTTAGATTTTGACGCTA
1 GGGTCAATTCCAAGCGAGCTTACTTG-GTTCCGACCCGATCGGCGAACTTTCGATTTTGACGCTA
*
9584 AAAATTTAGTCCATGTAACTCCTGTCGATTTTTCTCAATTTGGGACTGAGAAAAAAATTTCGAGA
65 AAAATTTAGTCCATGTAACTCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGA
* * * *
9649 TTTCAGTCGCATCCTACGTAGTTGAAGGCGAAGAATCGATTCCGCACGGTCCCCACATTTGGCGA
130 TTTCAGTCGCATCCTACGTAGTCGAAGGCGTAGAATCGATTCCGCACGGTCCCGACATTCGGCGA
* * * *
9714 GGCTTCCTGAGCTAAGAATCAGTCAAAAATTGGTTC-AAAACTAGCTTTTCTGACCACTTTTTGT
195 GGCTTCCTGAGCTGAGAAACAGTCAAAAACTGG-TCAAAAACGAGCTTTTCTGACCACTTTTTG-
* * * ** *
9778 CTCTTTTTTC-GGAGCGTTTTCAGCGGATAACTCGTAGCGAGGGACTCAAGGAGCTTTCCCGACT
258 CTCTTTTCTCTGGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCTTT-TCGACT
*
9842 GGAAAATCCCACTCAGC
322 -GAAAATCGCACTCAGC
*
9859 GGGTCAATTCCAAGCGAGCTTACTTGGTTCCGACCCGATCGGCGAACTATCGATTTTGACGCTAA
1 GGGTCAATTCCAAGCGAGCTTACTTGGTTCCGACCCGATCGGCGAACTTTCGATTTTGACGCTAA
* * *
9924 TAATTTAGTCCATGTAACCCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCAAGAT
66 AAATTTAGTCCATGTAACTCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGAT
** ** * * *
9989 TTCAGTCGCATCCTATATAGTCGGTGGCGTAGAATCGGTTCCGCACGCTCCCGACACTCGGCGAG
131 TTCAGTCGCATCCTACGTAGTCGAAGGCGTAGAATCGATTCCGCACGGTCCCGACATTCGGCGAG
* * *
10054 GCTTCCCGAG-TCGAGAAACAGTCAAAAGCTGGTCAAAAAGGAGCTTTTCTGACCACTTTTTGC-
196 GCTTCCTGAGCT-GAGAAACAGTCAAAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGCT
*
10117 CTGTTTCTCTGGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCTTTTCCAACTC
260 CT-TTTCTCTGGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCTTTT-CGACT-
* *
10182 GAAAATCGAACACAGC
322 GAAAATCGCACTCAGC
*
10198 GGGTCAATTCCATGCGAGCT
1 GGGTCAATTCCAAGCGAGCT
10218 CAGATCCAAA
Statistics
Matches: 603, Mismatches: 79, Indels: 31
0.85 0.11 0.04
Matches are distributed among these distances:
337 2 0.00
338 118 0.20
339 472 0.78
340 11 0.02
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (337 bp):
GGGTCAATTCCAAGCGAGCTTACTTGGTTCCGACCCGATCGGCGAACTTTCGATTTTGACGCTAA
AAATTTAGTCCATGTAACTCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGAT
TTCAGTCGCATCCTACGTAGTCGAAGGCGTAGAATCGATTCCGCACGGTCCCGACATTCGGCGAG
GCTTCCTGAGCTGAGAAACAGTCAAAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGCTC
TTTTCTCTGGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCTTTTCGACTGAAA
ATCGCACTCAGC
Found at i:13251 original size:318 final size:323
Alignment explanation
Indices: 12530--13258 Score: 808
Period size: 318 Copynumber: 2.2 Consensus size: 323
12520 TTACATAGTT
** * * *
12530 GGAGGCGTAGAATCGATTCCGCACGGTCTTGACTCTCGGCGAGGCTTCCTGAGCCGAGAAACAGT
1 GGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGA-AAA-A--
* * *
12595 CAGAAACTGGTCAAAAACGAGCATTTCCGACCACTTTTTGACTCTTTTTCTGGAGCATTTTCAGC
62 C----A---GTCAAAAACGAGCATTTCCGAACACTTTTTGACTCTTTCTCCGGAGCATTTTCAGC
* * *
12660 AGATTGCTGTAAGCGAGGGACTTGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAAT
120 AGATAGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAAT
* * * * * *
12725 TCAAAGCGAGCTTACTTGGTTTTATCCCGATGGGCGAACTTTCGATTTCGACCCGAAAAATTTAG
185 TCAAAGCGAGCTAACTTGCTTTCAGCCCGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAG
* ** * *
12790 TCCATGTAACCCATGTCAGTTTTTCTCCAGTTTGGACTGAGAAAAAACGTTTGAAATTTCAGTTG
250 TCCATGT-A--CA-G-CAGTTTTTCTCCAGTTTGGACTGAAAAAAAAAATTCGAAACTTCAGTTG
* *
12855 CATCCTACGTAGTT
310 CATCCTACGCAGTC
* * *
12869 GGAGGCGTAGAATCGCTTCCGCACGGTCCCGACTCTCTGCGAGACTTCCTGAGCCGAGAAACAGT
1 GGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAAAAACAGT
* * *
12934 CAAAAACGAGCATTTCTGAACACTTTTTGACTCTTTCTCCGTAGCGTTTTCAGCAGATAGCTCTA
66 CAAAAACGAGCATTTCCGAACACTTTTTGACTCTTTCTCCGGAGCATTTTCAGCAGATAGCTCTA
*
12999 AGCGAGGGACTCGCGGAGC-TTTCGGACTCGAAAATCGCACTCAGCGGGTCAATTCAAAGCG-GC
131 AGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCAAAGCGAG-
* * * * * * *
13062 CTAACTTGCTTTCGGCTCGATCGGCGTACTATCGATTTTGACGCTAAAAGTTTAGTCCATGT-C-
195 CTAACTTGCTTTCAGCCCGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGTCCATGTACA
* *
13125 G-A-TTTTTCTCGA-TTTGGGACTGAAAAAAAAAATTCGAGACTTCAGTCT-CATCCTACGCAGT
260 GCAGTTTTTCTCCAGTTT-GGACTGAAAAAAAAAATTCGAAACTTCAGT-TGCATCCTACGCAGT
13186 C
323 C
* ** * * * *
13187 GGAGGCGTAGAATCGATTGCGCACGGTCTTGGCGCTCTGCGAGGCTTTCTTAGCCGAAAAACAGT
1 GGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAAAAACAGT
13252 CAAAAAC
66 CAAAAAC
13259 AGGTCAAAAA
Statistics
Matches: 339, Mismatches: 48, Indels: 27
0.82 0.12 0.07
Matches are distributed among these distances:
317 3 0.01
318 107 0.32
319 2 0.01
321 1 0.00
323 1 0.00
326 1 0.00
327 90 0.27
328 77 0.23
331 1 0.00
335 1 0.00
337 1 0.00
338 2 0.01
339 52 0.15
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (323 bp):
GGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAAAAACAGT
CAAAAACGAGCATTTCCGAACACTTTTTGACTCTTTCTCCGGAGCATTTTCAGCAGATAGCTCTA
AGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCAAAGCGAGC
TAACTTGCTTTCAGCCCGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGTCCATGTACAG
CAGTTTTTCTCCAGTTTGGACTGAAAAAAAAAATTCGAAACTTCAGTTGCATCCTACGCAGTC
Found at i:16446 original size:339 final size:322
Alignment explanation
Indices: 16275--16911 Score: 658
Period size: 314 Copynumber: 2.0 Consensus size: 322
16265 GACTCGAAAA
* * ** * *
16275 TCGCACTCAGCGAGTCAATTCAAAGCGAG-CTTACTTGGTTTTTGCCCGATGGGCGAACTTTCGA
1 TCGCACTCAGCGAGTCAATTCAAAGCG-GCCTAACTTGCTTTCGGCCCGATCGGCGAACTATCGA
16339 TTTCGACCCGAAAAATTTAGTCCATGTAACCCATGTC-AGTTTTTCTCCAGTTT-GGACTGAGAA
65 TTTCGACCCGAAAAATTTAGTCCATGTAACCCATGTCGA-TTTTTCTCCA-TTTGGGACTGA-AA
**
16402 AAAACGTTT-GAAATTTCAGT-TGCATCCTACGTAGTTGGAGGCGTAGAATCGATTCCGCACGGT
127 AAAAAATTTCGAAATTTCAGTCT-CATCCTACGTAGTTGGAGGCGTAGAATCGATTCCGCACGGT
** * * *
16465 CCCGACTCTCTGCGAGAC-TTC---CTGAG---CCG--AGAAACAGTCAAAAACGAGCATTTCTG
191 CCCGAGGCTCTGCGAG-CTTTCTTGCCGAGAAACAGTCAGAAACGGTCAAAAACGAGCATTTCTG
* * * *
16521 AACACTTTTTGACTCTTTCTCCGTAGCGTTTTCAGCAGATAGCTCTAAGCGAGGGACTAGCGGAG
255 ACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCAGATAGCTGTAAGCGAGGGACTAGCGGAG
16586 CTT
320 CTT
* * *
16589 TCGCACTCAGCGGGTCAATTCCAAGCGGCCTAACTTGCTTTCGGCTCGATCGGCGAACTATCGAT
1 TCGCACTCAGCGAGTCAATTCAAAGCGGCCTAACTTGCTTTCGGCCCGATCGGCGAACTATCGAT
* * * * * *
16654 TTTGACGCTAAAAGTTTAGTCCATGTAACCCCTGTCGATTTTTCTCGATTTGGGACTGAAAAAAA
66 TTCGACCCGAAAAATTTAGTCCATGTAACCCATGTCGATTTTTCTCCATTTGGGACTGAAAAAAA
* * **
16719 AATTTCGAGATTTCAGTCTCATCCTACGCAGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTG-
131 AATTTCGAAATTTCAGTCTCATCCTACGTAGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGA
* * * * *
16783 GCGCTCTGCGAGGCTTCCTTAGCCGAAAAACACTCAAAAACAGGTCAAAAACGAGCTTTTCTGAC
196 G-GCTCTGCGA-GCTTTCTT-GCCGAGAAACAGTCAGAAAC-GGTCAAAAACGAGCATTTCTGAC
** * ** * * * * *
16848 CAAATCTTGACTCTTTGGCTAGAGCGTTTTCAGCGGACAGCCCG-AAGCGAGGGACTCGCGGAGC
257 CACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCAGATAG-CTGTAAGCGAGGGACTAGCGGAGC
Statistics
Matches: 259, Mismatches: 45, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
313 13 0.05
314 162 0.63
315 5 0.02
319 3 0.01
322 1 0.00
324 5 0.02
325 69 0.27
326 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (322 bp):
TCGCACTCAGCGAGTCAATTCAAAGCGGCCTAACTTGCTTTCGGCCCGATCGGCGAACTATCGAT
TTCGACCCGAAAAATTTAGTCCATGTAACCCATGTCGATTTTTCTCCATTTGGGACTGAAAAAAA
AATTTCGAAATTTCAGTCTCATCCTACGTAGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGA
GGCTCTGCGAGCTTTCTTGCCGAGAAACAGTCAGAAACGGTCAAAAACGAGCATTTCTGACCACT
TTTTGACTCTTTCTCTGGAGCGTTTTCAGCAGATAGCTGTAAGCGAGGGACTAGCGGAGCTT
Done.