Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013749.1 Corchorus capsularis cultivar CVL-1 contig13770, 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: 63850
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:283 original size:33 final size:33
Alignment explanation
Indices: 211--284 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
201 TTCTAGCTCA
* *
211 GAAACTTTATGAACTTTAGGTTTCGACAACTCT
1 GAAACTTTATGAAATTCAGGTTTCGACAACTCT
* *
244 GGAACTTTA-GACAATTCAGGTTTTGACAAAC-CT
1 GAAACTTTATGA-AATTCAGGTTTCGAC-AACTCT
277 GAAACTTT
1 GAAACTTT
285 TTGTTCTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
32 2 0.06
33 29 0.85
34 3 0.09
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (33 bp):
GAAACTTTATGAAATTCAGGTTTCGACAACTCT
Found at i:386 original size:213 final size:212
Alignment explanation
Indices: 7--923 Score: 914
Period size: 213 Copynumber: 4.4 Consensus size: 212
1 ACTTGT
* * * * * *
7 GGAACTTCAGGCTTCGACAACTCCGGAACTTTCGAAAATTCAAGTTTTGACAACTCAGAAACCTT
1 GGAACTTCAGGTTTCGACAACTCCAGAACTTTAGAAAATTCAGGTTTTGACAACTCTGAAACTTT
* * *
72 TTGTTCTTCAGGTTTT-GTCAACTTAGGC-TTGAGAAACTTCGGGTTAGGCAACTCAGGCTGGTT
66 TTGTTGTTCAGGTTTTGGT-AACTCAGGCTTTG-GAAAC-TCAGGTTAGGCAACTCAGGCTGGTT
* * * * *
135 AGATATGTTTGACTTTAGAACATTTGGGTGCTCTAGTTTTGAAAGTTTATCTGGAACATTCGACT
128 AGGTATGTTTGGCTTTGGAACATTTGGGTGCTCTAGTTTTGAAAGTTCATCTGGAACTTTCGACT
200 TTTCTAGCTCAGAAACTTTA
193 TTTCTAGCTCAGAAACTTTA
* * ** *
220 TGAACTTTAGGTTTCGACAACTCTGGAACTTTAGACAATTCAGGTTTTGACAAAC-CTGAAACTT
1 GGAACTTCAGGTTTCGACAACTCCAGAACTTTAGAAAATTCAGGTTTTGAC-AACTCTGAAACTT
* * *
284 TTTGTTCTTCAGGTTTTGGTAACTCAGGCTTTGGAAACACCAGGTTAGGCAACTCAGGCTGGTCA
65 TTTGTTGTTCAGGTTTTGGTAACTCAGGCTTTGGAAAC-TCAGGTTAGGCAACTCAGGCTGGTTA
349 GGTATGTTTGGCTTTGGAACATTTGGGTGAC-CTAGTTTTGAAAGTTCATCTGGAACTTTCGACT
129 GGTATGTTTGGCTTTGGAACATTTGGGTG-CTCTAGTTTTGAAAGTTCATCTGGAACTTTCGACT
*
413 TTTCTAGTTCAGAAACTTTA
193 TTTCTAGCTCAGAAACTTTA
** * * *
433 GGAACTTCAGACTTCGATAA--CC----C--T-G-GAA--CAGGTTTTGACAAATCTGAAACTTT
1 GGAACTTCAGGTTTCGACAACTCCAGAACTTTAGAAAATTCAGGTTTTGACAACTCTGAAACTTT
* * ** * * * *
486 TTGTTGTTCAGGTTTTGGCAACTCAGGCTTTGGTAACTTTGGCTTAGACAACTTAGG-TTGTTGG
66 TTGTTGTTCAGGTTTTGGTAACTCAGGCTTTGGAAACTCAGG-TTAGGCAACTCAGGCTGGTTAG
* * ** * * * *
550 GTATG-TTGGTTTTGGAACAATTAGACT-CTCTGGTTTTGAGAGTTCATCCGGAATTTTCGACTT
130 GTATGTTTGGCTTTGGAAC-ATTTGGGTGCTCTAGTTTTGAAAGTTCATCTGGAACTTTCGACTT
* * *
613 TTCTAGGTCAGAATCTTTT
194 TTCTAGCTCAGAAACTTTA
* * *
632 GGAACTTCAGGTTTCGACAACTCCAAAACTTTGGAAAATTCAGGTTTTGACAACTCAGAAGA-TT
1 GGAACTTCAGGTTTCGACAACTCCAGAACTTTAGAAAATTCAGGTTTTGACAACTCTGAA-ACTT
* *
696 TTTGTTGTTCAGGTTTTGGTAACTCA-GC-TT------T-A---T--GCAACTCAGGTTGGTTGG
65 TTTGTTGTTCAGGTTTTGGTAACTCAGGCTTTGGAAACTCAGGTTAGGCAACTCAGGCTGGTTAG
* * * *
747 GTATGTTTTGCTTTGGAACATTTTGGCGCTCTGGTTTTGAAAGTTCATCTGGAACTTTCGACTTT
130 GTATGTTTGGCTTTGGAACATTTGGGTGCTCTAGTTTTGAAAGTTCATCTGGAACTTTCGACTTT
* *
812 TGTATCTCAGAAACTTTA
195 TCTAGCTCAGAAACTTTA
* * * * *
830 GGAACTTCA-ATCTTCGAAAACTCTAGAGCTTTAGAAAATTCATGTTTTGACAACTCTGAAACTT
1 GGAACTTCAGGT-TTCGACAACTCCAGAACTTTAGAAAATTCAGGTTTTGACAACTCTGAAACTT
**
894 TTTGTTGTTCAGGTTTTGACAACTCAGGCT
65 TTTGTTGTTCAGGTTTTGGTAACTCAGGCT
924 GGTTGGGTAT
Statistics
Matches: 590, Mismatches: 86, Indels: 69
0.79 0.12 0.09
Matches are distributed among these distances:
196 8 0.01
197 16 0.03
198 136 0.23
199 77 0.13
200 18 0.03
201 69 0.12
203 3 0.01
204 1 0.00
205 2 0.00
207 2 0.00
208 1 0.00
209 4 0.01
210 2 0.00
211 46 0.08
212 1 0.00
213 195 0.33
214 9 0.02
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (212 bp):
GGAACTTCAGGTTTCGACAACTCCAGAACTTTAGAAAATTCAGGTTTTGACAACTCTGAAACTTT
TTGTTGTTCAGGTTTTGGTAACTCAGGCTTTGGAAACTCAGGTTAGGCAACTCAGGCTGGTTAGG
TATGTTTGGCTTTGGAACATTTGGGTGCTCTAGTTTTGAAAGTTCATCTGGAACTTTCGACTTTT
CTAGCTCAGAAACTTTA
Found at i:808 original size:198 final size:196
Alignment explanation
Indices: 534--1899 Score: 797
Period size: 198 Copynumber: 6.8 Consensus size: 196
524 TTGGCTTAGA
* * * * * *
534 CAACTTAGGTT-GTTGGGTATG-TTGGTTTTGGAACAATTAGACTCTCTGGTTTTGAGAGTTCAT
1 CAACTCAGGTTGGTTGGGTATGTTTGGCTTTGGAAC-ATTTGGCGCTCTGGTTTTGAAAGTTCAT
* * * * *
597 CCGGAATTTTCGACTTTTCTAGGTCAGAATCTTTTGGAACTTCAGGTTTCGACAACTCCAAAACT
65 CTGGAATTTTCGACTTTTCTAGCTCAGAAACTTTTGGAACTTCAGGCTTCGACAACTCCAGAACT
*
662 TTGGAAAATTCAGGTTTTGACAACTCAGAAGA-TTTTTGTTGTTCAGGTTTTGGTAACTCAGCTT
130 TTAGAAAATTCAGGTTTTGACAACTCAGAA-ACTTTTTGTTGTTCAGGTTTT-GTAACTCAGCTT
726 TATG
193 TATG
*
730 CAACTCAGGTTGGTTGGGTATGTTTTGCTTTGGAACATTTTGGCGCTCTGGTTTTGAAAGTTCAT
1 CAACTCAGGTTGGTTGGGTATGTTTGGCTTTGGAACA-TTTGGCGCTCTGGTTTTGAAAGTTCAT
* * * * ** * * *
795 CTGGAACTTTCGACTTTTGTATCTCAGAAACTTTAGGAACTTCAATCTTCGAAAACTCTAGAGCT
65 CTGGAATTTTCGACTTTTCTAGCTCAGAAACTTTTGGAACTTCAGGCTTCGACAACTCCAGAACT
* *
860 TTAGAAAATTCATGTTTTGACAACTCTGAAACTTTTTGTTGTTCAGG--TT-T---T--G----A
130 TTAGAAAATTCAGGTTTTGACAACTCAGAAACTTTTTGTTGTTCAGGTTTTGTAACTCAGCTTTA
913 --
195 TG
* * * *
913 CAACTCAGGCTGGTTGGGTATGTTTGGCTTTGAAACAATTGG-GCCTTCTGGTTTTGACAGTTCA
1 CAACTCAGGTTGGTTGGGTATGTTTGGCTTTGGAACATTTGGCG-C-TCTGGTTTTGAAAGTTCA
* * * * *
977 TCTGGAATTTTCGACTTTTCTAGCTCAAAAACTTTTGGAACTTTAGACTTCGACAGCT-CAGGAT
64 TCTGGAATTTTCGACTTTTCTAGCTCAGAAACTTTTGGAACTTCAGGCTTCGACAACTCCA-GAA
* ** * *
1041 CTTTCA-ACAATTCAGGTTTTGACAGA-TTGGAAACTTTTTGTTGTTTAGGTTTTGACAACTCAG
128 CTTT-AGAAAATTCAGGTTTTGACA-ACTCAGAAACTTTTTGTTGTTCAGGTTTTG-TAACTCAG
1104 ACTTTGCTAACTCCGACTTAGG
190 -C--T--T---T---A--T--G
* * * *
1126 CAACTCAGGCTGGTTGGGTATG-TTGGACTTTGGAACATTTGGCAGCTCTGATTCT-AAGAATTC
1 CAACTCAGGTTGGTTGGGTATGTTTGG-CTTTGGAACATTTGGC-GCTCTGGTTTTGAA-AGTTC
* * *** * * *
1189 ATCCT-CAGCTAAGCAAGGTTTCTCTATAAGTTCATCTGAAACTTTT-G-ACTTTTCTA-GC-TC
63 AT-CTGGA-ATTTTCGA-CTTT-TC--T-AG--C-TCAGAAACTTTTGGAAC--TTC-AGGCTTC
** * ** * *
1249 GGA-AACTTTAGGAACTTCAGGCTTCGATAACCCTAGAACAGGTTTTGACAAATCTGAAACTTTT
115 -GACAACTCCA-GAAC-T-----TTAGA-AA----A-TTCAGGTTTTGACAACTCAGAAACTTTT
*
1313 TGTTGTTCAGGTTTTGACAACTCAGGCTTTGGTAACTCTGGCTTAGG
166 TGTTGTTCAGGTTTTG-TAACTCA-GC-TT--T-A--------T--G
* * * **
1360 CAACTCAGGTTGGTTGGTTATGTTTGGCTTTGGAACAATTGGACTCTCTGGTTTTGAGTGTTCAT
1 CAACTCAGGTTGGTTGGGTATGTTTGGCTTTGGAACATTTGG-CGCTCTGGTTTTGAAAGTTCAT
** * * * *
1425 CCAGAATTTTCGACTTTTCTAGGTCAGAATCTTTTGGAACTTCAGGCTTCGACAACTCCGGACCT
65 CTGGAATTTTCGACTTTTCTAGCTCAGAAACTTTTGGAACTTCAGGCTTCGACAACTCCAGAACT
* * * * *
1490 TTGGACAATTCAGGTTTAGACAATTCAGAAACTTTTTGTTGTTCAGGTTTTGGTAACTCAGGTTT
130 TTAGAAAATTCAGGTTTTGACAACTCAGAAACTTTTTGTTGTTCAGGTTTT-GTAACTCAGCTTT
*
1555 AGG
194 ATG
**
1558 CAACTCAGGTTGGTTGGGTATGTTTTTCTTTGGAACATTTTGGCGCTCTGGTTTTGAAAGTTCAT
1 CAACTCAGGTTGGTTGGGTATGTTTGGCTTTGGAACA-TTTGGCGCTCTGGTTTTGAAAGTTCAT
* * * * * * * * * **
1623 CTGAAACTTTCGACCTTTGTATCTCAGAAACTTTAGAAACTTCAGTCTTCGAAAACTCTGGAACT
65 CTGGAATTTTCGACTTTTCTAGCTCAGAAACTTTTGGAACTTCAGGCTTCGACAACTCCAGAACT
* * *
1688 TTAGACAATTCAAGTTTTGACAACTCTGAAACTTTTTGTTGTTCAGG--TT-T---T--G----A
130 TTAGAAAATTCAGGTTTTGACAACTCAGAAACTTTTTGTTGTTCAGGTTTTGTAACTCAGCTTTA
1741 --
195 TG
* * * * * *
1741 CAACTTAGGCTGGTTGGGTATATTTGGCTTTGAAACAATTGG-GTCTTCTGGTTTTGACAGTTCA
1 CAACTCAGGTTGGTTGGGTATGTTTGGCTTTGGAACATTTGGCG-C-TCTGGTTTTGAAAGTTCA
* * * *
1805 TCTGGAATTTTCGACTTTTCTAGCTCAGAAATTTTTGGAACTTTAGGCTTCGGCAGCT-CAGAAT
64 TCTGGAATTTTCGACTTTTCTAGCTCAGAAACTTTTGGAACTTCAGGCTTCGACAACTCCAGAA-
* *
1869 CTTTCGACAATTCAGGTTTTGACAACTCAGA
128 CTTTAGAAAATTCAGGTTTTGACAACTCAGA
1900 TTTTACTAAC
Statistics
Matches: 913, Mismatches: 164, Indels: 199
0.72 0.13 0.16
Matches are distributed among these distances:
181 2 0.00
182 14 0.02
183 262 0.29
184 2 0.00
185 4 0.00
189 2 0.00
190 1 0.00
191 2 0.00
192 1 0.00
194 2 0.00
196 14 0.02
197 12 0.01
198 273 0.30
199 4 0.00
207 1 0.00
208 1 0.00
209 1 0.00
211 2 0.00
212 6 0.01
213 93 0.10
214 8 0.01
215 4 0.00
216 2 0.00
218 2 0.00
219 6 0.01
220 2 0.00
221 7 0.01
222 20 0.02
223 2 0.00
224 2 0.00
225 20 0.02
226 7 0.01
227 2 0.00
228 6 0.01
229 2 0.00
230 1 0.00
231 3 0.00
232 3 0.00
233 8 0.01
234 100 0.11
235 7 0.01
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (196 bp):
CAACTCAGGTTGGTTGGGTATGTTTGGCTTTGGAACATTTGGCGCTCTGGTTTTGAAAGTTCATC
TGGAATTTTCGACTTTTCTAGCTCAGAAACTTTTGGAACTTCAGGCTTCGACAACTCCAGAACTT
TAGAAAATTCAGGTTTTGACAACTCAGAAACTTTTTGTTGTTCAGGTTTTGTAACTCAGCTTTAT
G
Found at i:1062 original size:183 final size:183
Alignment explanation
Indices: 730--1103 Score: 490
Period size: 183 Copynumber: 2.0 Consensus size: 183
720 CAGCTTTATG
* * * * *
730 CAACTCAGGTTGGTTGGGTATGTTTTGCTTTGGAACATTTTGGCGCTCTGGTTTTGAAAGTTCAT
1 CAACTCAGGCTGGTTGGGTATGTTTGGCTTTGAAACAATTGGGCGCTCTGGTTTTGAAAGTTCAT
* * *
795 CTGGAACTTTCGACTTTTGTATCTCAGAAACTTTAGGAACTTCAATCTTCGAAAACTCTAGAGCT
66 CTGGAACTTTCGACTTTTCTAGCTCAAAAACTTTAGGAACTTCAATCTTCGAAAACTCTAGAGCT
*
860 TTAGAAAATTCATGTTTTGACA-ACTCT-GAAACTTTTTGTTGTTCAGGTTTTGA
131 TTAGAAAATTCAGGTTTTGACAGA-T-TGGAAACTTTTTGTTGTTCAGGTTTTGA
*
913 CAACTCAGGCTGGTTGGGTATGTTTGGCTTTGAAACAATTGGGC-CTTCTGGTTTTGACAGTTCA
1 CAACTCAGGCTGGTTGGGTATGTTTGGCTTTGAAACAATTGGGCGC-TCTGGTTTTGAAAGTTCA
* * * * *
977 TCTGGAATTTTCGACTTTTCTAGCTCAAAAACTTTTGGAACTTTAGA-CTTCGACAGCTC-AGGA
65 TCTGGAACTTTCGACTTTTCTAGCTCAAAAACTTTAGGAACTTCA-ATCTTCGAAAACTCTA-GA
* * *
1040 TCTTTCA-ACAATTCAGGTTTTGACAGATTGGAAACTTTTTGTTGTTTAGGTTTTGA
128 GCTTT-AGAAAATTCAGGTTTTGACAGATTGGAAACTTTTTGTTGTTCAGGTTTTGA
1096 CAACTCAG
1 CAACTCAG
1104 ACTTTGCTAA
Statistics
Matches: 167, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
182 3 0.02
183 161 0.96
184 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.39
Consensus pattern (183 bp):
CAACTCAGGCTGGTTGGGTATGTTTGGCTTTGAAACAATTGGGCGCTCTGGTTTTGAAAGTTCAT
CTGGAACTTTCGACTTTTCTAGCTCAAAAACTTTAGGAACTTCAATCTTCGAAAACTCTAGAGCT
TTAGAAAATTCAGGTTTTGACAGATTGGAAACTTTTTGTTGTTCAGGTTTTGA
Found at i:1349 original size:15 final size:15
Alignment explanation
Indices: 1330--1368 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1320 CAGGTTTTGA
*
1330 CAACTCAGGCTTTGG
1 CAACTCAGGCTTAGG
* *
1345 TAACTCTGGCTTAGG
1 CAACTCAGGCTTAGG
1360 CAACTCAGG
1 CAACTCAGG
1369 TTGGTTGGTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (15 bp):
CAACTCAGGCTTAGG
Found at i:1550 original size:15 final size:15
Alignment explanation
Indices: 1532--1568 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1522 TTTTTGTTGT
* *
1532 TCAGGTTTTGGTAAC
1 TCAGGTTTAGGCAAC
1547 TCAGGTTTAGGCAAC
1 TCAGGTTTAGGCAAC
1562 TCAGGTT
1 TCAGGTT
1569 GGTTGGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (15 bp):
TCAGGTTTAGGCAAC
Found at i:1688 original size:33 final size:33
Alignment explanation
Indices: 1649--1722 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
1639 TTGTATCTCA
1649 GAAACTTTAGA-AACTTC-AGTCTTCGAAAACTCT
1 GAAACTTTAGACAA-TTCAAGT-TTCGAAAACTCT
* * *
1682 GGAACTTTAGACAATTCAAGTTTTGACAACTCT
1 GAAACTTTAGACAATTCAAGTTTCGAAAACTCT
1715 GAAACTTT
1 GAAACTTT
1723 TTGTTGTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 30 0.86
34 5 0.14
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (33 bp):
GAAACTTTAGACAATTCAAGTTTCGAAAACTCT
Found at i:1799 original size:828 final size:826
Alignment explanation
Indices: 390--1892 Score: 2594
Period size: 828 Copynumber: 1.8 Consensus size: 826
380 CTAGTTTTGA
* *
390 AAGTTCATCTGGAACTTTCGACTTTTCTAGTTCAGAAACTTTAGGAACTTCAGACTTCGATAACC
1 AAGTTCATCTGAAACTTTCGACTTTTCTAGCTCAGAAACTTTAGGAACTTCAGACTTCGATAACC
* *
455 CTGGAACAGGTTTTGACAAATCTGAAACTTTTTGTTGTTCAGGTTTTGGCAACTCAGGCTTTGGT
66 CTAGAACAGGTTTTGACAAATCTGAAACTTTTTGTTGTTCAGGTTTTGACAACTCAGGCTTTGGT
* * *
520 AACTTTGGCTTAGACAACTTAGGTTGTTGGGTATGTTGGTTTTGGAACAATTAGACTCTCTGGTT
131 AACTCTGGCTTAGACAACTCAGGTTGTTGGGTATGTTGGCTTTGGAACAATTAGACTCTCTGGTT
* *
585 TTGAGAGTTCATCCGGAATTTTCGACTTTTCTAGGTCAGAATCTTTTGGAACTTCAGGTTTCGAC
196 TTGAGAGTTCATCCAGAATTTTCGACTTTTCTAGGTCAGAATCTTTTGGAACTTCAGGCTTCGAC
*
650 AACTCCAAAACTTTGGAAAATTCAGGTTTTGACAACTCAGAAGATTTTTGTTGTTCAGGTTTTGG
261 AACTCCAAAACTTTGGAAAATTCAGGTTTAGACAACTCAGAAGATTTTTGTTGTTCAGGTTTTGG
*
715 TAACTCAGCTTTATGCAACTCAGGTTGGTTGGGTATGTTTTGCTTTGGAACATTTTGGCGCTCTG
326 TAACTCAGCTTTAGGCAACTCAGGTTGGTTGGGTATGTTTTGCTTTGGAACATTTTGGCGCTCTG
* * *
780 GTTTTGAAAGTTCATCTGGAACTTTCGACTTTTGTATCTCAGAAACTTTAGGAACTTCAATCTTC
391 GTTTTGAAAGTTCATCTGAAACTTTCGACCTTTGTATCTCAGAAACTTTAGAAACTTCAATCTTC
* *
845 GAAAACTCTAGAGCTTTAGAAAATTCATGTTTTGACAACTCTGAAACTTTTTGTTGTTCAGGTTT
456 GAAAACTCTAGAACTTTAGAAAATTCAAGTTTTGACAACTCTGAAACTTTTTGTTGTTCAGGTTT
*
910 TGACAACTCAGGCTGGTTGGGTATGTTTGGCTTTGAAACAATTGGGCCTTCTGGTTTTGACAGTT
521 TGACAACTCAGGCTGGTTGGGTATATTTGGCTTTGAAACAATTGGGCCTTCTGGTTTTGACAGTT
*
975 CATCTGGAATTTTCGACTTTTCTAGCTCAAAAACTTTTGGAACTTTAGACTTCGACAGCTCAGGA
586 CATCTGGAATTTTCGACTTTTCTAGCTCAAAAACTTTTGGAACTTTAGACTTCGACAGCTCAGAA
1040 TCTTTCAACAATTCAGGTTTTGACAGATTGGAAACTTTTTGTTGTTTAGGTTTTGACAACTCAGA
651 TCTTTCAACAATTCAGGTTTTGACAGATTGGAAACTTTTTGTTGTTTAGGTTTTGACAACTCAGA
1105 CTTTGCTAACTCCGACTTAGGCAACTCAGGCTGGTTGGGTATGTTGGACTTTGGAACATTTGGCA
716 CTTTGCTAACTCCGACTTAGGCAACTCAGGCTGGTTGGGTATGTTGGACTTTGGAACATTTGGCA
1170 GCTCTGATTCTAAGAATTCATCCTCAGCTAAGCAAGGTTTCTCTAT
781 GCTCTGATTCTAAGAATTCATCCTCAGCTAAGCAAGGTTTCTCTAT
* * *
1216 AAGTTCATCTGAAACTTTTGACTTTTCTAGCTCGGAAACTTTAGGAACTTCAGGCTTCGATAACC
1 AAGTTCATCTGAAACTTTCGACTTTTCTAGCTCAGAAACTTTAGGAACTTCAGACTTCGATAACC
1281 CTAGAACAGGTTTTGACAAATCTGAAACTTTTTGTTGTTCAGGTTTTGACAACTCAGGCTTTGGT
66 CTAGAACAGGTTTTGACAAATCTGAAACTTTTTGTTGTTCAGGTTTTGACAACTCAGGCTTTGGT
* * *
1346 AACTCTGGCTTAGGCAACTCAGGTTGGTTGGTTATGTTTGGCTTTGGAACAATTGGACTCTCTGG
131 AACTCTGGCTTAGACAACTCAGGTT-GTTGGGTATG-TTGGCTTTGGAACAATTAGACTCTCTGG
*
1411 TTTTGAGTGTTCATCCAGAATTTTCGACTTTTCTAGGTCAGAATCTTTTGGAACTTCAGGCTTCG
194 TTTTGAGAGTTCATCCAGAATTTTCGACTTTTCTAGGTCAGAATCTTTTGGAACTTCAGGCTTCG
** * * *
1476 ACAACTCCGGACCTTTGGACAATTCAGGTTTAGACAATTCAGAA-ACTTTTTGTTGTTCAGGTTT
259 ACAACTCCAAAACTTTGGAAAATTCAGGTTTAGACAACTCAGAAGA-TTTTTGTTGTTCAGGTTT
* *
1540 TGGTAACTCAGGTTTAGGCAACTCAGGTTGGTTGGGTATGTTTTTCTTTGGAACATTTTGGCGCT
323 TGGTAACTCAGCTTTAGGCAACTCAGGTTGGTTGGGTATGTTTTGCTTTGGAACATTTTGGCGCT
*
1605 CTGGTTTTGAAAGTTCATCTGAAACTTTCGACCTTTGTATCTCAGAAACTTTAGAAACTTCAGTC
388 CTGGTTTTGAAAGTTCATCTGAAACTTTCGACCTTTGTATCTCAGAAACTTTAGAAACTTCAATC
* *
1670 TTCGAAAACTCTGGAACTTTAGACAATTCAAGTTTTGACAACTCTGAAACTTTTTGTTGTTCAGG
453 TTCGAAAACTCTAGAACTTTAGAAAATTCAAGTTTTGACAACTCTGAAACTTTTTGTTGTTCAGG
* *
1735 TTTTGACAACTTAGGCTGGTTGGGTATATTTGGCTTTGAAACAATTGGGTCTTCTGGTTTTGACA
518 TTTTGACAACTCAGGCTGGTTGGGTATATTTGGCTTTGAAACAATTGGGCCTTCTGGTTTTGACA
* * * *
1800 GTTCATCTGGAATTTTCGACTTTTCTAGCTCAGAAATTTTTGGAACTTTAGGCTTCGGCAGCTCA
583 GTTCATCTGGAATTTTCGACTTTTCTAGCTCAAAAACTTTTGGAACTTTAGACTTCGACAGCTCA
*
1865 GAATCTTTCGACAATTCAGGTTTTGACA
648 GAATCTTTCAACAATTCAGGTTTTGACA
1893 ACTCAGATTT
Statistics
Matches: 632, Mismatches: 42, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
826 145 0.23
827 10 0.02
828 477 0.75
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (826 bp):
AAGTTCATCTGAAACTTTCGACTTTTCTAGCTCAGAAACTTTAGGAACTTCAGACTTCGATAACC
CTAGAACAGGTTTTGACAAATCTGAAACTTTTTGTTGTTCAGGTTTTGACAACTCAGGCTTTGGT
AACTCTGGCTTAGACAACTCAGGTTGTTGGGTATGTTGGCTTTGGAACAATTAGACTCTCTGGTT
TTGAGAGTTCATCCAGAATTTTCGACTTTTCTAGGTCAGAATCTTTTGGAACTTCAGGCTTCGAC
AACTCCAAAACTTTGGAAAATTCAGGTTTAGACAACTCAGAAGATTTTTGTTGTTCAGGTTTTGG
TAACTCAGCTTTAGGCAACTCAGGTTGGTTGGGTATGTTTTGCTTTGGAACATTTTGGCGCTCTG
GTTTTGAAAGTTCATCTGAAACTTTCGACCTTTGTATCTCAGAAACTTTAGAAACTTCAATCTTC
GAAAACTCTAGAACTTTAGAAAATTCAAGTTTTGACAACTCTGAAACTTTTTGTTGTTCAGGTTT
TGACAACTCAGGCTGGTTGGGTATATTTGGCTTTGAAACAATTGGGCCTTCTGGTTTTGACAGTT
CATCTGGAATTTTCGACTTTTCTAGCTCAAAAACTTTTGGAACTTTAGACTTCGACAGCTCAGAA
TCTTTCAACAATTCAGGTTTTGACAGATTGGAAACTTTTTGTTGTTTAGGTTTTGACAACTCAGA
CTTTGCTAACTCCGACTTAGGCAACTCAGGCTGGTTGGGTATGTTGGACTTTGGAACATTTGGCA
GCTCTGATTCTAAGAATTCATCCTCAGCTAAGCAAGGTTTCTCTAT
Found at i:1819 original size:183 final size:183
Alignment explanation
Indices: 1547--1896 Score: 418
Period size: 183 Copynumber: 1.9 Consensus size: 183
1537 TTTTGGTAAC
* * * ** * *
1547 TCAGGTTTAGGCAACTCAGGTTGGTTGGGTATGTTTTTCTTTGGAACATTTTGGCGCTCTGGTTT
1 TCAGGTTTAGACAACTCAGGCTGGTTGGGTATATTTGGCTTTGAAACATATTGGCGCTCTGGTTT
* * *
1612 TGAAAGTTCATCTGAAACTTTCGACCTTTGTATCTCAGAAACTTTAGAAACTTCAGTCTTCGAAA
66 TGAAAGTTCATCTGAAACTTTCGACCTTTCTAGCTCAGAAACTTTAGAAACTTCAGGCTTCGAAA
*
1677 ACTCTGGAA-CTTTAGACAATTCAAGTTTTGACAACTCTGAAACTTTTTGTTGT
131 ACTC-AGAATCTTTAGACAATTCAAGTTTTGACAACTCTGAAACTTTTTGTTGT
* *
1730 TCAGGTTTTGACAACTTAGGCTGGTTGGGTATATTTGGCTTTGAAACA-ATTGG-GTCTTCTGGT
1 TCAGGTTTAGACAACTCAGGCTGGTTGGGTATATTTGGCTTTGAAACATATTGGCG-C-TCTGGT
* * * * * * * * *
1793 TTTGACAGTTCATCTGGAATTTTCGACTTTTCTAGCTCAGAAATTTTTGGAACTTTAGGCTTCGG
64 TTTGAAAGTTCATCTGAAACTTTCGACCTTTCTAGCTCAGAAACTTTAGAAACTTCAGGCTTCGA
* * * *
1858 CAGCTCAGAATCTTTCGACAATTCAGGTTTTGACAACTC
129 AAACTCAGAATCTTTAGACAATTCAAGTTTTGACAACTC
1897 AGATTTTACT
Statistics
Matches: 138, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
181 1 0.01
182 8 0.06
183 129 0.93
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (183 bp):
TCAGGTTTAGACAACTCAGGCTGGTTGGGTATATTTGGCTTTGAAACATATTGGCGCTCTGGTTT
TGAAAGTTCATCTGAAACTTTCGACCTTTCTAGCTCAGAAACTTTAGAAACTTCAGGCTTCGAAA
ACTCAGAATCTTTAGACAATTCAAGTTTTGACAACTCTGAAACTTTTTGTTGT
Found at i:3048 original size:31 final size:32
Alignment explanation
Indices: 3010--3103 Score: 104
Period size: 31 Copynumber: 3.0 Consensus size: 32
3000 AGTTAGGTCA
3010 GGTTAAATTTGGGAT-AGGTTGAATC-GGTTCG
1 GGTTAAATTTGGG-TCAGGTTGAATCGGGTTCG
* *
3041 GGTTAAATTTGGGTCAGGTTGATTCGGGTTTG
1 GGTTAAATTTGGGTCAGGTTGAATCGGGTTCG
* * *
3073 GGTCAATTTTGGGTCA-GTTTAATTCGGGTTC
1 GGTTAAATTTGGGTCAGGTTGAA-TCGGGTTC
3104 AGATTGGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
30 1 0.02
31 26 0.49
32 26 0.49
ACGTcount: A:0.18, C:0.09, G:0.34, T:0.39
Consensus pattern (32 bp):
GGTTAAATTTGGGTCAGGTTGAATCGGGTTCG
Found at i:3089 original size:32 final size:32
Alignment explanation
Indices: 3014--3103 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
3004 AGGTCAGGTT
* *
3014 AAATTTGGGAT-AGGTTGAATC-GGTTCGGGTT
1 AAATTTGGG-TCAGGTTGATTCGGGTTCGGGTC
*
3045 AAATTTGGGTCAGGTTGATTCGGGTTTGGGTC
1 AAATTTGGGTCAGGTTGATTCGGGTTCGGGTC
* * *
3077 AATTTTGGGTCAGTTTAATTCGGGTTC
1 AAATTTGGGTCAGGTTGATTCGGGTTC
3104 AGATTGGGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.02
31 18 0.36
32 31 0.62
ACGTcount: A:0.19, C:0.09, G:0.33, T:0.39
Consensus pattern (32 bp):
AAATTTGGGTCAGGTTGATTCGGGTTCGGGTC
Found at i:4363 original size:103 final size:102
Alignment explanation
Indices: 4180--4367 Score: 288
Period size: 103 Copynumber: 1.8 Consensus size: 102
4170 CTACTTTATG
* *
4180 AAAATTGTAGATCATGAAACGACTTTTTAAAAGACACTTAAATCACCTCAAACAGATATCTGCAG
1 AAAATTGTAGATCATGAAACAACCTTTTAAAAGACACTTAAATCACCTCAAACAGATATCTGCAG
4245 CAAAAATTATGTAATATTAAGCTTTTGAATCCTTCAT
66 CAAAAATTATGTAATATTAAGCTTTTGAATCCTTCAT
* * * *
4282 AAAAGTTGTAGATCATTG-AACAACCTTTTAAGAGACACTTAAATCACCTTAATCAGATATCTGG
1 AAAA-TTGTAGATCA-TGAAACAACCTTTTAAAAGACACTTAAATCACCTCAAACAGATATCTGC
*
4346 AGCAAAAGTTATGTAATATTAA
64 AGCAAAAATTATGTAATATTAA
4368 TTGGACCACT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
102 4 0.05
103 71 0.92
104 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (102 bp):
AAAATTGTAGATCATGAAACAACCTTTTAAAAGACACTTAAATCACCTCAAACAGATATCTGCAG
CAAAAATTATGTAATATTAAGCTTTTGAATCCTTCAT
Found at i:7105 original size:37 final size:37
Alignment explanation
Indices: 7031--7105 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
7021 GGTTACTGTA
* **
7031 TGATCTACGACTTTCATGAAGAACTCGAAAGTTAATT
1 TGATCTACGACTTTCATGAAGAACTCAAAAGGGAATT
* * *
7068 TGATCTACGAGTTTCATGAAGGATTCAAAAGGGAATT
1 TGATCTACGACTTTCATGAAGAACTCAAAAGGGAATT
7105 T
1 T
7106 TTATGTTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (37 bp):
TGATCTACGACTTTCATGAAGAACTCAAAAGGGAATT
Found at i:7371 original size:6 final size:6
Alignment explanation
Indices: 7362--7414 Score: 72
Period size: 6 Copynumber: 8.7 Consensus size: 6
7352 CGTTTCTGTT
*
7362 TTTTTG TTTTTTG TTTTTTG TTTTTG TTTTTG TTTTTG -TTTCG TTTTTG
1 TTTTTG -TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
7411 TTTT
1 TTTT
7415 GCTGTCAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
5 4 0.09
6 26 0.60
7 13 0.30
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:7540 original size:53 final size:52
Alignment explanation
Indices: 7429--7528 Score: 173
Period size: 53 Copynumber: 1.9 Consensus size: 52
7419 TCAAAATTTT
*
7429 GAAAACAAAAACACGTTTGGTTGTATAAAGTTGTTGCACGTTTTAAAAAACA
1 GAAAACAAAAACACGTTTGGATGTATAAAGTTGTTGCACGTTTTAAAAAACA
*
7481 GAAAACAGAAAACACGTTTGGATGTATAAAGTTGTTGCATGTTTTAAA
1 GAAAACA-AAAACACGTTTGGATGTATAAAGTTGTTGCACGTTTTAAA
7529 TTGATGTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 7 0.16
53 38 0.84
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (52 bp):
GAAAACAAAAACACGTTTGGATGTATAAAGTTGTTGCACGTTTTAAAAAACA
Found at i:9325 original size:54 final size:54
Alignment explanation
Indices: 9255--9365 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
9245 GTCAAATAGG
* *
9255 AAATTATCCATACAACCAAAGTTAAAAAATCATGTCATCCATGCAAATAAAATA
1 AAATCATCCATACAACCAAAGTTAAAAAATCATGCCATCCATGCAAATAAAATA
*
9309 AAATCATCCATACAACCAAAGTTAAAAAGTCATGCCATCCATGCAAATAAAATA
1 AAATCATCCATACAACCAAAGTTAAAAAATCATGCCATCCATGCAAATAAAATA
9363 AAA
1 AAA
9366 CAACATCATC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (54 bp):
AAATCATCCATACAACCAAAGTTAAAAAATCATGCCATCCATGCAAATAAAATA
Found at i:9346 original size:27 final size:27
Alignment explanation
Indices: 9262--9346 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
9252 AGGAAATTAT
9262 CCATACAACCAAAGTTAAAAAATCATG
1 CCATACAACCAAAGTTAAAAAATCATG
* * ** *
9289 TCATCCATGCAAA-TAAAATAAAATCAT-
1 CCATACAACCAAAGT-TAA-AAAATCATG
*
9316 CCATACAACCAAAGTTAAAAAGTCATG
1 CCATACAACCAAAGTTAAAAAATCATG
9343 CCAT
1 CCAT
9347 CCATGCAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
26 8 0.19
27 26 0.60
28 9 0.21
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.21
Consensus pattern (27 bp):
CCATACAACCAAAGTTAAAAAATCATG
Found at i:9355 original size:27 final size:27
Alignment explanation
Indices: 9271--9355 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
9261 TCCATACAAC
*
9271 CAAAGTTAAAAAATCATGTCATCCATG
1 CAAAGTTAAAAAATCATGCCATCCATG
* * **
9298 CAAA-TAAAATAAAATCAT-CCATACAAC
1 CAAAGT-TAA-AAAATCATGCCATCCATG
*
9325 CAAAGTTAAAAAGTCATGCCATCCATG
1 CAAAGTTAAAAAATCATGCCATCCATG
9352 CAAA
1 CAAA
9356 TAAAATAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
26 8 0.18
27 27 0.61
28 9 0.20
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.21
Consensus pattern (27 bp):
CAAAGTTAAAAAATCATGCCATCCATG
Found at i:9816 original size:30 final size:30
Alignment explanation
Indices: 9782--9854 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
9772 CCAATAATGC
9782 CATCTTCATCACTTAATGGTTGATCCCTCG
1 CATCTTCATCACTTAATGGTTGATCCCTCG
* * * *
9812 CATCTTCCTCCCTTATTGGTTGATCCCTTG
1 CATCTTCATCACTTAATGGTTGATCCCTCG
9842 CATCTTCATCACT
1 CATCTTCATCACT
9855 ATCGGAGGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.33, G:0.11, T:0.40
Consensus pattern (30 bp):
CATCTTCATCACTTAATGGTTGATCCCTCG
Found at i:11233 original size:24 final size:24
Alignment explanation
Indices: 11205--11250 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
11195 ACAGGGAAAA
11205 CAAGAAAGGAGATAGAAGAAGACG
1 CAAGAAAGGAGATAGAAGAAGACG
11229 CAAGAAAGGAGATAGAAGAAGA
1 CAAGAAAGGAGATAGAAGAAGA
11251 ACATGAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.07, G:0.33, T:0.04
Consensus pattern (24 bp):
CAAGAAAGGAGATAGAAGAAGACG
Found at i:15126 original size:76 final size:76
Alignment explanation
Indices: 15000--15147 Score: 208
Period size: 76 Copynumber: 1.9 Consensus size: 76
14990 CAACGTCATT
* * *
15000 AATTGACAGATTTGGAAGACTTGCAATTGATGAGGAATATGACTGTTGGAGGCAGATCTAAGTAT
1 AATTGACAGATTTGAAAGACTTGCAATTAATGAGGAATATGACCGTTGGAGGCAGATCTAAGTAT
*
15065 TTAAGGAAACA
66 ATAAGGAAACA
* * * *
15076 AATTGACAGATTTGAAAGATTTGCATTTAATGTGGAGA-ATGACCGTTGGAGGCAGATCTGAGTA
1 AATTGACAGATTTGAAAGACTTGCAATTAATGAGGA-ATATGACCGTTGGAGGCAGATCTAAGTA
15140 TATAAGGA
65 TATAAGGA
15148 CCCAAGAGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 62 0.98
77 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (76 bp):
AATTGACAGATTTGAAAGACTTGCAATTAATGAGGAATATGACCGTTGGAGGCAGATCTAAGTAT
ATAAGGAAACA
Found at i:16908 original size:41 final size:41
Alignment explanation
Indices: 16852--16938 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
16842 CATTAACTAG
16852 AGAAACTTTAAAAGAGATAAATATAGAAATGATGACTTCAA
1 AGAAACTTTAAAAGAGATAAATATAGAAATGATGACTTCAA
* *
16893 AGAAGCTTTGAAAGAGATAAATATAGAAATGATGACTTCAA
1 AGAAACTTTAAAAGAGATAAATATAGAAATGATGACTTCAA
16934 AGAAA
1 AGAAA
16939 ACCAGCCTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.53, C:0.07, G:0.17, T:0.23
Consensus pattern (41 bp):
AGAAACTTTAAAAGAGATAAATATAGAAATGATGACTTCAA
Found at i:20704 original size:22 final size:22
Alignment explanation
Indices: 20676--20719 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20666 CAAAACTAAA
*
20676 TTGCATTGTGTCTTCTTTACTT
1 TTGCATTGTGTCTTCTCTACTT
20698 TTGCATTGTGTCTTCTCTACTT
1 TTGCATTGTGTCTTCTCTACTT
20720 ATGGTCTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.14, T:0.57
Consensus pattern (22 bp):
TTGCATTGTGTCTTCTCTACTT
Found at i:23987 original size:26 final size:25
Alignment explanation
Indices: 23958--24222 Score: 158
Period size: 26 Copynumber: 10.1 Consensus size: 25
23948 ATAGTAAATT
*
23958 AGTAATCAATAAAAAAAGTAAGAAA
1 AGTAATCAATAAAAAGAGTAAGAAA
* *
23983 TAGTATTCAGTAAAAAGAGTAAGAAA
1 -AGTAATCAATAAAAAGAGTAAGAAA
24009 AG-AATCATCAGTAAAAAGAGTAAGAAA
1 AGTAATCA--A-TAAAAAGAGTAAGAAA
* *
24036 CAGTATTCAGTAAAAAGAGTAAGAAA
1 -AGTAATCAATAAAAAGAGTAAGAAA
*
24062 AG-AATCACCAGTAAAAAGAGCAAGAAA
1 AGTAATCA--A-TAAAAAGAGTAAGAAA
* * * * *
24089 CAATATTCAGTAAAAGGATTAAGAAA
1 -AGTAATCAATAAAAAGAGTAAGAAA
*
24115 AG-AGCCATCAGTAAAAAGAGTAAGAAA
1 AGTA---ATCAATAAAAAGAGTAAGAAA
* * * *
24142 CAGTATTCAGTAAGAATAGTAAGAAAA
1 -AGTAATCAATAAAAAGAGTAAG-AAA
* * *
24169 GAGTCATCAGTAAAAAGAGTAGGAAA
1 -AGTAATCAATAAAAAGAGTAAGAAA
* * * *
24195 CAATATTCAGTGAAAAGAGTAAGAAA
1 -AGTAATCAATAAAAAGAGTAAGAAA
24221 AG
1 AG
24223 CGCAATAGTA
Statistics
Matches: 187, Mismatches: 36, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
24 9 0.05
25 6 0.03
26 89 0.48
27 69 0.37
28 5 0.03
29 9 0.05
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (25 bp):
AGTAATCAATAAAAAGAGTAAGAAA
Found at i:24031 original size:53 final size:53
Alignment explanation
Indices: 23962--24222 Score: 378
Period size: 53 Copynumber: 4.9 Consensus size: 53
23952 TAAATTAGTA
* * *
23962 ATCAATAAAAAAAGTAAGAAATAGTATTCAGTAAAAAGAGTAAGAAAAGAATC
1 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAATC
24015 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAATC
1 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAATC
* * * * * **
24068 ACCAGTAAAAAGAGCAAGAAACAATATTCAGTAAAAGGATTAAGAAAAGAGCC
1 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAATC
* * *
24121 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAATAGTAAGAAAAGAGTC
1 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAATC
* * *
24174 ATCAGTAAAAAGAGTAGGAAACAATATTCAGTGAAAAGAGTAAGAAAAG
1 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAG
24223 CGCAATAGTA
Statistics
Matches: 185, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 185 1.00
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (53 bp):
ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAATC
Found at i:24339 original size:34 final size:31
Alignment explanation
Indices: 24300--24408 Score: 114
Period size: 34 Copynumber: 3.4 Consensus size: 31
24290 AAAGGCAATC
24300 AGTAAAGAGTAATTAGTGAAGAAGAATGGTAAAG
1 AGTAAAGAGTAATTAGT-AA-AA-AATGGTAAAG
*
24334 AGTAAAGAGTAATCAGTAAAAAAAAATGGTAAAG
1 AGTAAAGAGTAATTAGT---AAAAAATGGTAAAG
* * *
24368 AATGAGGAGTAATTAGT--AAAATGGTAAAG
1 AGTAAAGAGTAATTAGTAAAAAATGGTAAAG
24397 AGTAAAGAGTAA
1 AGTAAAGAGTAA
24409 AGTAAAGAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
29 21 0.33
34 39 0.61
35 2 0.03
36 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.26, T:0.20
Consensus pattern (31 bp):
AGTAAAGAGTAATTAGTAAAAAATGGTAAAG
Found at i:24504 original size:20 final size:20
Alignment explanation
Indices: 24456--24600 Score: 96
Period size: 20 Copynumber: 7.0 Consensus size: 20
24446 TAAAGTAAAA
**
24456 AGTAATCAGTAAAGAAAAAAAT
1 AGTAATCAGTAAAG--AGTAAT
*
24478 GGTAATCAGTAAAGAGTAAT
1 AGTAATCAGTAAAGAGTAAT
24498 AGTAATCAGT-AAGAAGTAAT
1 AGTAATCAGTAAAG-AGTAAT
* * *
24518 GGTAATCAGTAAAAAGTAAAA
1 AGTAATCAGTAAAGAGT-AAT
* *
24539 AGGTAATCACTAAAAAGTAAAAT
1 A-GTAATCAGTAAAGAGT--AAT
* *
24562 GGTAATCAGTAAAAAGTAA-
1 AGTAATCAGTAAAGAGTAAT
* *
24581 AGGTAATTAGTGAAGAGTAA
1 A-GTAATCAGTAAAGAGTAA
24601 AATGGTAATT
Statistics
Matches: 101, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
19 3 0.03
20 48 0.48
21 4 0.04
22 43 0.43
23 3 0.03
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTAATCAGTAAAGAGTAAT
Found at i:24579 original size:64 final size:65
Alignment explanation
Indices: 24407--24681 Score: 257
Period size: 64 Copynumber: 4.4 Consensus size: 65
24397 AGTAAAGAGT
* * ** *
24407 AAAGTAAAGAGG-GATCAGTAAAAAG-AAAATGGTAAAAAGT--AAAGTAAAAAGTAATCAGTAA
1 AAAGTAAAAAGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAAGGTAATCAGTAA
* * * *
24468 AGAA--AAAAATGGTAATCAGTAAAGAGT--AATAGTAATCAGTAAGAAGT-AATGGTAATCAGT
1 A-AAGTAAAAA-GGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAAGGTAATCAGT
24528 AA
64 AA
* * *
24530 AAAGTAAAAAGGTAATCACTAAAAAGTAAAATGGTAATCAGTAAAAAGT-AAAGGTAATTAGTGA
1 AAAGTAAAAAGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAAGGTAATCAGTAA
* * * ** * * *
24594 AGAGTAAAATGGTAATTACAAAAAAGTAAAAGGGTGATCAGTAAAAAGTAAAATGGTAATTAGTA
1 AAAGTAAAAAGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAA-GGTAATCAGTA
24659 A
65 A
*
24660 AAAGTAAAGA-GTAATCAGTAAA
1 AAAGTAAAAAGGTAATCAGTAAA
24682 GAAAAAAATA
Statistics
Matches: 173, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
60 4 0.02
61 15 0.09
62 42 0.24
63 9 0.05
64 73 0.42
65 12 0.07
66 18 0.10
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (65 bp):
AAAGTAAAAAGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAAGGTAATCAGTAA
Found at i:24601 original size:20 final size:21
Alignment explanation
Indices: 24407--24681 Score: 235
Period size: 22 Copynumber: 13.0 Consensus size: 21
24397 AGTAAAGAGT
*
24407 AAAGTAAAGAGG-GATCAGTAA
1 AAAGTAAA-AGGTAATCAGTAA
**
24428 AAAG-AAAATGGTAAAAAGT--
1 AAAGTAAAA-GGTAATCAGTAA
*
24447 AAAGTAAAAAGTAATCAGTAA
1 AAAGTAAAAGGTAATCAGTAA
*
24468 AGAA-AAAAATGGTAATCAGTAA
1 A-AAGTAAAA-GGTAATCAGTAA
* *
24490 AGAGTAATA-GTAATCAGTAA
1 AAAGTAAAAGGTAATCAGTAA
* *
24510 GAAGT-AATGGTAATCAGTAA
1 AAAGTAAAAGGTAATCAGTAA
*
24530 AAAGTAAAAAGGTAATCACTAA
1 AAAGT-AAAAGGTAATCAGTAA
24552 AAAGTAAAATGGTAATCAGTAA
1 AAAGTAAAA-GGTAATCAGTAA
* *
24574 AAAGT-AAAGGTAATTAGTGA
1 AAAGTAAAAGGTAATCAGTAA
* * **
24594 AGAGTAAAATGGTAATTACAAA
1 AAAGTAAAA-GGTAATCAGTAA
*
24616 AAAGTAAAAGGGTGATCAGTAA
1 AAAGTAAAA-GGTAATCAGTAA
*
24638 AAAGTAAAATGGTAATTAGTAA
1 AAAGTAAAA-GGTAATCAGTAA
24660 AAAGT-AAAGAGTAATCAGTAA
1 AAAGTAAAAG-GTAATCAGTAA
24681 A
1 A
24682 GAAAAAAATA
Statistics
Matches: 204, Mismatches: 35, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
19 13 0.06
20 53 0.26
21 38 0.19
22 100 0.49
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (21 bp):
AAAGTAAAAGGTAATCAGTAA
Found at i:24672 original size:14 final size:14
Alignment explanation
Indices: 24655--24741 Score: 66
Period size: 14 Copynumber: 6.1 Consensus size: 14
24645 AATGGTAATT
24655 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
**
24669 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
**
24683 AAAAAAATAGTAAAG
1 AGTAAAA-AGTAAAG
* **
24698 AATAATCAGTAAAG
1 AGTAAAAAGTAAAG
*
24712 AGTAAAATAGTAAAA
1 AGTAAAA-AGTAAAG
**
24727 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
24741 A
1 A
24742 AAAAAAATAG
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
14 33 0.60
15 22 0.40
ACGTcount: A:0.61, C:0.03, G:0.17, T:0.18
Consensus pattern (14 bp):
AGTAAAAAGTAAAG
Found at i:24694 original size:29 final size:29
Alignment explanation
Indices: 24658--24759 Score: 143
Period size: 29 Copynumber: 3.5 Consensus size: 29
24648 GGTAATTAGT
24658 AAAA-AGTAAAGAGTAATCAGTAAAGAAA
1 AAAATAGTAAAGAGTAATCAGTAAAGAAA
* **
24686 AAAATAGTAAAGAATAATCAGTAAAGAGT
1 AAAATAGTAAAGAGTAATCAGTAAAGAAA
*
24715 AAAATAGTAAAAAGTAATCAGTAAAGAAAA
1 AAAATAGTAAAGAGTAATCAGTAAAG-AAA
*
24745 AAAATAGTAAGGAGT
1 AAAATAGTAAAGAGT
24760 GAGAAGAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.06
29 45 0.71
30 14 0.22
ACGTcount: A:0.62, C:0.03, G:0.18, T:0.18
Consensus pattern (29 bp):
AAAATAGTAAAGAGTAATCAGTAAAGAAA
Found at i:24696 original size:15 final size:15
Alignment explanation
Indices: 24676--24754 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 15
24666 AAGAGTAATC
24676 AGTAAAGAAAAAAAT
1 AGTAAAGAAAAAAAT
*
24691 AGTAAAG--AATAAT
1 AGTAAAGAAAAAAAT
**
24704 CAGTAAAGAGTAAAAT
1 -AGTAAAGAAAAAAAT
**
24720 AGT-AA-AAAGTAAT
1 AGTAAAGAAAAAAAT
24733 CAGTAAAGAAAAAAAAT
1 -AGTAAAG-AAAAAAAT
24750 AGTAA
1 AGTAA
24755 GGAGTGAGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 13
0.69 0.13 0.19
Matches are distributed among these distances:
13 9 0.19
14 12 0.25
15 12 0.25
16 9 0.19
17 6 0.12
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (15 bp):
AGTAAAGAAAAAAAT
Found at i:24888 original size:42 final size:43
Alignment explanation
Indices: 24814--24903 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 43
24804 GAGAAAAATG
* * *
24814 GTAAAGAGAAAAATCTTAATTAGTAAAAAGTAATG-GCAATCA
1 GTAAAGAGAAAAATATTAACTAGTAAAAAGTAAAGAGCAATCA
** *
24856 GTAAAGA-ATAAAATATTAACTAGTAATCAGTAAAGAGTAATCA
1 GTAAAGAGA-AAAATATTAACTAGTAAAAAGTAAAGAGCAATCA
24899 GTAAA
1 GTAAA
24904 AAGTGAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.03
42 28 0.70
43 11 0.28
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (43 bp):
GTAAAGAGAAAAATATTAACTAGTAAAAAGTAAAGAGCAATCA
Found at i:24896 original size:14 final size:14
Alignment explanation
Indices: 24877--24903 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24867 AATATTAACT
24877 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
24891 AGTAATCAGTAAA
1 AGTAATCAGTAAA
24904 AAGTGAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:26434 original size:201 final size:199
Alignment explanation
Indices: 26065--26822 Score: 953
Period size: 201 Copynumber: 3.8 Consensus size: 199
26055 ACTTCTTAAC
* * * *
26065 CCGTAAGTGGGGTTTATCAGACTGCACGTGCGTGGTTTAATTTTAAGGGTTGACATGTGTACCCT
1 CCGTTAGTGGAGTTTAGCAGACTGCACGTGCG-GGGTTAA-TTTAAGGGTTGACATGTGTACCCT
* * *
26130 TAGAGAATATGTATTAATATTAA-ATATTTAATCATGGAATGAGGTATGTGTCAACTTCTTAATC
64 TAGGGAATATGTATTAATATTAATATATTTAATCATGAAATG-GGTATGTGTCAACTTCTTAACC
* *
26194 CGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTACAATAATCCTACAAGAAAATTTATA
128 CGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAATTTATA
26259 CAATACA
193 CAATACA
*
26266 CCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGGGTTGACATATGTACCCT
1 CCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGG-TTAA-TTTAAGGGTTGACATGTGTACCCT
*
26331 TAGGGAATATGTATTAATATT-ATATATTTAATCATGAAATGGAGTATGTGTCAACTTCTTAATC
64 TAGGGAATATGTATTAATATTAATATATTTAATCATGAAATGG-GTATGTGTCAACTTCTTAACC
* * * * *
26395 TGCTTATGGAATCCAAAATTTACACTGACAGTATATTGTATAATAATCCTTTAAGAAAAATTATA
128 CGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAATTTATA
26460 CAATAC-
193 CAATACA
* * * * * * *
26466 CCGTTAGTGGATTTTAGCAAACTGCACGTAC----ATGATTTAAGAGTTGACATGTGTCCCCTTA
1 CCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTAATTTAAGGGTTGACATGTGTACCCTTA
* *
26527 GGGAATATGTATTAATATTAAATATATAATTAATTATGAAATAGGGTATATGTCAACTTCTTAAC
66 GGGAATATGTATTAATATT-AATATAT--TTAATCATGAAAT-GGGTATGTGTCAACTTCTTAAC
* * * * * *
26592 CCGCTTATGGCGTCCAAAATTTATAATGATAGTGTATTGTATAATAACCCTATAAGAAAAATTAA
127 CCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAG-AAAATTTA
**
26657 TGGAATACA
191 TACAATACA
* * *
26666 CCGTCAGTGGAGTTTAGTAGACTGCACGTGCGGGG----TTTAAGGGTTGACATGTGTCCCCTTA
1 CCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTAATTTAAGGGTTGACATGTGTACCCTTA
* * *
26727 GGGAATATGCATTAATATTAAATATTTAATTAATTATGAAATGTGGTATGTGTCAACTTCTTAAC
66 GGGAATATGTATTAATATT-AATA--TATTTAATCATGAAATG-GGTATGTGTCAACTTCTTAAC
26792 CCGCTTATGGAGTCCAAAATTTACACTGACA
127 CCGCTTATGGAGTCCAAAATTTACACTGACA
26823 CGCGCGAGGT
Statistics
Matches: 488, Mismatches: 52, Indels: 35
0.85 0.09 0.06
Matches are distributed among these distances:
194 42 0.09
195 2 0.00
196 6 0.01
198 77 0.16
199 15 0.03
200 166 0.34
201 178 0.36
202 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (199 bp):
CCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTAATTTAAGGGTTGACATGTGTACCCTTA
GGGAATATGTATTAATATTAATATATTTAATCATGAAATGGGTATGTGTCAACTTCTTAACCCGC
TTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAATTTATACAA
TACA
Found at i:26765 original size:200 final size:197
Alignment explanation
Indices: 26106--26822 Score: 944
Period size: 200 Copynumber: 3.6 Consensus size: 197
26096 GTGGTTTAAT
* *
26106 TTTAAGGGTTGACATGTGTACCCTTAGAGAATATGTATTAATATTAAATAT--TTAATCATGGAA
1 TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATAATTAATCATGAAA
*
26169 TGAGGTATGTGTCAACTTCTTAATCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTA
66 TGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTA
* * *
26234 CAATAATCCTACAAGAAAATTTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGG
131 TAATAATCCTATAAGAAAAATTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGG
26299 GG
196 GG
* *
26301 TTTAACTTTAAGGGTTGACATATGTACCCTTAGGGAATATGTATTAATATT--ATATATTTAATC
1 ------TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATAATTAATC
* * * *
26364 ATGAAATG-GAGTATGTGTCAACTTCTTAATCTGCTTATGGAATCCAAAATTTACACTGACAGTA
60 ATGAAATGAG-GTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTG
* * *
26428 TATTGTATAATAATCCTTTAAGAAAAATTATACAATAC-CCGTTAGTGGATTTTAGCAAACTGCA
124 TATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCA
* ** *
26492 CGTACATGA
189 CGTGCGGGG
* * *
26501 TTTAAGAGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATAATTAATTATGA
1 TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATT-AA-ATATAATTAATCATGA
* * * * *
26566 AAT-AGGGTATATGTCAACTTCTTAACCCGCTTATGGCGTCCAAAATTTATAATGATAGTGTATT
64 AATGA-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATT
* ** * *
26630 GTATAATAACCCTATAAGAAAAATTAATGGAATACACCGTCAGTGGAGTTTAGTAGACTGCACGT
128 GTATAATAATCCTATAAGAAAAATT-ATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGT
26695 GCGGGG
192 GCGGGG
* * *
26701 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGCATTAATATTAAATATTTAATTAATTATGA
1 TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATA--TAATTAATCATGA
*
26766 AATGTGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACA
64 AATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACA
26823 CGCGCGAGGT
Statistics
Matches: 452, Mismatches: 50, Indels: 29
0.85 0.09 0.05
Matches are distributed among these distances:
194 42 0.09
198 92 0.20
199 14 0.03
200 163 0.36
201 141 0.31
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (197 bp):
TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATAATTAATCATGAAA
TGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTA
TAATAATCCTATAAGAAAAATTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGG
GG
Found at i:26929 original size:127 final size:131
Alignment explanation
Indices: 26708--26941 Score: 379
Period size: 127 Copynumber: 1.8 Consensus size: 131
26698 GGGTTTAAGG
* *
26708 GTTGACATGTGTCCCCTTAGGGAATATGCATTAATATTAAATATTTAATTAATTATGAAATGTGG
1 GTTGACATGTATCCCCTTAGGGAATATGCATTAATATTAAATATTTAAATAATTATGAAATGTGG
*
26773 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACACGCGCGAGGTTTGAA
66 TATGTGTCAACTTCTTAACCCGCTCATGGAGTCCAAAATTTACACTGACACGCGCGAGGTTTGAA
26838 A
131 A
* *
26839 GTTGACATGTATCCCCTTAGGGAATATGCA-T-AT-TT-TATGTTTAAATAATTATGAAATAG-G
1 GTTGACATGTATCCCCTTAGGGAATATGCATTAATATTAAATATTTAAATAATTATGAAAT-GTG
26899 GTATGTGTCAACTTCTTAACCCGCTCATGGAGTCCAAAATTTA
65 GTATGTGTCAACTTCTTAACCCGCTCATGGAGTCCAAAATTTA
26942 TAATGATAGT
Statistics
Matches: 97, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
127 62 0.64
128 3 0.03
129 2 0.02
130 1 0.01
131 29 0.30
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (131 bp):
GTTGACATGTATCCCCTTAGGGAATATGCATTAATATTAAATATTTAAATAATTATGAAATGTGG
TATGTGTCAACTTCTTAACCCGCTCATGGAGTCCAAAATTTACACTGACACGCGCGAGGTTTGAA
A
Found at i:27537 original size:16 final size:16
Alignment explanation
Indices: 27512--27542 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27502 ATTATAAATT
27512 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
27528 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
27543 TATTTTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:37571 original size:18 final size:19
Alignment explanation
Indices: 37537--37577 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
37527 ACGAGAAAAA
37537 AAAATTCTCACAAATTT-C
1 AAAATTCTCACAAATTTAC
*
37555 AAAATTC-CGACATATTTAC
1 AAAATTCTC-ACAAATTTAC
37574 AAAA
1 AAAA
37578 CCAAGTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.70
19 5 0.25
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATTCTCACAAATTTAC
Found at i:39802 original size:156 final size:155
Alignment explanation
Indices: 39493--39858 Score: 375
Period size: 156 Copynumber: 2.3 Consensus size: 155
39483 CCGAACCTCT
* *
39493 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTGAATGAGCTGA
1 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACGAGCTG-
* * * * *
39558 AACTTTACCAAGGGACTTACATTATCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACCGAGC
65 AACTTTACCAAGAGAATTACATTATCCCCATGAGACTATGGAAAAAATTCTAAGTAAAACCAAAC
* * * *
39623 TCCCCTTGATGGTGAACTAGGTTTCT
130 TCCCCTAGATAGAGAACTAGGTTTCA
* *** *
39649 CTCC-CTAGGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAGGCT
1 CACCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACGA-GCT
* * *
39712 G-A-TTTTCCACCAGTAGAATTAGATTATCCCCATGA-AGCTATGGGAAAAATTCTAAGTAAAAC
64 GAACTTTACCA--AG-AGAATTACATTATCCCCATGAGA-CTATGGAAAAAATTCTAAGTAAAAC
* * * *
39774 CAAACT-CTCTAGCATAGAGAAGTTGGTTTGA
125 CAAACTCCCCTAG-ATAGAGAACTAGGTTTCA
* * * *
39805 CACCTCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCATACAAAGTCT
1 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCT
39859 GTTTGAGATG
Statistics
Matches: 170, Mismatches: 31, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
153 6 0.04
154 1 0.01
155 12 0.07
156 150 0.88
157 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (155 bp):
CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACGAGCTGA
ACTTTACCAAGAGAATTACATTATCCCCATGAGACTATGGAAAAAATTCTAAGTAAAACCAAACT
CCCCTAGATAGAGAACTAGGTTTCA
Found at i:46278 original size:136 final size:135
Alignment explanation
Indices: 45985--46346 Score: 553
Period size: 136 Copynumber: 2.7 Consensus size: 135
45975 TGGAGGTGGA
* * * * *** *
45985 ACTTGTTGGTTATTCACCTCATTGTTGACTTGTTGAAGAGGAAGAGGGTCGGGATGGGCACCAAG
1 ACTTGTTGGTTGTTCACCTGATGGTTGACTTGTTGAAGAGGCAGAGCACCGGGCTGGGCACCAAG
* * *
46050 CAGTTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATAAGACCAATCTGAC
66 CAGCTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGCCTTTCATCAATAAGACCAATCTGAC
46115 CCATG
131 CCATG
46120 ACTTGTTGGTTGTTCACCTGATGGTTGACTTGTTGAAGAGGCAGAGCACCGGGCTGGGCACCAAG
1 ACTTGTTGGTTGTTCACCTGATGGTTGACTTGTTGAAGAGGCAGAGCACCGGGCTGGGCACCAAG
* * *
46185 CAGCTATTGGTTTTTCCCCCCGAGTCCTTGCCCCCCCAAGCCTTTCATCAATGAGACCAATCTGA
66 CAGCTGTTGGTTTTGCCCCCCGAGTCCTTG-CCCCCCAAGCCTTTCATCAATAAGACCAATCTGA
46250 CCCATG
130 CCCATG
* * * *
46256 ACTTGTTGGTTGTTCACTTGATGATTGACTTGTTGAAGAGGCAAAGCACCGGGCTGGGCGCCAAG
1 ACTTGTTGGTTGTTCACCTGATGGTTGACTTGTTGAAGAGGCAGAGCACCGGGCTGGGCACCAAG
46321 CAGCTGTTGGTTTTGCCCCCCGAGTC
66 CAGCTGTTGGTTTTGCCCCCCGAGTC
46347 TTTCTTCGAT
Statistics
Matches: 206, Mismatches: 20, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
135 84 0.41
136 122 0.59
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (135 bp):
ACTTGTTGGTTGTTCACCTGATGGTTGACTTGTTGAAGAGGCAGAGCACCGGGCTGGGCACCAAG
CAGCTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGCCTTTCATCAATAAGACCAATCTGAC
CCATG
Found at i:48139 original size:156 final size:155
Alignment explanation
Indices: 47840--48139 Score: 324
Period size: 156 Copynumber: 1.9 Consensus size: 155
47830 TCACCTCAAC
* *
47840 TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTGAATGAGCTGAAACTTTACCA
1 TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACGAGCTG-AACTTTACCA
* * * * *
47905 AGGGACCTAGATTATCTCCATGAGAATATGGAAAAAATTCTAGGTAAAACCGAGCTCCCCTTGAT
65 AGGGACCTAGATTATCCCCATGAGAACATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTAGAT
* * *
47970 GGTGAACTAGGTTTCTCTCCCTAGGT
130 AGAGAAATAGGTTTCTCTCCCTAGGT
* *
47996 TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAGGCTG-A-TTTTCCA
1 TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACGA-GCTGAACTTTACCA
* * ** *
48058 CCAGTAGG-CTTAGATTATCCCCATGA-AGCCATGTTAAAAATTCTAAGTAAAACCGAACT-CTC
65 --AG--GGACCTAGATTATCCCCATGAGA-ACATGGAAAAAATTCTAAGTAAAACCGAACTCCCC
*
48120 TAGTATAGAGAAATTGGTTT
125 TAG-ATAGAGAAATAGGTTT
48140 GACACCTCAA
Statistics
Matches: 119, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
153 6 0.05
154 1 0.01
155 11 0.09
156 99 0.83
157 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (155 bp):
TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACGAGCTGAACTTTACCAA
GGGACCTAGATTATCCCCATGAGAACATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTAGATA
GAGAAATAGGTTTCTCTCCCTAGGT
Found at i:49724 original size:17 final size:17
Alignment explanation
Indices: 49699--49732 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
49689 CACCCTTCTT
49699 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
49716 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
49733 TAGCCGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Found at i:49820 original size:12 final size:12
Alignment explanation
Indices: 49805--49840 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
49795 AGTTATATCG
49805 AAAAATAT-AAA
1 AAAAATATAAAA
49816 AAAAA-ATAAAA
1 AAAAATATAAAA
49827 AAAAATA-AAAA
1 AAAAATATAAAA
49838 AAA
1 AAA
49841 TTTCGACCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.09
11 20 0.87
12 1 0.04
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAAATATAAAA
Found at i:49841 original size:9 final size:10
Alignment explanation
Indices: 49805--49840 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
49795 AGTTATATCG
*
49805 AAAAATATAA
1 AAAAAAATAA
49815 AAAAAAATAA
1 AAAAAAATAA
49825 AAAAAAATAA
1 AAAAAAATAA
49835 AAAAAA
1 AAAAAA
49841 TTTCGACCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:55206 original size:33 final size:33
Alignment explanation
Indices: 55125--55247 Score: 142
Period size: 33 Copynumber: 3.7 Consensus size: 33
55115 CCGCGCAACA
55125 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGT
55160 CCGGCCATC-ACCGGCCACGCGACATGGACATGT
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGT
* ** * *
55193 CCGGCTACAACCGGCCAAACGAC-TCGACCATGC
1 CCGGCCACAACCGGCCACGCGACATGGA-CATGT
*
55226 CCGGCCACAACTGGCCACGCGA
1 CCGGCCACAACCGGCCACGCGA
55248 TCCTTTGTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 4 0.05
33 64 0.84
35 7 0.09
36 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.26, T:0.09
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGT
Found at i:61661 original size:980 final size:980
Alignment explanation
Indices: 59763--61728 Score: 3720
Period size: 980 Copynumber: 2.0 Consensus size: 980
59753 ATCTTTTGGT
*
59763 GTAATGATGGGCTAAATTTACTCCATAAGTGTAATGTAGTTTATTCTTAAGTTTAGTGTATGGTT
1 GTAATGATGGGCTAAATTTACTCCATAAGTGTAATGTAGTTTATTCTTAAGTTTAGTGTATGATT
59828 AAACAAATTTGCTTATTAGTTTAATGATCTTTATATACTTTATCTATTTTATCCTCTGAAGGTTT
66 AAACAAATTTGCTTATTAGTTTAATGATCTTTATATACTTTATCTATTTTATCCTCTGAAGGTTT
59893 TAAAATTTAGATGTGGAAATCAACAATTAAAAAAGAAAGAAAAAGAGAAATTATGCTCTCGTTAA
131 TAAAATTTAGATGTGGAAATCAACAATTAAAAAAGAAAGAAAAAGAGAAATTATGCTCTCGTTAA
59958 TGCTACTATGTACCAACCGATTCTACCTATATTATCCTTTTTATTGTTGTTATAATTTATCGAGT
196 TGCTACTATGTACCAACCGATTCTACCTATATTATCCTTTTTATTGTTGTTATAATTTATCGAGT
*
60023 TTTTGTTCATGTGTTTAACGAAGTCTACATTCTTGCAAATCTCTGTCTAGTCTGGCACGTTCCAA
261 TTTTGTTCATGGGTTTAACGAAGTCTACATTCTTGCAAATCTCTGTCTAGTCTGGCACGTTCCAA
60088 CCAATTTTAATTACCAAACAACTAATAAAAAAAATCAATCATGGTAAGAGATGCATAGATATATA
326 CCAATTTTAATTACCAAACAACTAATAAAAAAAATCAATCATGGTAAGAGATGCATAGATATATA
60153 CCGGTTTGGGTAAGCTAGATCTATCACTATCCTCTTATGCTTTCCCTAGTAAATCTAGGATTATG
391 CCGGTTTGGGTAAGCTAGATCTATCACTATCCTCTTATGCTTTCCCTAGTAAATCTAGGATTATG
60218 CCGATTTTGGATTGTTGCTACATCTTTTTTATTGAGGAAAAATGAGTCCAAAATCATCATCTCCC
456 CCGATTTTGGATTGTTGCTACATCTTTTTTATTGAGGAAAAATGAGTCCAAAATCATCATCTCCC
60283 TACTCTGTCTATATATAATGGTATAACAGAGTATAACTAAAAATATATTAATATATCTTCATAAT
521 TACTCTGTCTATATATAATGGTATAACAGAGTATAACTAAAAATATATTAATATATCTTCATAAT
*
60348 ACTTTTTTTGCGGTTGGACTGGTGGAACATGGTTTCACTCTAACAATCTCATAGTTGTCACTTTT
586 ACTTTTTTTGCGGTTGGACTGGTGGAACATGGTTTCACCCTAACAATCTCATAGTTGTCACTTTT
*
60413 TTTTCGGGTATCTCATTTTACTTAGCTATTAAAAGATTTTTAGAATAGATAAATTATAACCTTGA
651 TTTTCGGGTATCTCATGTTACTTAGCTATTAAAAGATTTTTAGAATAGATAAATTATAACCTTGA
60478 TTGAATCATATTTTTCACCTTAATGTAGGGATAAGGCATTAATCAGATCCTATTTTCATAATCTT
716 TTGAATCATATTTTTCACCTTAATGTAGGGATAAGGCATTAATCAGATCCTATTTTCATAATCTT
60543 AGGATTAAGCCAATGATTCTTTGGATTTGATATTTTATAGCTACTAATTAACGCTAATGTGGAAA
781 AGGATTAAGCCAATGATTCTTTGGATTTGATATTTTATAGCTACTAATTAACGCTAATGTGGAAA
60608 TTCTGTTGTAAGTTTTTAATTATAATGTTTTACTTTAAATTTTATAATTTTGATGGTTATTGCTT
846 TTCTGTTGTAAGTTTTTAATTATAATGTTTTACTTTAAATTTTATAATTTTGATGGTTATTGCTT
*
60673 TATAATCAAGTTAGAGTTTCATAATTATTTTAGTGATCAATTAGTTATGCTTGAAATTCAATTAT
911 TATAATCAAGTTAGAGTTTCATAATTATTTTAGTGATCAATTAGTTATGCTTGAAATTCAAGTAT
60738 ATGAG
976 ATGAG
*
60743 GTAATGATGGGCTAAATTTATTCCATAAGTGTAATGTAGTTTATTCTTAAGTTTAGTGTATGATT
1 GTAATGATGGGCTAAATTTACTCCATAAGTGTAATGTAGTTTATTCTTAAGTTTAGTGTATGATT
60808 AAACAAATTTGCTTATTAGTTTAATGATCTTTATATACTTTATCTATTTTATCCTCTGAAGGTTT
66 AAACAAATTTGCTTATTAGTTTAATGATCTTTATATACTTTATCTATTTTATCCTCTGAAGGTTT
60873 TAAAATTTAGATGTGGAAATCAACAATTAAAAAAGAAAG-AAAAGAGAAATTATGCTCTCGTTAA
131 TAAAATTTAGATGTGGAAATCAACAATTAAAAAAGAAAGAAAAAGAGAAATTATGCTCTCGTTAA
* *
60937 TGCTACTATGTACCGACCGATTCTGCCTATATTATCCTTTTTATTGTTGTTATAATTTATCGAGT
196 TGCTACTATGTACCAACCGATTCTACCTATATTATCCTTTTTATTGTTGTTATAATTTATCGAGT
61002 TTTTGTTCATGGGTTTAACGAAGTCTACATTCTTGCAAATCTCTGTCTAGTCTGGCACGTTCCAA
261 TTTTGTTCATGGGTTTAACGAAGTCTACATTCTTGCAAATCTCTGTCTAGTCTGGCACGTTCCAA
* * * *
61067 CCAATTTTAATTACCAAAGAACTGATAAAAAAAAATCGATCATGGTAAGAGATGCATAGATATGT
326 CCAATTTTAATTACCAAACAACTAAT-AAAAAAAATCAATCATGGTAAGAGATGCATAGATATAT
* *
61132 ACCGGTTTTGGTAAGCTAGATCTATCACTATCCTCTTATGGTTTCCCTAGTAAATCTAGGATTAT
390 ACCGGTTTGGGTAAGCTAGATCTATCACTATCCTCTTATGCTTTCCCTAGTAAATCTAGGATTAT
*
61197 GCCGATTTTGGATTGTTGCTACATCTTTTTTATTGAGGAAAAATGAGTCCAAAATCATCATTTCC
455 GCCGATTTTGGATTGTTGCTACATCTTTTTTATTGAGGAAAAATGAGTCCAAAATCATCATCTCC
61262 CTACTCTGTCTATATATAATGGTATAACAGAGTATAACTAAAAATATATTAATATATCTTCATAA
520 CTACTCTGTCTATATATAATGGTATAACAGAGTATAACTAAAAATATATTAATATATCTTCATAA
*
61327 TACTTTTTTTGCGGTTGGAGTGGTGGAACATGGTTTCACCCTAACAATCTCATAGTTGTCACTTT
585 TACTTTTTTTGCGGTTGGACTGGTGGAACATGGTTTCACCCTAACAATCTCATAGTTGTCACTTT
*
61392 TTTTTCGGGTATCTCATGTTACTTAGCTATTAAAATATTTTTAGAATAGATAAATTATAACCTTG
650 TTTTTCGGGTATCTCATGTTACTTAGCTATTAAAAGATTTTTAGAATAGATAAATTATAACCTTG
* *
61457 ATTGAATCATATTTTTCACCTTAATGTAGGGAT-ATGCTATTAATCATATCCTATTTTCATAATC
715 ATTGAATCATATTTTTCACCTTAATGTAGGGATAAGGC-ATTAATCAGATCCTATTTTCATAATC
*
61521 TTAGGATTAAGCCAATGATTCTTTGGATTTGATATTTTATGGCTACTAATTAACGCTAATGTGGA
779 TTAGGATTAAGCCAATGATTCTTTGGATTTGATATTTTATAGCTACTAATTAACGCTAATGTGGA
61586 AATTCTGTTGTAAGTTTTTAATTATAATGTTTTACTTTAAATTTTATAATTTTGATGGTTATTGC
844 AATTCTGTTGTAAGTTTTTAATTATAATGTTTTACTTTAAATTTTATAATTTTGATGGTTATTGC
61651 TTTATAATCAAGTTAGAGTTTCATAATTATTTTAGTGATCAATTAGTTATGCTTGAAATTCAAGT
909 TTTATAATCAAGTTAGAGTTTCATAATTATTTTAGTGATCAATTAGTTATGCTTGAAATTCAAGT
61716 ATATGAG
974 ATATGAG
61723 GTAATG
1 GTAATG
61729 GTATTTTGAT
Statistics
Matches: 964, Mismatches: 20, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
979 179 0.19
980 785 0.81
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.41
Consensus pattern (980 bp):
GTAATGATGGGCTAAATTTACTCCATAAGTGTAATGTAGTTTATTCTTAAGTTTAGTGTATGATT
AAACAAATTTGCTTATTAGTTTAATGATCTTTATATACTTTATCTATTTTATCCTCTGAAGGTTT
TAAAATTTAGATGTGGAAATCAACAATTAAAAAAGAAAGAAAAAGAGAAATTATGCTCTCGTTAA
TGCTACTATGTACCAACCGATTCTACCTATATTATCCTTTTTATTGTTGTTATAATTTATCGAGT
TTTTGTTCATGGGTTTAACGAAGTCTACATTCTTGCAAATCTCTGTCTAGTCTGGCACGTTCCAA
CCAATTTTAATTACCAAACAACTAATAAAAAAAATCAATCATGGTAAGAGATGCATAGATATATA
CCGGTTTGGGTAAGCTAGATCTATCACTATCCTCTTATGCTTTCCCTAGTAAATCTAGGATTATG
CCGATTTTGGATTGTTGCTACATCTTTTTTATTGAGGAAAAATGAGTCCAAAATCATCATCTCCC
TACTCTGTCTATATATAATGGTATAACAGAGTATAACTAAAAATATATTAATATATCTTCATAAT
ACTTTTTTTGCGGTTGGACTGGTGGAACATGGTTTCACCCTAACAATCTCATAGTTGTCACTTTT
TTTTCGGGTATCTCATGTTACTTAGCTATTAAAAGATTTTTAGAATAGATAAATTATAACCTTGA
TTGAATCATATTTTTCACCTTAATGTAGGGATAAGGCATTAATCAGATCCTATTTTCATAATCTT
AGGATTAAGCCAATGATTCTTTGGATTTGATATTTTATAGCTACTAATTAACGCTAATGTGGAAA
TTCTGTTGTAAGTTTTTAATTATAATGTTTTACTTTAAATTTTATAATTTTGATGGTTATTGCTT
TATAATCAAGTTAGAGTTTCATAATTATTTTAGTGATCAATTAGTTATGCTTGAAATTCAAGTAT
ATGAG
Done.