Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_389 ID=scaffold_389-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: 7563
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Found at i:19 original size:6 final size:7
Alignment explanation
Indices: 1--33 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1 GAAAAAG
1 GAAAAAG
8 GAAAAAG
1 GAAAAAG
*
15 GAAAAAA
1 GAAAAAG
22 GAAAAA-
1 GAAAAAG
28 GAAAAA
1 GAAAAA
34 AAAATATACC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
GAAAAAG
Found at i:1073 original size:109 final size:109
Alignment explanation
Indices: 879--1091 Score: 381
Period size: 109 Copynumber: 2.0 Consensus size: 109
869 GCGCCACTTG
*
879 CGCACATAAAACGCCTTCAGAGAGTCGAGTATGTAATGACCTGAAACCAGCACGCACAACATATT
1 CGCACATAAAACGCCTTCAGAGAGTCGAGTAAGTAATGACCTGAAACCAGCACGCACAACATATT
* *
944 CGTAACAACAATTGCTGCAGACGCAGCTGAAGGCGAATTGCTCT
66 CGTAACAACAATTGCCGCAGACGCAGCTGAAGACGAATTGCTCT
* *
988 CGCACATAAAACGCCTTCAGAGATTCGTGTAAGTAATGACCTGAAACCAGCACGCACAACATATT
1 CGCACATAAAACGCCTTCAGAGAGTCGAGTAAGTAATGACCTGAAACCAGCACGCACAACATATT
1053 CGTAACAACAATTGCCGCAGACGCAGCTGAAGACGAATT
66 CGTAACAACAATTGCCGCAGACGCAGCTGAAGACGAATT
1092 TTTCAGTTAA
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 99 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (109 bp):
CGCACATAAAACGCCTTCAGAGAGTCGAGTAAGTAATGACCTGAAACCAGCACGCACAACATATT
CGTAACAACAATTGCCGCAGACGCAGCTGAAGACGAATTGCTCT
Found at i:2193 original size:343 final size:337
Alignment explanation
Indices: 1569--2270 Score: 807
Period size: 343 Copynumber: 2.1 Consensus size: 337
1559 AATCGGCCAA
* *
1569 GGGTCAATTCCAAGCGAGCTTACTTGGTTCCGACCATATCGGCGAAATTTCCATTTTGACCCGAA
1 GGGTCAATTCCAAGCGAGCTTACTTGGTTCAGACCATATCGGCGAAATTTCCATTTCGACCCGAA
* * * * * * *
1634 AAATTTAGTCCATGTTATACGTGTCGATTTTTCTTGATTTGGGACGGAGAAAAATATTCGAGATT
66 AAATTTAGTCCATGGTATACCTGTAGATTTTTCTCGATTTAGGACGGAGAAAAAAATTCAAGATT
* *
1699 TCAGTTGCATTCTACGTTGCTGGAAGCGTAGAATCGATTCCGCACGCTCTTGACACTCGGCGAGG
131 TCAGTCGCATCCTACGTTGCTGGAAGCGTAGAATCGATTCCGCACGCTCTTGACACTCGGCGAGG
* *
1764 CTTCCTTAGCCGAAAAACAGTCGAAAACAGGTCAAAACGGAGCTTTTCTGACGAATTTTTGACTC
196 CTTCCTGAGCCGAAAAACAGTCGAAAACAGGTCAAAACGGAGCTTTTCTGACCAATTTTTGACTC
** * * *
1829 TTTGTCTAGAGCGTTTTCAGCGGACAGCCCGAAGCTAGGGACTCGCGGAGC-TTTCCAGACAGGA
261 TTTGTCTAGAGCGAATTCAGCGGACAGCCCAAAGCGAGGGACTCGCGGAGCTTTTCCA-ACACGA
* * *
1893 GAATCGCACTTAGC
325 AAAT-GAACTCAGC
* * *
1907 GGGTCAATTCCAAGCGAGCTTCCTTGGTTTCAG-CC-TAATCGGCGAACTTTCGATTTCGACCCC
1 GGGTCAATTCCAAGCGAGCTTACTTGG-TTCAGACCAT-ATCGGCGAAATTTCCATTTCGA-CCC
*
1970 G-AAAATTTAGTCCATGGTACGTACCCCTGTAGATTTTTCTCGATTTAGGACTGAGAAAAAAATT
63 GAAAAATTTAGTCCATGGTA--TA--CCTGTAGATTTTTCTCGATTTAGGACGGAGAAAAAAA-T
* * *
2034 TCAAGATTTCAGTCGCATCCTA--TTTCGTGCGAGGCGTAGAATCGATTCCGCACAG-TCTTGGC
123 TCAAGATTTCAGTCGCATCCTACGTTGC-TG-GAAGCGTAGAATCGATTCCGCAC-GCTCTTGAC
* * *
2096 TCTCTGCGAGGCTTCCTGAG-CTAAAGAACAGTC-AAAA-AGTTGTCAAAAAC-GAGCTTTTCTG
185 ACTCGGCGAGGCTTCCTGAGCCGAAA-AACAGTCGAAAACAG--GTC-AAAACGGAGCTTTTCTG
* * * * * *
2157 ACCACTTTTTG-CTTGTTTTTCTGGAGCGAATTCAGCGGATAGCTCAAAGCGAGGGACTCGCGGA
246 ACCAATTTTTGAC-TCTTTGTCTAGAGCGAATTCAGCGGACAGCCCAAAGCGAGGGACTCGCGGA
*
2221 GCTTTTCCAACTCGAAAATGAACTCAGC
310 GCTTTTCCAACACGAAAATGAACTCAGC
*
2249 GGGTCAATCCCAAGCGAGCTTA
1 GGGTCAATTCCAAGCGAGCTTA
2271 GATCCAAAGG
Statistics
Matches: 307, Mismatches: 40, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
337 1 0.00
338 64 0.21
339 8 0.03
340 2 0.01
341 5 0.02
342 69 0.22
343 146 0.48
344 12 0.04
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (337 bp):
GGGTCAATTCCAAGCGAGCTTACTTGGTTCAGACCATATCGGCGAAATTTCCATTTCGACCCGAA
AAATTTAGTCCATGGTATACCTGTAGATTTTTCTCGATTTAGGACGGAGAAAAAAATTCAAGATT
TCAGTCGCATCCTACGTTGCTGGAAGCGTAGAATCGATTCCGCACGCTCTTGACACTCGGCGAGG
CTTCCTGAGCCGAAAAACAGTCGAAAACAGGTCAAAACGGAGCTTTTCTGACCAATTTTTGACTC
TTTGTCTAGAGCGAATTCAGCGGACAGCCCAAAGCGAGGGACTCGCGGAGCTTTTCCAACACGAA
AATGAACTCAGC
Found at i:5387 original size:339 final size:336
Alignment explanation
Indices: 4331--5830 Score: 1538
Period size: 339 Copynumber: 4.4 Consensus size: 336
4321 GACTTCAGGC
* * * * **
4331 AAACTGGTCAAAAACGAG-TGTTTCTGGCCACTTTTTGAGT-TTCTCTCTGGATCGTCTTCCGCG
1 AAACTGGTCAAAAACGAGCT-TTTCAGACCACTTTTTGACTCTT-TCTCTGGAGCGT-TTTAGCG
* *
4394 GATAGCTCGAAGCGAGGGACTCGCGGA-CCTTTCCGGACTCGAAAATCGCACTCAGCGGGTCAAT
63 GATAGCTCGAAGCGAGGGACTCGCGGAGCTTTTCC-GACTGGAAAATCGCACTCAGCGGGTCAAT
* * * * * * *
4458 ACCAAGCGAGCTTACTTTGTTCCGACCCGATCGGGGAACTATCTATTTTGACGCTAAAAATTTAG
127 TCCAAGCGAGCTTACTTGGTTCCGGCCCGATCAGCGAACTTTCGATTTTGACGCTAAAAATTTAG
* *
4523 TCCAA-GTAATC--CTAG-TCGATTTTCCTCGATTTGGGACTGAGAAAAAAATGTCGAGA-TACA
192 T-CAATGTAA-CGACT-GTTC-ATTTT-CTCGATTTGGGACTGAGAAAAAAATTTCGAGATTTCA
* * * * * *
4583 GTCGCATCCTACGCATTTTGAGGCGTAGAATCAATTCCGCACGGTCCCGACTC-AGAAAC-AGTC
252 GTCGCATCCTACGTA-GTGGAAGCGTAGAATCAATTCCGCACGGTCCCGACTCTCG--GCGAG--
** ** * *
4646 GCTGAAC-GAAACGCTCCCGAAACAGTCAG
312 GCT-TCCTG-AA--C-CGAGAAACAGTAAA
* * *
4675 AAACTGGTCAAAAACCAGCTTTTCAGACCGA-TTTTTTACTCTTTCTCTAGAGCGTTTTCAGCGG
1 AAACTGGTCAAAAACGAGCTTTTCAGACC-ACTTTTTGACTCTTTCTCTGGAGCGTTTT-AGCGG
* * * *
4739 AAAGCTCGAAGCGAGGGACTCGCGGAGCTTTACCGAATGGAAAATCGCACTCAGCGGGTCATTTC
64 ATAGCTCGAAGCGAGGGACTCGCGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCAATTC
* * * * * *
4804 CAAGCGACCTTACTTGGTTTCTGCCCGATCAGCGAATTTTCGATTTTGATGCTAAAAATTTGGTC
129 CAAGCGAGCTTACTTGGTTCCGGCCCGATCAGCGAACTTTCGATTTTGACGCTAAAAATTTAGTC
** *
4869 CCTGT--CGA---TT--TTTT-TCGATTTGGGACTGAGAAAAAAATTTCAAGATTTCAGTCGCAT
194 AATGTAACGACTGTTCATTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGATTTCAGTCGCAT
* * * * *
4926 CCTACGTAGTTGAAGGCGTAGAATCGATTCCGCACGGTCTCGACTCTCGGCGAGACTTCCTGAGC
259 CCTACGTAGTGGAA-GCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGCTTCCTGAAC
*
4991 CTAGAAACAG-AATA
323 CGAGAAACAGTAA-A
* * * *
5005 AAACTGGTCAAACACGAGCTTTTCAGACCAATTTTTTACTCTTTCTCTGGAGCGTGTTTAGCGAA
1 AAACTGGTCAAAAACGAGCTTTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGT-TTTAGCGGA
* * *
5070 TAGCTCGAAGCGAGGGACTCGCGGAGCTTTTTCGACTGGAGAATCGCACTCAGCGGGTCATTTCC
65 TAGCTCGAAGCGAGGGACTCGCGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCAATTCC
* * * * * *
5135 AAGCG-GCATAACTTGCTTCCGGCTCGATCGGCGAACTTTCGATTTTGACGCTTAAAATTTAGTT
130 AAGCGAGC-TTACTTGGTTCCGGCCCGATCAGCGAACTTTCGATTTTGACGCTAAAAATTTAGTC
*
5199 AATGTAACGACTGTTCATTTTACTCGATTTTGGACTGAGAAAAATAA-TTCGAGATTTCAGTCGC
194 AATGTAACGACTGTTCATTTT-CTCGATTTGGGACTGAGAAAAA-AATTTCGAGATTTCAGTCGC
* * * * ** *
5263 ATTCTACGTTGCTGGAAGCGTAGAATCGATTCAGCACGGTCCTAACTCTTGGCGAGGCTTCCTGA
257 ATCCTACGTAG-TGGAAGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGCTTCCTGA
5328 ACCGAGAAACAGTAAA
321 ACCGAGAAACAGTAAA
* * * *
5344 AAACTAGTCAAAAACGAGCTTTTCTGACCACTTTTTGACTCTTTCTCTGGAGCGTATTCAGCGGC
1 AAACTGGTCAAAAACGAGCTTTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGT-TTTAGCGGA
* * * * *
5409 TAGCTCGAAACAAGGGACTTGCGGAGCTATTCCGACTGGAAAATCGCACTCGGCGGGTCAATTCC
65 TAGCTCGAAGCGAGGGACTCGCGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCAATTCC
* *
5474 AAGCGAGCTTACTTGGTTTCGGCCCGATCAGCGAACTTTTGATTTTGACGCTAAAAAATTTAGTC
130 AAGCGAGCTTACTTGGTTCCGGCCCGATCAGCGAACTTTCGATTTTGACGCT-AAAAATTTAGTC
* ** ** * *
5539 CATGTAACCCCTGTAGATTTTTCTCCATTTGGGACTGAGAAAAAAATTTCGAG-TTATCGGTCGC
194 AATGTAACGACTGTTCA-TTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGATT-TCAGTCGC
* * *
5603 TTCCCACGTAGTTGGAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGC-TCTCTG
257 ATCCTACGTAG-TGGAAGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGCTTC-CTG
* * *
5667 AGCCGAGAAACAGTCAG
320 AACCGAGAAACAGTAAA
* * * *
5684 AAACTGGTCAAAAACGAGCATTTCCGACCACTTTTTGACTCTTTTTCTTGAGCGTTTTCAGCGGA
1 AAACTGGTCAAAAACGAGCTTTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGTTTT-AGCGGA
* * * * *
5749 TAGCTCGAACCGAGGGAGTCGCGGACCTTTTCCGACTCGAAAATCGCACTCAGCGGGTCAATTCA
65 TAGCTCGAAGCGAGGGACTCGCGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCAATTCC
** *
5814 AAGTTACCTTACTTGGT
130 AAGCGAGCTTACTTGGT
5831 GTTGGTCCGA
Statistics
Matches: 969, Mismatches: 150, Indels: 78
0.81 0.13 0.07
Matches are distributed among these distances:
329 3 0.00
330 176 0.18
331 4 0.00
332 3 0.00
333 2 0.00
334 3 0.00
335 36 0.04
336 48 0.05
337 9 0.01
339 262 0.27
340 255 0.26
341 5 0.01
343 3 0.00
344 151 0.16
345 9 0.01
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (336 bp):
AAACTGGTCAAAAACGAGCTTTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTAGCGGAT
AGCTCGAAGCGAGGGACTCGCGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCAATTCCA
AGCGAGCTTACTTGGTTCCGGCCCGATCAGCGAACTTTCGATTTTGACGCTAAAAATTTAGTCAA
TGTAACGACTGTTCATTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGATTTCAGTCGCATCC
TACGTAGTGGAAGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGCTTCCTGAACCGA
GAAACAGTAAA
Found at i:5723 original size:340 final size:337
Alignment explanation
Indices: 4331--5860 Score: 1663
Period size: 340 Copynumber: 4.5 Consensus size: 337
4321 GACTTCAGGC
* * * * * *
4331 AAACTGGTCAAAAACGAG-TGTTTCTGGCCACTTTTTGAGT-TTCTCTCTGGATCGTCTTCCGCG
1 AAACTGGTCAAAAACGAGCT-TTTCAGACCACTTTTTGACTCTT-TCTCTGGAGCGTTTTCAGCG
* * *
4394 GATAGCTCGAAGCGAGGGACTCGCGGACCTTTCCGGACTCGAAAATCGCACTCAGCGGGTCAATA
64 GATAGCTCGAAGCGAGGGACTCGCGGAGCTTTCC-GACTGGAAAATCGCACTCAGCGGGTCAATT
* * * * *
4459 CCAAGCGAGCTTACTTTGTTCCGACCCGATCGGGGAACTATCT-ATTTTGACGCTAAAAATTTAG
128 CCAAGCGAGCTTACTTGGTTTCGGCCCGATCGGCGAACT-TTTGATTTTGACGCTAAAAATTTAG
* * * * *
4523 TCCAAGTAATCCTAGTCGATTTTCCTCGATTTGGGACTGAGAAAAAAATGTCGAGA-TACAGTCG
192 TCCATGTAACCCT-GTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGATTTCAGTCG
* * * * *
4587 CATCCTACGCATTTTGAGGCGTAGAATCAATTCCGCACGGTCCCGACTC-AGAAAC-AGTCGCTG
256 CATCCTACGTAGTTGGAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCG--GCGAG--GCT-
** **
4650 AAC-GAAACGCTCCCGAAACAGTCAG
316 TCCTG--A-GC-CGAGAAACAGTCAG
* * *
4675 AAACTGGTCAAAAACCAGCTTTTCAGACCGA-TTTTTTACTCTTTCTCTAGAGCGTTTTCAGCGG
1 AAACTGGTCAAAAACGAGCTTTTCAGACC-ACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCGG
* * *
4739 AAAGCTCGAAGCGAGGGACTCGCGGAGCTTTACCGAATGGAAAATCGCACTCAGCGGGTCATTTC
65 ATAGCTCGAAGCGAGGGACTCGCGGAGCTTT-CCGACTGGAAAATCGCACTCAGCGGGTCAATTC
* * * *
4804 CAAGCGACCTTACTTGGTTTCTGCCCGATCAGCGAA-TTTTCGATTTTGATGCTAAAAATTT-G-
129 CAAGCGAGCTTACTTGGTTTCGGCCCGATCGGCGAACTTTT-GATTTTGACGCTAAAAATTTAGT
* *
4866 ----GT--CCCTGTCGATTTTTTTCGATTTGGGACTGAGAAAAAAATTTCAAGATTTCAGTCGCA
193 CCATGTAACCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGATTTCAGTCGCA
* * * *
4925 TCCTACGTAGTTGAAGGCGTAGAATCGATTCCGCACGGTCTCGACTCTCGGCGAGACTTCCTGAG
258 TCCTACGTAGTTGGAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGCTTCCTGAG
*
4990 CCTAGAAACAGAAT-A-
323 CCGAGAAACAG--TCAG
* * * *
5005 AAACTGGTCAAACACGAGCTTTTCAGACCAATTTTTTACTCTTTCTCTGGAGCGTGTTT-AGCGA
1 AAACTGGTCAAAAACGAGCTTTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGT-TTTCAGCGG
* * *
5069 ATAGCTCGAAGCGAGGGACTCGCGGAGCTTTTTCGACTGGAGAATCGCACTCAGCGGGTCATTTC
65 ATAGCTCGAAGCGAGGGACTCGCGGAGC-TTTCCGACTGGAAAATCGCACTCAGCGGGTCAATTC
* * * * * *
5134 CAAGCG-GCATAACTTGCTTCCGGCTCGATCGGCGAACTTTCGATTTTGACGCTTAAAATTTAGT
129 CAAGCGAGC-TTACTTGGTTTCGGCCCGATCGGCGAACTTTTGATTTTGACGCTAAAAATTTAGT
** * * *
5198 TAATGTAACGACTGTTC-ATTTTACTCGATTTTGGACTGAGAAAAATAA-TTCGAGATTTCAGTC
193 CCATGTAAC-CCTG-TCGATTTTTCTCGATTTGGGACTGAGAAAAA-AATTTCGAGATTTCAGTC
* * * * * * ** *
5261 GCATTCTACGTTGCTGGAAGCGTAGAATCGATTCAGCACGGTCCTAACTCTTGGCGAGGCTTCCT
255 GCATCCTACGTAGTTGGAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGCTTCCT
* * *
5326 GAACCGAGAAACAGTAAA
320 GAGCCGAGAAACAGTCAG
* * * *
5344 AAACTAGTCAAAAACGAGCTTTTCTGACCACTTTTTGACTCTTTCTCTGGAGCGTATTCAGCGGC
1 AAACTGGTCAAAAACGAGCTTTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCGGA
* * * *
5409 TAGCTCGAAACAAGGGACTTGCGGAGCTATTCCGACTGGAAAATCGCACTCGGCGGGTCAATTCC
66 TAGCTCGAAGCGAGGGACTCGCGGAGCT-TTCCGACTGGAAAATCGCACTCAGCGGGTCAATTCC
*
5474 AAGCGAGCTTACTTGGTTTCGGCCCGATCAGCGAACTTTTGATTTTGACGCTAAAAAATTTAGTC
130 AAGCGAGCTTACTTGGTTTCGGCCCGATCGGCGAACTTTTGATTTTGACGCT-AAAAATTTAGTC
* * *
5539 CATGTAACCCCTGTAGATTTTTCTCCATTTGGGACTGAGAAAAAAATTTCGAG-TTATCGGTCGC
194 CATGTAA-CCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGATT-TCAGTCGC
* *
5603 TTCCCACGTAGTTGGAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGC-TCTCTG
257 ATCCTACGTAGTTGGAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGCTTC-CTG
5667 AGCCGAGAAACAGTCAG
321 AGCCGAGAAACAGTCAG
* * * *
5684 AAACTGGTCAAAAACGAGCATTTCCGACCACTTTTTGACTCTTTTTCTTGAGCGTTTTCAGCGGA
1 AAACTGGTCAAAAACGAGCTTTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCGGA
* * * * *
5749 TAGCTCGAACCGAGGGAGTCGCGGACCTTTTCCGACTCGAAAATCGCACTCAGCGGGTCAATTCA
66 TAGCTCGAAGCGAGGGACTCGCGGAGC-TTTCCGACTGGAAAATCGCACTCAGCGGGTCAATTCC
** * * *
5814 AAGTTACCTTACTTGGTGTT-GGTCCGATTGGCGAACTTTTGATTTTG
130 AAGCGAGCTTACTTGGT-TTCGGCCCGATCGGCGAACTTTTGATTTTG
5861 TCGAGCCGAG
Statistics
Matches: 1001, Mismatches: 144, Indels: 86
0.81 0.12 0.07
Matches are distributed among these distances:
329 2 0.00
330 164 0.16
331 13 0.01
332 2 0.00
333 1 0.00
334 3 0.00
335 39 0.04
336 57 0.06
337 2 0.00
338 7 0.01
339 268 0.27
340 278 0.28
341 4 0.00
342 2 0.00
343 2 0.00
344 151 0.15
345 6 0.01
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (337 bp):
AAACTGGTCAAAAACGAGCTTTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCGGA
TAGCTCGAAGCGAGGGACTCGCGGAGCTTTCCGACTGGAAAATCGCACTCAGCGGGTCAATTCCA
AGCGAGCTTACTTGGTTTCGGCCCGATCGGCGAACTTTTGATTTTGACGCTAAAAATTTAGTCCA
TGTAACCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCGAGATTTCAGTCGCATCC
TACGTAGTTGGAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGGCTTCCTGAGCCG
AGAAACAGTCAG
Found at i:5796 original size:679 final size:669
Alignment explanation
Indices: 4331--5810 Score: 1746
Period size: 679 Copynumber: 2.2 Consensus size: 669
4321 GACTTCAGGC
** * * * * * *
4331 AAACTGGTCAAAAACGAGTGTTTCTGGCCACTTTTTGAGT-TTCTCTCTGGATCGTCTTCCGCGG
1 AAACTGGTCAAAAACGAGCATTTCAGACCACTTTTTGACTCTT-TCTCTGGAGCGTTTTCAGCGG
4395 ATAGCTCGAAGCGAGGGACTCGCGGACC-TTTCCGGACTCGAAAATCGCACTCAGCGGGTCAATA
65 ATAGCTCGAAGCGAGGGACTCGCGGACCTTTTCC-GACTCGAAAATCGCACTCAGCGGGTCAATA
* * *
4459 CCAAGCGAGCTTACTTTGTTCCGACCCGATCGGGGAACTATCTATTTTGACGCTAAAAATTTAGT
129 CCAAGCGAGCTAACTTTGTTCCGACCCGATCGGCGAACTATCGATTTTGACGCTAAAAATTTAGT
*
4524 CCAAGTAATCCTAGTCGATTTTCCTCGATTTGGGACTGAGAAAAAAATGTCGAGATACAGTCGCA
194 CCAAGTAATCCTAGTCGATTTTACTCGATTTGGGACTGAGAAAAAAATGTCGAGATACAGTCGCA
* * * *
4589 TCCTACGCATTTTGAGGCGTAGAATCAATTCCGCACGGTCCCGACTCAGAAACAGTCGCTGAACG
259 TCCTACG-ATTTGGAAGCGTAGAATCAATTCAGCACGGTCCCAACTCAG-AACAG-CGCTGAACG
* * * * *
4654 AAACGCTCCCGAAACAGTCAGAAACTGGTCAAAAACCAGCTTTTCAGACCGATTTTTTACTCTTT
321 AAAC-CTCCAGAAACAGTAAAAAACTAGTCAAAAACCAGCTTTTCAGACCGATTTTTGACTCTTT
* * *
4719 CTCTAGAGCGTTTTCAGCGGAAAGCTCGAAGCGAGGGACTCGCGGAGCTTTACCGAATGGAAAAT
385 CTCTAGAGCGTATTCAGCGGAAAGCTCGAAACAAGGGACTCGCGGAGCTTTACCGAATGGAAAAT
* *
4784 CGCACTCAGCGGGTCATTTCCAAGCGACCTTACTTGGTTTCTGCCCGATCAGCGAATTTTCGATT
450 CGCACTCAGCGGGTCAATTCCAAGCGACCTTACTTGGTTTCGGCCCGATCAGCGAATTTTCGATT
* * * *
4849 TTGATGCTAAAAATTTGGTCCCTGTCGATTTTTTTCGATTTGGGACTGAGAAAAAAATTTCAAGA
515 TTGACGCTAAAAATTTGGTCCCTGTAGATTTTTCTCCATTTGGGACTGAGAAAAAAATTTCAAGA
* * *
4914 TTTCAGTCGCATCCTACGTAGTTGAAGGCGTAGAATCGATTCCGCACGGTCTCGACTCTCGGCGA
580 TTTCAGTCGCATCCCACGTAGTTGAAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGA
*
4979 GACTTCCTGAGCCTAGAAACAGAATA
645 GACTTCCTGAGCCGAGAAACAG-ATA
* * * * *
5005 AAACTGGTCAAACACGAGCTTTTCAGACCAATTTTTTACTCTTTCTCTGGAGCGTGTTT-AGCGA
1 AAACTGGTCAAAAACGAGCATTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGT-TTTCAGCGG
* * * * * *
5069 ATAGCTCGAAGCGAGGGACTCGCGGAGCTTTTTCGACTGGAGAATCGCACTCAGCGGGTCATTTC
65 ATAGCTCGAAGCGAGGGACTCGCGGACCTTTTCCGACTCGAAAATCGCACTCAGCGGGTCAATAC
* * * *
5134 CAAGCG-GCATAAC-TTGCTTCCGGCTCGATCGGCGAACTTTCGATTTTGACGCTTAAAATTTAG
130 CAAGCGAGC-TAACTTTG-TTCCGACCCGATCGGCGAACTATCGATTTTGACGCTAAAAATTTAG
* * *
5197 T-TAATGTAA-CGACT-GTTC-ATTTTACTCGATTTTGGACTGAGAAAAATAAT-TCGAGATTTC
193 TCCAA-GTAATC--CTAG-TCGATTTTACTCGATTTGGGACTGAGAAAAA-AATGTCGAGA-TAC
* * * * *
5257 AGTCGCATTCTACG-TTGCTGGAAGCGTAGAATCGATTCAGCACGGTCCTAACTCTTG-GCGAG-
252 AGTCGCATCCTACGATT--TGGAAGCGTAGAATCAATTCAGCACGGTCCCAACTC-AGAAC-AGC
** * * *
5319 GCT-TCCTG-AA-C-CGAGAAACAGTAAAAAACTAGTCAAAAACGAGCTTTTCTGACC-ACTTTT
313 GCTGAAC-GAAACCTCCAGAAACAGTAAAAAACTAGTCAAAAACCAGCTTTTCAGACCGA-TTTT
* ** *
5379 TGACTCTTTCTCTGGAGCGTATTCAGCGGCTAGCTCGAAACAAGGGACTTGCGGAGCTATT-CCG
376 TGACTCTTTCTCTAGAGCGTATTCAGCGGAAAGCTCGAAACAAGGGACTCGCGGAGCT-TTACCG
* * *
5443 ACTGGAAAATCGCACTCGGCGGGTCAATTCCAAGCGAGCTTACTTGGTTTCGGCCCGATCAGCGA
440 AATGGAAAATCGCACTCAGCGGGTCAATTCCAAGCGACCTTACTTGGTTTCGGCCCGATCAGCGA
5508 ACTTTT-GATTTTGACGCTAAAAAATTTAGTCCATGTAACCCCTGTAGATTTTTCTCCATTTGGG
505 A-TTTTCGATTTTGACGCT-AAAAATTT-G-----GT---CCCTGTAGATTTTTCTCCATTTGGG
* * * *
5572 ACTGAGAAAAAAATTTCGAG-TTATCGGTCGCTTCCCACGTAGTTGGAGGCGTAGAATCAATTCC
559 ACTGAGAAAAAAATTTCAAGATT-TCAGTCGCATCCCACGTAGTTGAAGGCGTAGAATCAATTCC
*
5636 GCACGGTCCCGACTCTCGGCGAGGC-TCTCTGAGCCGAGAAACAG-TCA
623 GCACGGTCCCGACTCTCGGCGAGACTTC-CTGAGCCGAGAAACAGAT-A
* * *
5683 GAAACTGGTCAAAAACGAGCATTTCCGACCACTTTTTGACTCTTTTTCTTGAGCGTTTTCAGCGG
1 -AAACTGGTCAAAAACGAGCATTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCGG
* *
5748 ATAGCTCGAACCGAGGGAGTCGCGGACCTTTTCCGACTCGAAAATCGCACTCAGCGGGTCAAT
65 ATAGCTCGAAGCGAGGGACTCGCGGACCTTTTCCGACTCGAAAATCGCACTCAGCGGGTCAAT
5811 TCAAAGTTAC
Statistics
Matches: 684, Mismatches: 88, Indels: 63
0.82 0.11 0.08
Matches are distributed among these distances:
668 1 0.00
669 165 0.24
670 15 0.02
671 1 0.00
672 3 0.00
673 14 0.02
674 188 0.27
675 62 0.09
676 3 0.00
677 1 0.00
678 8 0.01
679 223 0.33
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (669 bp):
AAACTGGTCAAAAACGAGCATTTCAGACCACTTTTTGACTCTTTCTCTGGAGCGTTTTCAGCGGA
TAGCTCGAAGCGAGGGACTCGCGGACCTTTTCCGACTCGAAAATCGCACTCAGCGGGTCAATACC
AAGCGAGCTAACTTTGTTCCGACCCGATCGGCGAACTATCGATTTTGACGCTAAAAATTTAGTCC
AAGTAATCCTAGTCGATTTTACTCGATTTGGGACTGAGAAAAAAATGTCGAGATACAGTCGCATC
CTACGATTTGGAAGCGTAGAATCAATTCAGCACGGTCCCAACTCAGAACAGCGCTGAACGAAACC
TCCAGAAACAGTAAAAAACTAGTCAAAAACCAGCTTTTCAGACCGATTTTTGACTCTTTCTCTAG
AGCGTATTCAGCGGAAAGCTCGAAACAAGGGACTCGCGGAGCTTTACCGAATGGAAAATCGCACT
CAGCGGGTCAATTCCAAGCGACCTTACTTGGTTTCGGCCCGATCAGCGAATTTTCGATTTTGACG
CTAAAAATTTGGTCCCTGTAGATTTTTCTCCATTTGGGACTGAGAAAAAAATTTCAAGATTTCAG
TCGCATCCCACGTAGTTGAAGGCGTAGAATCAATTCCGCACGGTCCCGACTCTCGGCGAGACTTC
CTGAGCCGAGAAACAGATA
Done.