Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011514.1 Kokia drynarioides strain JFW-HI SEQ_126499, 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: 3496
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:473 original size:215 final size:216
Alignment explanation
Indices: 1--1261 Score: 1517
Period size: 216 Copynumber: 5.8 Consensus size: 216
* * * * ** **
1 CTTTTATAACTTCAGTTCCTGAGGGTATTTAATACGATCCATTCCTTCGACTTATTTTTCCAACA
1 CTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTTTGAACA
* * * * * * * * *
66 TTTCATTCTTGGGAAATCGCATCACTTGGTTTAAAAAGTTTGGCATGTTGTAAAAAAAACTTTTG
66 TTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT--AAAAAGCTTTTG
* *
131 GTCTTTGATTTAAAAACTTTTTTACGTGAGAATTGGTTCTCTCTTGGTTCTTGGAAAAACTTTCG
129 GTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAAAACTTTCG
196 AACTTGTCAAACATTTA-TGAGTT
194 AACTTGTCAAACATTTACT-AGTT
* *
219 CTTTTATAACATT-GGTTTCTGAGAGTATTCAATACGATCCATTCCTTCGACCAATTTTTTGAAC
1 CTTTTATAAC-TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTTTGAAC
*
283 ATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAA-ACGTTTGTCATTTTGTAAAAAGCTTTTG
65 ATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAAAAAGCTTTTG
* * * ** *
347 GTCTTTGAGTTAAAAAC-TTTTTATGTGAGAATTGTTTCTCTCTTGGTTATTGGATGAAGTTTCG
129 GTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAAAACTTTCG
* **
411 ATCTTGTCAAACATTTACTAAAT
194 AACTTGTCAAACATTTACTAGTT
* * * *
434 CTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGACCAATTTTTCT-AGC
1 CTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTT-TGAAC
* * *
498 ATTCCAT-CATCGGGATATCGCATCATTTGGTGTAAATATTTTGTCATTTTGTAAACAA-CTTTT
65 ATTCCATGC-TCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGCTTTT
* ** *
561 GGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGACAAACTTTC
128 GGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAAAACTTTC
** * *
626 GAACACGTCAAACATTTTCGAGTT
193 GAACTTGTCAAACATTTACTAGTT
* *
650 CTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTC-AGCCAATTTTTTGAAC
1 CTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGA-CCAATTTTTTGAAC
**
714 ATTCCATGCTTAGGAAATCGCATCATTTGGTCTAAA-ACGTTTGTCATTTTGTAAAAAGCTTTTG
65 ATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAAAAAGCTTTTG
* * ** * *
778 GTCTTTGAGTTAAAAAC-TTTTTACGTGAGAATTGTTTCTCTCTTGGTTATTGGATGAAGTTCCG
129 GTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAAAACTTTCG
**
842 AACTTGTCAAACATTTACTAAAT
194 AACTTGTCAAACATTTACTAGTT
* * * *
865 CTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCTACCAATTTTTCT-AAC
1 CTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTT-TGAAC
* * *
929 ATTCCAT-CATCGGGATATCGCATCATTTGGTGTAAATATTTTGTCATTTTGTAAACAA-CTTTT
65 ATTCCATGC-TCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGCTTTT
* **
992 GGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGAAAAACTTTC
128 GGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAAAACTTTC
** * *
1057 GAACACGTCAAACATTTTCGAGTT
193 GAACTTGTCAAACATTTACTAGTT
* *
1081 CTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTC-AGCCAATTTTTTGAAC
1 CTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGA-CCAATTTTTTGAAC
* * * * * * *
1145 ATTCCATGCTCGGGAAATCGCTTCATTTGATTTAAATAGTTTATCATTTTGTGTACAAG-TTTTA
65 ATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT-AAAAAGCTTTTG
* * * *
1209 GTCTTTGAATTAAATACTTATTTACGTGAGAATTATTTCCCTCTTGGTTCTTG
129 GTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTG
1262 TACAACTTGT
Statistics
Matches: 895, Mismatches: 123, Indels: 52
0.84 0.11 0.05
Matches are distributed among these distances:
214 4 0.00
215 367 0.41
216 421 0.47
217 4 0.00
218 97 0.11
219 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (216 bp):
CTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTTTGAACA
TTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAGCTTTTGGT
CTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAAAACTTTCGAA
CTTGTCAAACATTTACTAGTT
Found at i:808 original size:431 final size:431
Alignment explanation
Indices: 1--1257 Score: 1941
Period size: 431 Copynumber: 2.9 Consensus size: 431
* ** * * * * ** *
1 CTTTTATAACTTCAGTTCCTGAGGGTATTTAATACGATCCATTCCTTCGACTTATTTTTCCAACA
1 CTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGACCAATTTTTCTAACA
* * * * * * * * * *
66 TTTCATTC-TTGGGAAATCGCATCACTTGGTTTAAAAAGTTTGGCATGTTGTAAAAAAAACTTTT
66 TTCCA-TCATCGGGATATCGCATCATTTGGTGTAAATATTTTGTCATTTTGT--AAACAACTTTT
* * * **
130 GGTCTTTGATTTAAAAACTTTTTTACGTGAGAATTGGTTCTCTCTTGGTTCTTGGAAAAACTTTC
128 GGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGAAAAACTTTC
** * * * *
195 GAACTTGTCAAACATTTAT-GAGTTCTTTTATAACATT-GGTTTCTGAGAGTATTCAATACGATC
193 GAACACGTCAAACATTT-TCGAGTTCTTTTATAAC-TTCGATTCCTGAGAGTATTAAAGACGATC
258 CATTCCTTC-GACCAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAACG
256 CATTCCTTCAG-CCAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAACG
*
322 TTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAGTTAAAAACTTTTTATGTGAGAATTGTTTCTC
320 TTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAGTTAAAAACTTTTTACGTGAGAATTGTTTCTC
* *
387 TCTTGGTTATTGGATGAAGTTTCGATCTTGTCAAACATTTACTAAAT
385 TCTTGGTTATTGGATGAAGTTCCGAACTTGTCAAACATTTACTAAAT
*
434 CTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGACCAATTTTTCTAGCA
1 CTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGACCAATTTTTCTAACA
499 TTCCATCATCGGGATATCGCATCATTTGGTGTAAATATTTTGTCATTTTGTAAACAACTTTTGGT
66 TTCCATCATCGGGATATCGCATCATTTGGTGTAAATATTTTGTCATTTTGTAAACAACTTTTGGT
*
564 CTTTGAATTAAAAACTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGACAAACTTTCGAA
131 CTTTGAATTAAAAACTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGAAAAACTTTCGAA
629 CACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTC
196 CACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTC
*
694 CTTCAGCCAATTTTTTGAACATTCCATGCTTAGGAAATCGCATCATTTGGTCTAAAACGTTTGTC
261 CTTCAGCCAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAACGTTTGTC
759 ATTTTGTAAAAAGCTTTTGGTCTTTGAGTTAAAAACTTTTTACGTGAGAATTGTTTCTCTCTTGG
326 ATTTTGTAAAAAGCTTTTGGTCTTTGAGTTAAAAACTTTTTACGTGAGAATTGTTTCTCTCTTGG
824 TTATTGGATGAAGTTCCGAACTTGTCAAACATTTACTAAAT
391 TTATTGGATGAAGTTCCGAACTTGTCAAACATTTACTAAAT
*
865 CTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCTACCAATTTTTCTAACA
1 CTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGACCAATTTTTCTAACA
930 TTCCATCATCGGGATATCGCATCATTTGGTGTAAATATTTTGTCATTTTGTAAACAACTTTTGGT
66 TTCCATCATCGGGATATCGCATCATTTGGTGTAAATATTTTGTCATTTTGTAAACAACTTTTGGT
995 CTTTGAATTAAAAACTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGAAAAACTTTCGAA
131 CTTTGAATTAAAAACTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGAAAAACTTTCGAA
1060 CACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTC
196 CACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTC
* * * * *
1125 CTTCAGCCAATTTTTTGAACATTCCATGCTCGGGAAATCGCTTCATTTGATTTAAATA-GTTTAT
261 CTTCAGCCAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAA-ACGTTTGT
* * * * * * *
1189 CATTTTGTGTACAAG-TTTTAGTCTTTGAATTAAATACTTATTTACGTGAGAATTATTTCCCTCT
325 CATTTTGT-AAAAAGCTTTTGGTCTTTGAGTTAAAAACTT-TTTACGTGAGAATTGTTTCTCTCT
1253 TGGTT
388 TGGTT
1258 CTTGTACAAC
Statistics
Matches: 764, Mismatches: 53, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
430 3 0.00
431 633 0.83
432 35 0.05
433 93 0.12
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (431 bp):
CTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGACCAATTTTTCTAACA
TTCCATCATCGGGATATCGCATCATTTGGTGTAAATATTTTGTCATTTTGTAAACAACTTTTGGT
CTTTGAATTAAAAACTTTTTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGAAAAACTTTCGAA
CACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTC
CTTCAGCCAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAACGTTTGTC
ATTTTGTAAAAAGCTTTTGGTCTTTGAGTTAAAAACTTTTTACGTGAGAATTGTTTCTCTCTTGG
TTATTGGATGAAGTTCCGAACTTGTCAAACATTTACTAAAT
Found at i:1368 original size:135 final size:135
Alignment explanation
Indices: 1151--1396 Score: 318
Period size: 135 Copynumber: 1.8 Consensus size: 135
1141 GAACATTCCA
* * * *
1151 TGCTCGGGAAATCGCTTCATTTGATTTAAATAGTTTATCATTTTGTGTACAAGTTTTAGTCTTTG
1 TGCTCGGGAAATCGCATCATTTGATCTAAATAGTTTATCATTTTGTGAAAAAGTTTTAGTCTTTG
* *
1216 AATTAAATACTTATTTACGTGAGAATT-ATTTCCCTCTTGGTTCTTGTACAACTTGTCAAACATT
66 AATTAAAAACTTATTTACGTGACAATTGA-TTCCCTCTTGGTTCTTGTACAACTTGTCAAACATT
1280 TACTAG
130 TACTAG
* * * * *
1286 TGCTTGGGAAATTGCATCATTTGGTCTAAA-ACGTTTGTCATTTTGT-AAAAAGCTTTTGGTCTT
1 TGCTCGGGAAATCGCATCATTTGATCTAAATA-GTTTATCATTTTGTGAAAAAG-TTTTAGTCTT
* * *
1349 TGATTTAAAAACTTTTTTACGTGACAATTGATTCTCTCTTGGTTCTTG
64 TGAATTAAAAACTTATTTACGTGACAATTGATTCCCTCTTGGTTCTTG
1397 GAAAAACTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
134 5 0.05
135 88 0.94
136 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.44
Consensus pattern (135 bp):
TGCTCGGGAAATCGCATCATTTGATCTAAATAGTTTATCATTTTGTGAAAAAGTTTTAGTCTTTG
AATTAAAAACTTATTTACGTGACAATTGATTCCCTCTTGGTTCTTGTACAACTTGTCAAACATTT
ACTAG
Found at i:1591 original size:351 final size:351
Alignment explanation
Indices: 948--1608 Score: 913
Period size: 351 Copynumber: 1.9 Consensus size: 351
938 TCGGGATATC
* *
948 GCATCATTTGGTGTAAATATTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTT
1 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTT
* *
1013 TTTACGAGAGAATTGTTTCTCAATTGGTTCTTGGAAAAACTTTCGAACACGTCAAACATTTTCGA
66 TTTACGAGACAATTGATTCTCAATTGGTTCTTGGAAAAACTTTCGAACACGTCAAACATTTTCGA
* *
1078 GTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTCAGCCAATTTTTTGA
131 GTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCATTCAGACAATTTTTTGA
* * * * *
1143 ACATTCCATGCTCGGGAAATCGCTTCATTTGATTTAAATAGTTTATCATTTTGTGTACAAGTTTT
196 ACATTCCATCCTCGGGAAATCGCATCATTTGATCTAAATAGTTTATCATTTTGTGAAAAAGTTTT
*
1208 AGTCTTTGAATTAAATACTTATTTACGTGAGAATTATTTCCCTCTTGGTTCTTGTACAACTTGTC
261 AGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCCCTCTTGGTTCTTGTACAACTTGTC
1273 AAACATTTACTAGTGCTTGGGAAATT
326 AAACATTTACTAGTGCTTGGGAAATT
*
1299 GCATCATTTGGTCTAAA-ACGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGATTTAAAAACT
1 GCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGAATTAAAAACT
* ** **
1362 TTTTTACGTGACAATTGATTCTCTCTTGGTTCTTGGAAAAACTTTCGAACTTGTCAAACATTTAT
64 TTTTTACGAGACAATTGATTCTCAATTGGTTCTTGGAAAAACTTTCGAACACGTCAAACATTT-T
* * * *
1427 -GAGTTCTTTTATAACATT-GGTTTCTGAGAGTATTCAATACGATCCATTCATTC-GAACAATTT
128 CGAGTTCTTTTATAAC-TTCGATTCCTGAGAGTATTAAAGACGATCCATTCATTCAG-ACAATTT
* * * * * *
1489 TTTGAACATTCCATCCTTGGGAAATCGYATCATTTGGTCTAAA-ACRTTTGTCATTTTRT-AAAA
191 TTTGAACATTCCATCCTCGGGAAATCGCATCATTTGATCTAAATA-GTTTATCATTTTGTGAAAA
* * * * *
1552 AGCTTTTGGTCTTTGARTTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTT
255 AG-TTTTAGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCCCTCTTGGTT
1609 ATTGGATGAA
Statistics
Matches: 270, Mismatches: 33, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
350 9 0.03
351 258 0.96
352 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (351 bp):
GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTT
TTTACGAGACAATTGATTCTCAATTGGTTCTTGGAAAAACTTTCGAACACGTCAAACATTTTCGA
GTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCATTCAGACAATTTTTTGA
ACATTCCATCCTCGGGAAATCGCATCATTTGATCTAAATAGTTTATCATTTTGTGAAAAAGTTTT
AGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCCCTCTTGGTTCTTGTACAACTTGTC
AAACATTTACTAGTGCTTGGGAAATT
Found at i:1687 original size:216 final size:214
Alignment explanation
Indices: 1288--3494 Score: 2404
Period size: 216 Copynumber: 10.4 Consensus size: 214
1278 TTTACTAGTG
* *
1288 CTTGGGAAATTGCATCATTTGGTCTAAAACGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGA
1 CTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAATAA-CTTTTGGTCTTTGA
* * ** * *
1352 TTTAAAAACTTTTTTACGTGACAATTGATTCTCTCTTGGTTCTTGGAAAAACTTTCGAACTTGTC
65 ATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGG--AAACTTCCGAACTTGTC
* * *
1417 AAACATTTA-TGAGTTCTTTTATAACATT-GGTTTCTGAGAGTATTCAATACGATCCATTCATTC
128 AAACATTTACT-AGTTCTTTTATAAC-TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTC
*
1480 GAACAATTTTTTGAACATTCCATC
191 GACCAATTTTTTGAACATTCCATC
* ** *
1504 CTTGGGAAATCGYATCATTTGGTCTAAAACRTTTGTCATTTTRTAAA-AAGCTTTTGGTCTTTGA
1 CTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAATAA-CTTTTGGTCTTTGA
* * *
1568 RTTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTATTGGATGAAGTTCCGAACTTGTC
65 ATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGGA--AACTTCCGAACTTGTC
** * * *
1633 AAACATTTACTAAATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGA
128 AAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGA
1698 CCAATTTTTCT-AACATTCCATC
193 CCAATTTTT-TGAACATTCCATC
* * * * * * *
1720 ATCGGGATATCGCATCATTTGGTATAAATATTTTGTCATTTTGTAAATAACTTTTGGCCTTTGAA
1 CTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAA
* * * * * * * *
1785 ATAAAAGCTTTTTTACGTTAGAATTCATTCTCTCTTGG--A---CAAACTTCTGAACTAGTTAAA
66 TTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGGAAACTTCCGAACTTGTCAAA
* * * *
1845 CAATTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTTGACCA
131 CATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCA
*
1910 A-TTTTTGAAGATTCCATGAC
196 ATTTTTTGAACATTCCAT--C
* *
1930 C--GGGAAATCGCATCATTTGGTCAAAAAAGTTTGTCATTTTGTAAATAACTTTTGTTCTTTGAA
1 CTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAA
* * * * * *
1993 TTAAAAGCTTTTTTACGTTAGAATTCTTTCTCTCTTGG--A---CAAACTTCTGAACTAGTTAAA
66 TTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGGAAACTTCCGAACTTGTCAAA
* * * *
2053 CAATTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTTGACCA
131 CATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCA
*
2118 ATTTTTTGAAGATTCCATGAC
196 ATTTTTTGAACATTCCAT--C
* * *** *
2139 C--GAGTAATCATGTCAATTGGTC-AAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGA
1 CTTGGGAAATCGCATCATTTGGTCTAAAA-AGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGA
* * * *
2201 ATTAAAAAC-TTTTTACTTTAGAATTCTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTC
65 ATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGGA--AACTTCCGAACTTGTC
* * * * *
2265 AAACATTTACGAGTTCTTTTATAACTCCAGTTCCTGAGAGTATTTAATACGATCCATTCCTTCGA
128 AAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGA
** * * *
2330 CTTATTTTTCGAACATTTCATT
193 CCAATTTTTTGAACATTCCATC
* * * *
2352 CTTGGGAAATCGCATCACTTGGTCTAAAAAGTTTGGCATGTTGTAAAAAAACTTTTGGTCTTTGA
1 CTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGT-AAATAACTTTTGGTCTTTGA
* ** * **
2417 TTTAAAAACTTTTTTACGTGAGAATTGGTTCTCTCTTGGTTCTTGGAAAAACTTTTGAACTTGTC
65 ATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGG--AAACTTCCGAACTTGTC
* *
2482 AAACATTTA-TGAGTTCTTTTATAACATT-GGTTTCTGAGAGTATTCAATACGATCCATTCCTTC
128 AAACATTTACT-AGTTCTTTTATAAC-TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTC
*
2545 GACCAATTTTTTGAACATTCCATG
191 GACCAATTTTTTGAACATTCCATC
*
2569 CTTGGGAAATCGCATCATTTGGTCTAAAACGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGA
1 CTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAATAA-CTTTTGGTCTTTGA
* ** * *
2633 TTTAAAAACTTTTTTACGTGAGAATTGATTCTCTCTTGGTTCTTGGAAAAACTTTCGAACTTGTC
65 ATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGG--AAACTTCCGAACTTGTC
* * *
2698 AAACATTTA-TGAGTTCTTTTATAACATT-GGTTTCTGAGAGTATTCAATACGATCCATTCATTC
128 AAACATTTACT-AGTTCTTTTATAAC-TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTC
* *
2761 GAACAATGTTTTGAACATTCCATC
191 GACCAATTTTTTGAACATTCCATC
* *
2785 CTTGGGAAATCGTATCATTTGGTCTAAAACA-TTTGTCATTTTATAAA-AAGCTTTTGGTCTTTG
1 CTTGGGAAATCGCATCATTTGGTCTAAAA-AGTTTGTCATTTTGTAAATAA-CTTTTGGTCTTTG
* * *
2848 AGTTAAAAAC-TTTTTACGTGAGAATTGTTTCTCTCTTGGTTATTGGATGAAGTTCCGAACTTGT
64 AATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGGA--AACTTCCGAACTTGT
** * * *
2912 CAAACATTTACTAAATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCG
127 CAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCG
2977 ACCAATTTTTCT-AACATTCCATC
192 ACCAATTTTT-TGAACATTCCATC
* * * * * *
3000 ATCT-GGATATCGCATCATTTGGTATAAATATTTTGTCATTTTGTAAATAACTTTTGGCCTTTGA
1 CT-TGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGA
* ** * * * * * *
3064 AATAAATGCTTTTTTACGTTAGAATTCATTCTCTCTTGG--A---CAAACTTCTGAACTAGTTAA
65 ATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGGAAACTTCCGAACTTGTCAA
* * * *
3124 ACAATTACAAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTTGACC
130 ACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACC
*
3189 AA-TTTTTGAAGATTCCATGAC
195 AATTTTTTGAACATTCCAT--C
*
3210 C--GGGAAATCGCATCATTTGGTCAAAAAAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAA
1 CTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAA
* * * * * *
3273 TTAAAAGCTTTTTTACGTTAGAATTCTTTCTCTCTTGG--A---CAAACTTCTGAACTAGTTAAA
66 TTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGGAAACTTCCGAACTTGTCAAA
* * * *
3333 CAATTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTTGACCA
131 CATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCA
*
3398 ATTTTTTGAAGATTCCATGAC
196 ATTTTTTGAACATTCCAT--C
* * *** *
3419 C--GAGTAATCATGTCAATTGGTC-AAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGA
1 CTTGGGAAATCGCATCATTTGGTCTAAAA-AGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGA
3481 ATTAAAAACTTTTT
65 ATTAAAAACTTTTT
3495 AC
Statistics
Matches: 1759, Mismatches: 188, Indels: 95
0.86 0.09 0.05
Matches are distributed among these distances:
207 2 0.00
208 418 0.24
209 304 0.17
210 2 0.00
211 2 0.00
213 3 0.00
214 6 0.00
215 291 0.17
216 564 0.32
217 165 0.09
218 1 0.00
219 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (214 bp):
CTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAA
TTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTATTGGAAACTTCCGAACTTGTCAAA
CATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCA
ATTTTTTGAACATTCCATC
Found at i:3475 original size:848 final size:829
Alignment explanation
Indices: 1299--3494 Score: 2406
Period size: 848 Copynumber: 2.6 Consensus size: 829
1289 TTGGGAAATT
* *
1299 GCATCATTTGGTCTAAA-ACGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGATTTAAAAACT
1 GCATCATTTGGTATAAATA-GTTTGTCATTTTGTAAATAA-CTTTTGGTCTTTGAATTAAAAACT
* * * * *
1362 TTTTTACGTGACAATTGATTCTCTCTTGGTTCTTGGAAAAACTTTCGAACTTGTCAAACATTTAT
64 TTTTTACGTTAGAATTCA-T-TCTC-----TCTTGGACAAACTTTCGAACTTGTCAAACATTTAC
* *
1427 GAGTTCTTTTATAACATT-GGTT-TCTGAGAGTATTCAATACGATCCATTCATTCGAACAATTTT
122 GAGTTCTTTTATAAC-TTCGGTTCT-TGAGAGTATTCAATACGATCCATTCCTTCGACCAA-TTT
* ** *
1490 TTGAACATTCCATCCTTGGGAAATCGYATCATTTGGTCTAAAACRTTTGTCATTTTRTAAAAAGC
184 TTGAACATTCCATCC--GGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAAAA-C
* * *
1555 TTTTGGTCTTTGARTTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTATTGGATGAAG
246 TTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGG--A----A-AAAC
* * ** * * *
1620 TTCCGAACTTGTCAAACATTTACTAAATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGA
304 TTCTGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGA
* * * *
1685 TCCATTTCTTCGACCAATTTTTCT-AACATTCCATCATCGGGATATCGCATCATTTGGT-ATAAA
369 TCCATTCCTTCGACCAATTTTT-TGAACATTCCATGA-CCGGAAATCGCATCATTTGGTCA-AAA
* * * * *
1748 TATTTTGTCATTTTGTAAATAACTTTTGGCCTTTGAAATAAAAGCTTTTTTACGTTAGAATTCAT
431 TAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCAT
* *
1813 TCTCTCTTGGACAAACTTCTGAACTAGTTAAACAATTACGAGTTCTTTTATAACTTCGGTTCTTG
496 TCTCTCTTGGAAAAACTTCTGAACTAGTCAAACAATTACGAGTTCTTTTATAACTTCGGTTCTTG
* * * *
1878 AGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTGAAGATTCCATGACCGGGAAATCGCAT
561 AGAGTATTCAAGACGATCCATTCATTCGAACAATTTTTGAACATTCCAT-ACCGGGAAATCGCAT
* * *
1943 CATTTGGTCAAAAAAGTTTGTCATTTTGTAAATAACTTTTGTTCTTTGAATTAAAAGCTTTTTTA
625 CATTTGGTCAAAAAAGTTTGTCATTTTATAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTA
* * * **
2008 CGTTAGAATTCTTTCTCTCTTGGACAAACTTCTGAACTAGTTAAACAATTACGAGTTCTTTTATA
690 CGTGAGAATTCTTTCTCTCTTGGACAAACTTCCGAACTAGTCAAACAATTACGAAATCTTTTATA
* * * * *
2073 ACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTTGAAGATTCCATGA
755 ACTTCGGTTCCTGAGAGTAGTCAAGACGATCCATTCCTTCGACCAATTTTTTGAACATTCCATCA
2138 CCGAGTAATC
820 CCGAGTAATC
*** *
2148 ATGTCAATTGGTCA-AAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAAC-T
1 GCATCATTTGGT-ATAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTT
* * *
2211 TTTTACTTTAGAATTCTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCAAACATTTACG
65 TTTTACGTTAGAATTCATTCTCTCTTGG-AC----A--AACTTTCGAACTTGTCAAACATTTACG
* * * * **
2276 AGTTCTTTTATAACTCCAGTTCCTGAGAGTATTTAATACGATCCATTCCTTCGACTTATTTTTCG
123 AGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAATACGATCCATTCCTTCGACCAATTTTT-G
* * * * *
2341 AACATTTCATTCTTGGGAAATCGCATCACTTGGTCTAAAAAGTTTGGCATGTTGTAAAAAAACTT
187 AACATTCCA-TC-CGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGT--AAAAACTT
*
2406 TTGGTCTTTGATTTAAAAACTTTTTTACGTGAGAATTGGTTCTCTCTTGGTTCTTGGAAAAACTT
248 TTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATT-GTT-TCTC-----TCTTGGAAAAACTT
* * *
2471 TTGAACTTGTCAAACATTTATGAGTTCTTTTATAACATT-GGTT-TCTGAGAGTATTCAATACGA
306 CTGAACTTGTCAAACATTTACGAGTTCTTTTATAAC-TTCGGTTCT-TGAGAGTATTCAAGACGA
*
2534 TCCATTCCTTCGACCAATTTTTTGAACATTCCATG-CTTGGGAAATCGCATCATTTGGTCTAAAA
369 TCCATTCCTTCGACCAATTTTTTGAACATTCCATGAC--CGGAAATCGCATCATTTGGTC-AAAA
* * *
2598 -CGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGATTTAAAAACTTTTTTACGTGAGAATTGA
431 TAGTTTGTCATTTTGTAAATAA-CTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCA
* * *
2661 TTCTCTCTTGGTTCTTGGAAAAACTT-TCGAACTTGTCAAACATTTATGAGTTCTTTTATAACAT
495 -T-TCTC-----TCTTGGAAAAACTTCT-GAACTAGTCAAACAATTACGAGTTCTTTTATAAC-T
*
2725 T-GGTT-TCTGAGAGTATTCAATACGATCCATTCATTCGAACAATGTTTTGAACATTCCAT-CCT
551 TCGGTTCT-TGAGAGTATTCAAGACGATCCATTCATTCGAACAAT-TTTTGAACATTCCATACC-
* * *
2787 TGGGAAATCGTATCATTTGGTCTAAAACA-TTTGTCATTTTATAAA-AAGCTTTTGGTCTTTGAG
613 -GGGAAATCGCATCATTTGGTC-AAAAAAGTTTGTCATTTTATAAATAA-CTTTTGGTCTTTGAA
* * * *
2850 TTAAAAAC-TTTTTACGTGAGAATTGTTTCTCTCTTGGTTATTGGATGAAGTTCCGAACTTGTCA
675 TTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGG--A---CA--AACTTCCGAACTAGTCA
* * * *
2914 AACATTTACTAAATCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGAC
733 AACAATTACGAAATCTTTTATAACTTCGGTTCCTGAGAGTAGTCAAGACGATCCATTCCTTCGAC
*
2979 CAATTTTTCT-AACATTCCATCATCTG-G-ATATC
798 CAATTTTT-TGAACATTCCATCA-CCGAGTA-ATC
* * * **
3011 GCATCATTTGGTATAAATATTTTGTCATTTTGTAAATAACTTTTGGCCTTTGAAATAAATGCTTT
1 GCATCATTTGGTATAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTT
* * * *
3076 TTTACGTTAGAATTCATTCTCTCTTGGACAAAC-TTCTGAACTAGTTAAACAATTACAAGTTCTT
66 TTTACGTTAGAATTCATTCTCTCTTGGACAAACTTTC-GAACTTGTCAAACATTTACGAGTTCTT
* * *
3140 TTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTGAAGATTCC
130 TTATAACTTCGGTTCTTGAGAGTATTCAATACGATCCATTCCTTCGACCAATTTTTGAACATTCC
*
3205 ATGACCGGGAAATCGCATCATTTGGTCAAAAAAGTTTGTCATTTTGTAAATAACTTTTGGTCTTT
195 AT--CCGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAA-AACTTTTGGTCTTT
* * * * * *
3270 GAATTAAAAGCTTTTTTACGTTAGAATTCTTTCTCTCTTGGACAAACTTCTGAACTAGTTAAACA
257 GAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGAAAAACTTCTGAACTTGTCAAACA
* *
3335 ATTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTTGACCAAT
322 TTTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTCGACCAAT
* * *** *
3400 TTTTTGAAGATTCCATGACCGAGTAATCATGTCAATTGGTCAAAATAGTTTGTCATTTTGTAAAT
387 TTTTTGAACATTCCATGACCG-GAAATCGCATCATTTGGTCAAAATAGTTTGTCATTTTGTAAAT
3465 AACTTTTGGTCTTTGAATTAAAAACTTTTT
451 AACTTTTGGTCTTTGAATTAAAAACTTTTT
3495 AC
Statistics
Matches: 1136, Mismatches: 142, Indels: 139
0.80 0.10 0.10
Matches are distributed among these distances:
841 6 0.01
846 5 0.00
847 15 0.01
848 288 0.25
849 250 0.22
850 18 0.02
851 9 0.01
853 4 0.00
854 6 0.01
855 44 0.04
856 162 0.14
857 146 0.13
858 6 0.01
859 1 0.00
861 1 0.00
862 2 0.00
863 143 0.13
864 30 0.03
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (829 bp):
GCATCATTTGGTATAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTT
TTTACGTTAGAATTCATTCTCTCTTGGACAAACTTTCGAACTTGTCAAACATTTACGAGTTCTTT
TATAACTTCGGTTCTTGAGAGTATTCAATACGATCCATTCCTTCGACCAATTTTTGAACATTCCA
TCCGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAAAACTTTTGGTCTTTGAAT
TAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGAAAAACTTCTGAACTTGTCAAACATTTA
CGAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTT
TGAACATTCCATGACCGGAAATCGCATCATTTGGTCAAAATAGTTTGTCATTTTGTAAATAACTT
TTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCATTCTCTCTTGGAAAAACTTCTGAACT
AGTCAAACAATTACGAGTTCTTTTATAACTTCGGTTCTTGAGAGTATTCAAGACGATCCATTCAT
TCGAACAATTTTTGAACATTCCATACCGGGAAATCGCATCATTTGGTCAAAAAAGTTTGTCATTT
TATAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCTTGGACA
AACTTCCGAACTAGTCAAACAATTACGAAATCTTTTATAACTTCGGTTCCTGAGAGTAGTCAAGA
CGATCCATTCCTTCGACCAATTTTTTGAACATTCCATCACCGAGTAATC
Done.