Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007481.1 Corchorus capsularis cultivar CVL-1 contig07502, 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: 31023
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1188 original size:8 final size:8
Alignment explanation
Indices: 1160--1193 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1150 GAATCGGCTA
1160 TGAATTTT
1 TGAATTTT
*
1168 TGAAGTTTC
1 TGAA-TTTT
1177 TGAATTTT
1 TGAATTTT
1185 TGAATTTT
1 TGAATTTT
1193 T
1 T
1194 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:4853 original size:159 final size:158
Alignment explanation
Indices: 4552--8120 Score: 3482
Period size: 159 Copynumber: 22.6 Consensus size: 158
4542 CAGATGCGGT
* * * * * *
4552 TTTTTTGTGCAACGAGTGCTAAAAAGTCATGTGTCGGAGTGAGATGAACTTATTGGGCAGCCTTG
1 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
* * * * * * *
4617 TGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAAATTTGCACTTTTCT-TCGTAAAACAAC
66 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGT-GCAAAATATC
*
4681 GTTCTTAGCGAAAGGCTCATTCCAGAAGTG
130 GTTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * * * * *
4711 TTTTGTGCGCAACGAGTGCCCAAAAGCCTTGTGTCAGAGTGAGATGAGCATGTTTGACAGCCCTG
1 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
* * * * *
4776 TGCACAAACAATGCTCTCCTCGAACTCCAAAGCCTCAACTTTGCACTTTTGTGTGCACAACATCG
66 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATCG
*
4841 TTCTTAGTGAAAGGCTCATTCCAGAAGCA
131 TTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * * * * * **
4870 TTTATTGCG-AATGGAGTGCTTAAAAGCCTTGTGTCAGAGTGAGTTGAGCTTATTTGACAGCGTT
1 TTTTTTGCGCAA-CGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * * * *
4934 GTCCACAAAGAAAGCTCTCCTCGAAATCCAAAGCCTCAACTTTGCGCATTAGTGTGCAAAATATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
* * * *
4999 GTTTTTAGCACCA--CTCATACCA-AATGCGG
130 GTTCTTAGGA-AAGGCTCATTCCAGAA-GC-G
* * ** *
5028 TTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTATTGGGTAGACCT
1 -TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * *
5093 GTGCACAAACAAAGCTCTCCTCGAAGTTCAATGCCTCAA-------C--TT-TGTGCAAAACATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
5148 GTTCTTAGCGAAAGGCTCATTCCAGAAGCG
130 GTTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * * *
5178 TTTTTTGCGCAACGAGTGCCCAAAAGCCTTGTGTCGGAGTGAGATGAGCATGTTTGACAGCCCTG
1 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
* * * * *
5243 TGCACAAACAATGCTCTCCTCGAACTCCAAAGCCTCAACTTTGCACTTTTGTGTGCACAACATCG
66 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATCG
*
5308 TTCTTAGTG-AAGGCTCATTCCAGAAGCA
131 TTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * * * * *
5336 TTTATTGCG-AATGGAGTGCTTAAAAGCCTTGTGTCGG-GTGAGATGAGCTTATTTGACAACCAT
1 TTTTTTGCGCAA-CGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * *
5399 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCTTCAACTTTGTGCATTTGTGTGCAAAATATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
* ** * * *
5464 GTT-TTAGGCAACACTTA-TACATGATGCGG
130 GTTCTTAGGAAAGGCTCATTCCA-GAAGC-G
* * * * *
5493 TTTTTTTGCGCAACGAGTGCTCAAAAAGTCGTGTGTCGGAGTGAGATTAACTTGTTGGGCAGCCC
1 -TTTTTTGCGCAACGAGTGCTC-AAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCC
* * ** * ** * *
5558 TGCGCACAAACAAAGCTCTCCTCGAACTTTAAAGCCTCAAATTTGCATTTTTTTGTGCAAAACAT
64 TGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATAT
*
5623 CGTTCTTAGCGAAAGGCTCATTCTAGAAGCG
129 CGTTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * *
5654 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTA
1 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
* * *
5719 TGCACAAACAAAGCTCTCCTCGAAGCCCAAAGCCTCAACTTTGCACTTTTGTGTGCAAAACATCG
66 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATCG
5784 TTCTTAGTGAAAGGCTCATTCCAGAAGCG
131 TTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * * * * * *
5813 TTTTTTACGCAAGGAGTGCTCAAAAGCTTTGTGTCGGAGTGAGTTTAGCTTATTTGACAGCCTTG
1 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
* * * * *
5878 TGCACAAAGAAAACTCTCCTCAAAGTTCAAAGCCTCAACTTTGCGCATTTGTGTGCAAAATATCG
66 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATCG
* * * *
5943 TTTTTAGCAACA--CTCATACCAGATGCGG
131 TTCTTAGGAA-AGGCTCATTCCAGAAGC-G
* * * *
5971 TTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTGTTGGGCAGCCCT
1 -TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * * * * * * *
6036 GTACACAATCAAAGATCTCCTCGATGTTCAATGCCTCAACTTTGCGCTTTTCTGTGCAAAACATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
* *
6101 GTTCTTAGCGAAAGGCTCATTCCAAAACCG
130 GTTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * ** * * * *
6131 TTTTTCGTGCAA-GAAGTGCTCAAAATCCTTGTGTCATAGTGAGATGAGCTTATTTGATAGCCAT
1 TTTTTTGCGCAACG-AGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * **
6195 GTGCACAAACACAGCTCTCCTCGAAGTCCGAAGCCTCAACTTTGCGAATTTGTGTGCAAAATATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
* * * * * *
6260 GTTTTTAGCAACA--CTCATACCGGATGTGG
130 GTTCTTAGGAA-AGGCTCATTCCAGAAG-CG
* * ** * *
6289 TTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAACGAGATGAACTTGTTGGGCAGCCCT
1 -TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * * * * *
6354 ATGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAAATTTGCACTTTTTTGTGCAAAATATT
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
*
6419 GTCCTTAGCGAAAGGCTCATTCCAGAAGCG
130 GTTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * **
6449 TTTTTTGCACAAGGAGTGCTCAAAAGCCTTGTGCCGGAGTGAGATGAACTTATTTTACAGCCCTG
1 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
* * * ** *
6514 TGCACAAAGAAAGCTCTCCTCGAAGTCCAAATCCTCAACTTTGCGCATTTGTAAGCAAAATATCA
66 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATCG
* * * * *
6579 TTTTTAGCAACA--CTGATAT-CAGATGCT
131 TTCTTAGGAA-AGGCTCAT-TCCAGAAGCG
* * * * * *
6606 TCTTTTTGTGCAACGATTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCT
1 T-TTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * * * * *
6671 GGGCACAAACAAATCTCTCTTCGAAGTCCAAAGCCTAAACTTTGCGCGTTTGTGTGCAAATTATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
* * * *
6736 GTTTTTAGCAACA--CTCATACCAGATGCGG
130 GTTCTTAGGAA-AGGCTCATTCCAGAAGC-G
* * * * *
6765 TTTTTTTGCGCAACGAGTGCTCAAAAAGTCGTGTGTCGGAGTGAGATTAACTTGTTGGGCAGCCC
1 -TTTTTTGCGCAACGAGTGCTC-AAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCC
* ** * * * *
6830 TGCGCACAAACAAAGCTCTCCTCGAAGTTTAAAGCCTCAAATTTGCGTTTTTTTTGTGCAAAACA
64 TGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCG-CTTTTGTGTGCAAAATA
6895 TCGTTCTTAGCGAAAGGCTCATTCCAGAAGCG
128 TCGTTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * * * * *
6927 TTTTTTGCGCAAGGAGTGCTCAAAAGCTTTGTGTCGGTGTGAGTTGAGCTTATTTGACAGCCTTG
1 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
* * * *
6992 TGCACAAAGAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCATTTGTGGGCAAAATATCG
66 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATCG
* * * *
7057 TTTTTAGCAACA--CTCATACCAGATGCAG
131 TTCTTAGGAA-AGGCTCATTCCAGAAGC-G
* * * *
7085 TTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTGTTGGGCAGCCCT
1 -TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * * * * * * * * *
7150 GTACACAATCAAAGATCTCCTCGATGTTCTATGCCTCAACTCTGCGCTTTTCTGTGCAAAACATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
* *
7215 GTTCTTAGCGAAAGGCTCATTCCAAAACCG
130 GTTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * ** * * * *
7245 TTTTTCGCGCAA-GAAGTGCTCAAAATCCTTGTGTCATAGTGAGATGAGCTTATTTGATAGCCAT
1 TTTTTTGCGCAACG-AGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* ** *
7309 GTGCACAAACAAAGCTCTCCTCGAAGTCCGAAGCCTCAACTTTGCGAATTTGTGTGAAAAATATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
* * * * * * *
7374 GTTTTTAGCAACA--CCCATACCGGATGTGG
130 GTTCTTAGGAA-AGGCTCATTCCAGAAG-CG
* * * * * *
7403 TTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGCGAGATTAACTTGTTGGGCAGCCCT
1 -TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * * * * *
7468 GTGGACAAAAAAAGCTCTCCTCGAAGTTCAAAGCCTCAAATTTGCGCTTTTTTGTGCAAAACATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
7533 GTTCTTAGCGAAAGGCTCATTCCAGAAGCG
130 GTTCTTAG-GAAAGGCTCATTCCAGAAGCG
* * * ** *
7563 TTTTTTGTGCAAGGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGATCTTATTTTACAACCCTG
1 TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
* * *
7628 TGCACAAACAAAGCTCTCCTCGATGTCCAAATCCTCAACTTTGCGCATTTT-TGAGCAAAATATC
66 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGC-TTTTGTGTGCAAAATATC
* * * *
7692 GTTTTTAGCAACA--CTAATAT-CAGATGCG
130 GTTCTTAGGAA-AGGCTCAT-TCCAGAAGCG
* * * * * *
7720 TTTTTTTGTGCAACGATTGCTCAAAAGTCGTGTGTCGGAGTGAGATGATCTTGTTGGACAGCCCT
1 -TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
* * *
7785 GTGCACAAAGAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTGCAAATTATC
65 GTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATC
* * * *
7850 GTTTTTAGCAACA--CTCATACCAGATGCG
130 GTTCTTAGGAA-AGGCTCATTCCAGAAGCG
* * * *
7878 TTTTTTTGCACAACGAGTGCTCAAAAG-TTGTGTGTCGCAGTGAGATGAACTTATTGGGCAGCCC
1 -TTTTTTGCGCAACGAGTGCTCAAAAGCCT-TGTGTCGGAGTGAGATGAACTTATTGGACAGCCC
* * *
7942 TATGCACAAACAAAGCTCTCCTC---G----AAG--TCAACTTTGCGCATTTGTGTGCAAATTAT
64 TGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATAT
* * * *
7998 CGTTTTTAGCAACA--CTCATACCAGATGCAG
129 CGTTCTTAGGAA-AGGCTCATTCCAGAAGC-G
* * *
8028 TTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTATTGGGCAGCCCT
1 -TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCT
*
8093 GTGCACAAACAAAGCTTTCCTCGAAGTC
65 GTGCACAAACAAAGCTCTCCTCGAAGTC
8121 TCCTCTTGTT
Statistics
Matches: 2800, Mismatches: 525, Indels: 174
0.80 0.15 0.05
Matches are distributed among these distances:
149 166 0.06
150 84 0.03
151 13 0.00
152 3 0.00
153 1 0.00
155 5 0.00
156 16 0.01
157 158 0.06
158 429 0.15
159 1541 0.55
160 271 0.10
161 86 0.03
162 13 0.00
163 14 0.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (158 bp):
TTTTTTGCGCAACGAGTGCTCAAAAGCCTTGTGTCGGAGTGAGATGAACTTATTGGACAGCCCTG
TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCTTTTGTGTGCAAAATATCG
TTCTTAGGAAAGGCTCATTCCAGAAGCG
Found at i:6151 original size:477 final size:476
Alignment explanation
Indices: 4540--8120 Score: 4000
Period size: 477 Copynumber: 7.6 Consensus size: 476
4530 TTGGCGCATC
* * *
4540 ACCAGATGCGGTTTTTTTGTGCAACGAGTGCTAAAAAGTCATGTGTCGGAGTGAGATGAACTTAT
1 ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTAT
* * * *
4605 TGGGCAGCCTTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAAATTTGCACTTTTCT-
66 TGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTGTG
* * * * *
4669 TCGTAAAACAACGTTCTTAGCGAAAGGCTCATTCCAGAAGTGTTTTGTGCGCAACGAGTGCCCAA
131 T-GCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAGAAGCGTTTTTTGCGCAACGAGTGCTCAA
* * * *
4734 AAGCCTTGTGTCAGAGTGAGATGAGCATGTTTGACAGCCCTGTGCACAAACAATGCTCTCCTCGA
195 AAGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCTCGA
* *
4799 ACTCCAAAGCCTCAACTTTGCACTTTTGTGTGCACAACATCGTTCTTAGTGAAAGGCTCATTCCA
260 AGTCCAAAGCCTCAACTTTGCACTTTTGTGTGCAAAACATCGTTCTTAG-GAAAGGCTCATTCCA
* * * * * *
4864 GAAGCATTTATTGCG-AATGGAGTGCTTAAAAGCCTTGTGTCAGAGTGAGTTGAGCTTATTTGAC
324 GAAGCGTTTTTTGCGCAA-GGAGTGCTCAAAAGCTTTGTGTCGGAGTGAGATGAGCTTATTTGAC
** * * * *
4928 AGCGTTGTCCACAAAGAAAGCTCTCCTCGAAATCCAAAGCCTCAACTTTGCGCATTAGTGTGCAA
388 AGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTGCAA
*
4993 AATATCGTTTTTAGCACCACTCAT
453 AATATCGTTTTTAGCAACACTCAT
*
5017 ACCAAATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTAT
1 ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTAT
* * *
5082 TGGGTAGACCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAATGCCTCAA-------C--TT-TG
66 TGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTGTG
*
5137 TGCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAGAAGCGTTTTTTGCGCAACGAGTGCCCAAA
131 TGCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAGAAGCGTTTTTTGCGCAACGAGTGCTCAAA
* * *
5202 AGCCTTGTGTCGGAGTGAGATGAGCATGTTTGACAGCCCTGTGCACAAACAATGCTCTCCTCGAA
196 AGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCTCGAA
* *
5267 CTCCAAAGCCTCAACTTTGCACTTTTGTGTGCACAACATCGTTCTTAGTG-AAGGCTCATTCCAG
261 GTCCAAAGCCTCAACTTTGCACTTTTGTGTGCAAAACATCGTTCTTAG-GAAAGGCTCATTCCAG
* * * *
5331 AAGCATTTATTGCG-AATGGAGTGCTTAAAAGCCTTGTGTCGG-GTGAGATGAGCTTATTTGACA
325 AAGCGTTTTTTGCGCAA-GGAGTGCTCAAAAGCTTTGTGTCGGAGTGAGATGAGCTTATTTGACA
* * * *
5394 ACCATGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCTTCAACTTTGTGCATTTGTGTGCAAA
389 GCCCTGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTGCAAA
*
5459 ATATCG-TTTTAGGCAACACTTAT
454 ATATCGTTTTTA-GCAACACTCAT
*
5482 A-CATGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAAGTCGTGTGTCGGAGTGAGATTAACTT
1 ACCA-GATGCGGTTTTTTTGCGCAACGAGTGCTC-AAAAGTCGTGTGTCGGAGTGAGATGAACTT
* * * * * ** *
5546 GTTGGGCAGCCCTGCGCACAAACAAAGCTCTCCTCGAACTTTAAAGCCTCAAATTTGCATTTTTT
64 ATTGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTG
*
5611 TGTGCAAAACATCGTTCTTAGCGAAAGGCTCATTCTAGAAGCGTTTTTTGCGCAACGAGTGCTCA
129 TGTGCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAGAAGCGTTTTTTGCGCAACGAGTGCTCA
*
5676 AAAGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTATGCACAAACAAAGCTCTCCTCG
194 AAAGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCTCG
*
5741 AAGCCCAAAGCCTCAACTTTGCACTTTTGTGTGCAAAACATCGTTCTTAGTGAAAGGCTCATTCC
259 AAGTCCAAAGCCTCAACTTTGCACTTTTGTGTGCAAAACATCGTTCTTAG-GAAAGGCTCATTCC
* * *
5806 AGAAGCGTTTTTTACGCAAGGAGTGCTCAAAAGCTTTGTGTCGGAGTGAGTTTAGCTTATTTGAC
323 AGAAGCGTTTTTTGCGCAAGGAGTGCTCAAAAGCTTTGTGTCGGAGTGAGATGAGCTTATTTGAC
* * * * *
5871 AGCCTTGTGCACAAAGAAAACTCTCCTCAAAGTTCAAAGCCTCAACTTTGCGCATTTGTGTGCAA
388 AGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTGCAA
5936 AATATCGTTTTTAGCAACACTCAT
453 AATATCGTTTTTAGCAACACTCAT
*
5960 ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTGT
1 ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTAT
* * * * * *
6025 TGGGCAGCCCTGTACACAATCAAAGATCTCCTCGATGTTCAATGCCTCAACTTTGCGCTTTTCTG
66 TGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTGTG
* * * *
6090 TGCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAAAACCGTTTTTCGTGCAA-GAAGTGCTCAA
131 TGCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAGAAGCGTTTTTTGCGCAACG-AGTGCTCAA
* ** * * *
6154 AATCCTTGTGTCATAGTGAGATGAGCTTATTTGATAGCCATGTGCACAAACACAGCTCTCCTCGA
195 AAGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCTCGA
* * * * * *
6219 AGTCCGAAGCCTCAACTTTGCGA-ATTTGTGTGCAAAATATCGTTTTTAGCAACA--CTCATACC
260 AGTCCAAAGCCTCAACTTTGC-ACTTTTGTGTGCAAAACATCGTTCTTAGGAA-AGGCTCATTCC
* * * * * ** * * *
6281 GGATGTGGTTTTTTTGCGCAACGAGTGCTCAAAAG-TCGTGTGTCGGAACGAGATGAACTTGTTG
323 AGAAG-CG-TTTTTTGCGCAAGGAGTGCTCAAAAGCT-TTGTGTCGGAGTGAGATGAGCTTATTT
* * * * * * *
6345 GGCAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAAATTTGCACTTTTTTGTG
385 GACAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTG
* **
6410 CAAAATATTGTCCTTAGCGAA-AGGCTCAT
450 CAAAATATCGTTTTTAGC-AACA--CTCAT
* * * * * * *
6439 TCCAGAAGC-G-TTTTTTGCACAAGGAGTGCTCAAAAGCCTTGTGCCGGAGTGAGATGAACTTAT
1 ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTAT
*** * * * * *
6502 TTTACAGCCCTGTGCACAAAGAAAGCTCTCCTCGAAGTCCAAATCCTCAACTTTGCGCATTTGTA
66 TGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTGTG
* * * * * * * * *
6567 AGCAAAATATCATTTTTAGC-AACA--CTGATAT-CAGATGCTTCTTTTTGTGCAACGATTGCTC
131 TGCAAAACATCGTTCTTAGCGAA-AGGCTCAT-TCCAGAAGCGT-TTTTTGCGCAACGAGTGCTC
* * * * * * *
6628 AAAAGTCGTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGGGCACAAACAAATCTCTCTTC
193 AAAAGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCTC
* * * ** * * *
6693 GAAGTCCAAAGCCTAAACTTTGCGCGTTTGTGTGCAAATTATCGTTTTTAGCAACA--CTCATAC
258 GAAGTCCAAAGCCTCAACTTTGCACTTTTGTGTGCAAAACATCGTTCTTAGGAA-AGGCTCATTC
* * * * * *
6756 CAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAAG-TCGTGTGTCGGAGTGAGATTAACTTGT
322 CAGAAGC-G-TTTTTTGCGCAAGGAGTGCTC-AAAAGCT-TTGTGTCGGAGTGAGATGAGCTTAT
* * * ** * ** *
6820 TGGGCAGCCCTGCGCACAAACAAAGCTCTCCTCGAAGTTTAAAGCCTCAAATTTGCGTTTTTTTT
383 TTGACAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCG-CATTTGT
* *
6885 GTGCAAAACATCGTTCTTAGCGAA-AGGCTCAT
447 GTGCAAAATATCGTTTTTAGC-AACA--CTCAT
* * * * * * *
6917 TCCAGAAGC-G-TTTTTTGCGCAAGGAGTGCTCAAAAG-CTTTGTGTCGGTGTGAGTTGAGCTTA
1 ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTC-GTGTGTCGGAGTGAGATGAACTTA
* * * * *
6979 TTTGACAGCCTTGTGCACAAAGAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCATTTGT
65 TTGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTGT
* * * * *
7044 GGGCAAAATATCGTTTTTAGC-AACA--CTCATACCAGATGCAGTTTTTTTGCGCAACGAGTGCT
130 GTGCAAAACATCGTTCTTAGCGAA-AGGCTCATTCCAGAAGC-G-TTTTTTGCGCAACGAGTGCT
* * * * * * * * *
7106 CAAAAGTCGTGTGTCGGAGTGAGATGAACTTGTTGGGCAGCCCTGTACACAATCAAAGATCTCCT
192 CAAAAGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCT
* * * * * * *
7171 CGATGTTCTATGCCTCAACTCTGCGCTTTTCTGTGCAAAACATCGTTCTTAGCGAAAGGCTCATT
257 CGAAGTCCAAAGCCTCAACTTTGCACTTTTGTGTGCAAAACATCGTTCTTAG-GAAAGGCTCATT
* * * * * * **
7236 CCAAAACCGTTTTTCGCGCAAGAAGTGCTCAAAATCCTTGTGTCATAGTGAGATGAGCTTATTTG
321 CCAGAAGCGTTTTTTGCGCAAGGAGTGCTCAAAAGCTTTGTGTCGGAGTGAGATGAGCTTATTTG
* * * * *
7301 ATAGCCATGTGCACAAACAAAGCTCTCCTCGAAGTCCGAAGCCTCAACTTTGCGAATTTGTGTGA
386 ACAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTGC
*
7366 AAAATATCGTTTTTAGCAACACCCAT
451 AAAATATCGTTTTTAGCAACACTCAT
* * * * *
7392 ACCGGATGTGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGCGAGATTAACTTGT
1 ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTAT
* * * *
7457 TGGGCAGCCCTGTGGACAAAAAAAGCTCTCCTCGAAGTTCAAAGCCTCAAATTTGCGCTTTTTTG
66 TGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTGTG
* *
7522 TGCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAGAAGCGTTTTTTGTGCAAGGAGTGCTCAAA
131 TGCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAGAAGCGTTTTTTGCGCAACGAGTGCTCAAA
* * * *
7587 AGCCTTGTGTCGGAGTGAGATGATCTTATTTTACAACCCTGTGCACAAACAAAGCTCTCCTCGAT
196 AGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCTCGAA
* * * * * * *
7652 GTCCAAATCCTCAACTTTGCGCATTTT-TGAGCAAAATATCGTTTTTAGCAACA--CTAATAT-C
261 GTCCAAAGCCTCAACTTTGCAC-TTTTGTGTGCAAAACATCGTTCTTAGGAA-AGGCTCAT-TCC
* * * * * * * *
7713 AGATGCGTTTTTTTGTGCAACGATTGCTCAAAAG-TCGTGTGTCGGAGTGAGATGATCTTGTTGG
323 AGAAGCG-TTTTTTGCGCAAGGAGTGCTCAAAAGCT-TTGTGTCGGAGTGAGATGAGCTTATTTG
*
7777 ACAGCCCTGTGCACAAAGAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTGC
386 ACAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTGC
*
7842 AAATTATCGTTTTTAGCAACACTCAT
451 AAAATATCGTTTTTAGCAACACTCAT
* * *
7868 ACCAGATGC-GTTTTTTTGCACAACGAGTGCTCAAAAGTTGTGTGTCGCAGTGAGATGAACTTAT
1 ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTAT
* *
7932 TGGGCAGCCCTATGCACAAACAAAGCTCTCCTC---G----AAG--TCAACTTTGCGCATTTGTG
66 TGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTGTG
** * * *
7988 TGCAAATTATCGTTTTTAGC-AACA--CTCATACCAGATGCAGTTTTTTTGCGCAACGAGTGCTC
131 TGCAAAACATCGTTCTTAGCGAA-AGGCTCATTCCAGAAGC-G-TTTTTTGCGCAACGAGTGCTC
* * * * * *
8050 AAAAGTCGTGTGTCGGAGTGAGATGAACTTATTGGGCAGCCCTGTGCACAAACAAAGCTTTCCTC
193 AAAAGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCTC
8115 GAAGTC
258 GAAGTC
8121 TCCTCTTGTT
Statistics
Matches: 2692, Mismatches: 353, Indels: 129
0.85 0.11 0.04
Matches are distributed among these distances:
464 19 0.01
465 123 0.05
466 244 0.09
467 175 0.07
468 6 0.00
470 1 0.00
472 1 0.00
475 118 0.04
476 472 0.18
477 963 0.36
478 391 0.15
479 165 0.06
480 4 0.00
481 10 0.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (476 bp):
ACCAGATGCGGTTTTTTTGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTAT
TGGGCAGCCCTGTGCACAAACAAAGCTCTCCTCGAAGTTCAAAGCCTCAACTTTGCGCTTTTGTG
TGCAAAACATCGTTCTTAGCGAAAGGCTCATTCCAGAAGCGTTTTTTGCGCAACGAGTGCTCAAA
AGCCTTGTGTCGGAGTGAGATGAGCTTATTTGACAGCCCTGTGCACAAACAAAGCTCTCCTCGAA
GTCCAAAGCCTCAACTTTGCACTTTTGTGTGCAAAACATCGTTCTTAGGAAAGGCTCATTCCAGA
AGCGTTTTTTGCGCAAGGAGTGCTCAAAAGCTTTGTGTCGGAGTGAGATGAGCTTATTTGACAGC
CCTGTGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCCTCAACTTTGCGCATTTGTGTGCAAAAT
ATCGTTTTTAGCAACACTCAT
Found at i:8072 original size:150 final size:149
Alignment explanation
Indices: 7820--8120 Score: 548
Period size: 150 Copynumber: 2.0 Consensus size: 149
7810 GTCCAAAGCC
7820 TCAACTTTGCGCATTTGTGTGCAAATTATCGTTTTTAGCAACACTCATACCAGATGCGTTTTTTT
1 TCAACTTTGCGCATTTGTGTGCAAATTATCGTTTTTAGCAACACTCATACCAGATGCGTTTTTTT
*
7885 GCACAACGAGTGCTCAAAAGTTGTGTGTCGCAGTGAGATGAACTTATTGGGCAGCCCTATGCACA
66 GCACAACGAGTGCTCAAAAGTCGTGTGTCGCAGTGAGATGAACTTATTGGGCAGCCCTATGCACA
7950 AACAAAGCTCTCCTCGAAG
131 AACAAAGCTCTCCTCGAAG
7969 TCAACTTTGCGCATTTGTGTGCAAATTATCGTTTTTAGCAACACTCATACCAGATGCAGTTTTTT
1 TCAACTTTGCGCATTTGTGTGCAAATTATCGTTTTTAGCAACACTCATACCAGATGC-GTTTTTT
* * *
8034 TGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAGTGAGATGAACTTATTGGGCAGCCCTGTGCAC
65 TGCACAACGAGTGCTCAAAAGTCGTGTGTCGCAGTGAGATGAACTTATTGGGCAGCCCTATGCAC
*
8099 AAACAAAGCTTTCCTCGAAG
130 AAACAAAGCTCTCCTCGAAG
8119 TC
1 TC
8121 TCCTCTTGTT
Statistics
Matches: 146, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
149 57 0.39
150 89 0.61
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (149 bp):
TCAACTTTGCGCATTTGTGTGCAAATTATCGTTTTTAGCAACACTCATACCAGATGCGTTTTTTT
GCACAACGAGTGCTCAAAAGTCGTGTGTCGCAGTGAGATGAACTTATTGGGCAGCCCTATGCACA
AACAAAGCTCTCCTCGAAG
Found at i:10658 original size:49 final size:49
Alignment explanation
Indices: 10584--10681 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
10574 GACCATGATA
10584 AGCCCTTGGCGCATCAGCCCCTCATGTTTATAAGTTTTTTTTGGGGTTT
1 AGCCCTTGGCGCATCAGCCCCTCATGTTTATAAGTTTTTTTTGGGGTTT
* * *
10633 AGCCCTTGGCGCATCAGCCCTTCATGTTTATAATTTTTTTTTTGGGTTT
1 AGCCCTTGGCGCATCAGCCCCTCATGTTTATAAGTTTTTTTTGGGGTTT
10682 TGTGTAGCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.44
Consensus pattern (49 bp):
AGCCCTTGGCGCATCAGCCCCTCATGTTTATAAGTTTTTTTTGGGGTTT
Found at i:11022 original size:40 final size:40
Alignment explanation
Indices: 10959--11040 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
10949 CTAACAACTC
*
10959 GGGTGTTTTAAAAGTTTAAGTTAATTTATTGTTTATTTAT
1 GGGTGTTTTAAAAGTGTAAGTTAATTTATTGTTTATTTAT
* *
10999 GGGTGTTTTGAAAGTGTATGTTAATTTATTGTTTATTTAT
1 GGGTGTTTTAAAAGTGTAAGTTAATTTATTGTTTATTTAT
11039 GG
1 GG
11041 TAAGTGATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (40 bp):
GGGTGTTTTAAAAGTGTAAGTTAATTTATTGTTTATTTAT
Found at i:11888 original size:152 final size:153
Alignment explanation
Indices: 11589--11896 Score: 444
Period size: 152 Copynumber: 2.0 Consensus size: 153
11579 GACTCCATTG
* * *
11589 TGTTCTTCAAGACCGTGATAAGCCCTTGGCGCATCAGCCCTTCATGTTTAAAAGGTTTTTTTTTG
1 TGTTCTTCAAGACCATGATAAACCCTTGGCGCAT-AGCCCTTCATCTTTAAAAGGTTTTTTTTTG
* * * * *
11654 TGTTTAGCCCTTGGCGCATTAGCCCTTCATGTTTATATGTTTTTTTGGGGGGTTTTGTGTAGCGA
65 TGTTTAGCCCATGGCGCATCAACCCTTCATGTTTATAAGTTTTTTTGGGGGGTTTTGTATAGCGA
11719 TGTGACATAAAGTAATGATATATT
130 TGTGACATAAAGTAATGATATATT
**
11743 TGTTCTTCAAGACCATGATAAACCCTT-G-GCAT-GCCCTTCATCTTTATAAGATTTTTTTTTTT
1 TGTTCTTCAAGACCATGATAAACCCTTGGCGCATAGCCCTTCATCTTTA-AA-AGGTTTTTTTTT
* *
11805 TTGGTTTAGCCCATGGCGCATCAACCCTTCATGTTTATAAGTTTTTTT-TGGGGTTTTGTATAGC
64 GT-GTTTAGCCCATGGCGCATCAACCCTTCATGTTTATAAGTTTTTTTGGGGGGTTTTGTATAGC
11869 GATGTGACATAAAGTAATGATATATT
128 GATGTGACATAAAGTAATGATATATT
11895 TG
1 TG
11897 AAAGTTTAAG
Statistics
Matches: 139, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
150 13 0.09
151 2 0.01
152 57 0.41
153 42 0.30
154 25 0.18
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (153 bp):
TGTTCTTCAAGACCATGATAAACCCTTGGCGCATAGCCCTTCATCTTTAAAAGGTTTTTTTTTGT
GTTTAGCCCATGGCGCATCAACCCTTCATGTTTATAAGTTTTTTTGGGGGGTTTTGTATAGCGAT
GTGACATAAAGTAATGATATATT
Found at i:12196 original size:40 final size:40
Alignment explanation
Indices: 12136--12216 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
12126 CTAACAACTC
*
12136 GGGTGTTTTAAAAGTTTAAGTTAATTTATTGTTTATTTAT
1 GGGTGTTTTAAAAGTGTAAGTTAATTTATTGTTTATTTAT
*
12176 GGGTGTTTTGAAAGTGTAAGTTAATTTATTGTTTATTTAT
1 GGGTGTTTTAAAAGTGTAAGTTAATTTATTGTTTATTTAT
12216 G
1 G
12217 ATAAGTGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (40 bp):
GGGTGTTTTAAAAGTGTAAGTTAATTTATTGTTTATTTAT
Found at i:16295 original size:4 final size:4
Alignment explanation
Indices: 16286--16317 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
16276 GAAAATAAGA
16286 AAAC AAAC AAAC AAAC AAAC AAAC AACAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA-AC AAA
16318 AAAAAGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:18269 original size:81 final size:81
Alignment explanation
Indices: 18134--18290 Score: 255
Period size: 81 Copynumber: 1.9 Consensus size: 81
18124 GATTTCTAGT
18134 ACCAATTAATTTCAAGTATTAGTTATATTAAAATTTAAAATCAAAGAAAAATTAAATGTTTAAAA
1 ACCAATTAATTTCAAGTATTAGTTATATTAAAATTTAAAATCAAAGAAAAATTAAATGTTTAAAA
*
18199 TAAAATCTCACTCTGC
66 CAAAATCTCACTCTGC
* *
18215 ACCAATTAATTTCAAGTATTAGATT-TATTAAATTTTAAAATTC-AAGAAAAATTAATTGTTTAA
1 ACCAATTAATTTCAAGTATTAG-TTATATTAAAATTTAAAA-TCAAAGAAAAATTAAATGTTTAA
18278 AACAAAATCTCAC
64 AACAAAATCTCAC
18291 CATGTCAGTA
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
81 67 0.94
82 4 0.06
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.36
Consensus pattern (81 bp):
ACCAATTAATTTCAAGTATTAGTTATATTAAAATTTAAAATCAAAGAAAAATTAAATGTTTAAAA
CAAAATCTCACTCTGC
Found at i:26257 original size:370 final size:370
Alignment explanation
Indices: 25573--26317 Score: 1224
Period size: 370 Copynumber: 2.0 Consensus size: 370
25563 GACAATTAGG
* *
25573 TCTTAGAGTGCGTTTGTTTTGCTTAGTTTCCTGGGAAAGTAATAGGATGGAAACACTCTCCATCA
1 TCTTAGAGTGCGTTTATTTTGCTTACTTTCCTGGGAAAGTAATAGGATGGAAACACTCTCCATCA
* *
25638 TTTGTTTTGATAATCTTAGATGGGAAAATAATTTTAAGGGCACCTTGTAGGGCACCTACTTTCCT
66 TTCGTTTTGATAATCTTAGATGGGAAAATAATTTTAAGGGCACCTTATAGGGCACCTACTTTCCT
* * *
25703 TGCTAGATGGGAGAATACTTTCCCACATGAGGGGTAGGGAAAGTTTTTTCTTACCCATGGTAAGT
131 TGATAGATGGGAGAATACTTTCCCACATGAGGGGTAGGGAAAGTTTTTTCTCACCCATGGAAAGT
* * *
25768 GTAAATTTCATTAAAATTGGATTATTTTCCAAGAAAAATGCTGATAAACCAAACCATTGAAAGTA
196 ATAAATATCATTAAAATTGGATTATTTTCCAAGAAAAATGCTGATAAACCAAACCATTGAAACTA
* *
25833 CTCTCCATGGAATTTAATTGTTACTTTCCCTAGAGTTACTTTCCCTGGAATCACTCTCCCAAGAA
261 CTCTCCATGGAATTTAATTGTTACTTTCCCTAGAGTTACTTTCCCTGAAATCACTCTCCCAAAAA
* *
25898 TCACTCTCCTATGGAGAGTTATTCCATGGAAAGCAACAAACGACC
326 TCACTCTCCTATGGAGAGTTATTCCATGAAAAGCAACAAACCACC
* *
25943 TCTTAGAGTGCGTTTATTTTGCTTACTTTCTTGGGAAAGTAATAGGATGGAAACACTCTCCATCG
1 TCTTAGAGTGCGTTTATTTTGCTTACTTTCCTGGGAAAGTAATAGGATGGAAACACTCTCCATCA
* * *
26008 TTCGTTTTGATAATTTTAGATGGGAAAATAATTTTAAGGGCATCTTATAGGAGCACCTACTTTTC
66 TTCGTTTTGATAATCTTAGATGGGAAAATAATTTTAAGGGCACCTTATAGG-GCACCTACTTTCC
*
26073 TTGATAGATGGGAGAATACTTTTCCCACA-G-GGGGTAGGGAAATTTTTTTCTCACCCATGGAAA
130 TTGATAGATGGGAGAATAC-TTTCCCACATGAGGGGTAGGGAAAGTTTTTTCTCACCCATGGAAA
* * **
26136 GTATAAATATCATTAAAATTGGATTATTTTCTAAGGAAAATGCTGATAAATTAAACCATTGAAAC
194 GTATAAATATCATTAAAATTGGATTATTTTCCAAGAAAAATGCTGATAAACCAAACCATTGAAAC
*
26201 TACTCTCCATGGAATTTAATTGTTACTTTCCCTAGAGTTACTTTCCTTGAAATCACTCTCCCAAA
259 TACTCTCCATGGAATTTAATTGTTACTTTCCCTAGAGTTACTTTCCCTGAAATCACTCTCCCAAA
*
26266 AATCACTCTTCTATGGAGAGTTATTCCATGAAAAGCAACAAACCACC
324 AATCACTCTCCTATGGAGAGTTATTCCATGAAAAGCAACAAACCACC
26313 TCTTA
1 TCTTA
26318 TTTTTCTAAT
Statistics
Matches: 347, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
370 307 0.88
371 31 0.09
372 9 0.03
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (370 bp):
TCTTAGAGTGCGTTTATTTTGCTTACTTTCCTGGGAAAGTAATAGGATGGAAACACTCTCCATCA
TTCGTTTTGATAATCTTAGATGGGAAAATAATTTTAAGGGCACCTTATAGGGCACCTACTTTCCT
TGATAGATGGGAGAATACTTTCCCACATGAGGGGTAGGGAAAGTTTTTTCTCACCCATGGAAAGT
ATAAATATCATTAAAATTGGATTATTTTCCAAGAAAAATGCTGATAAACCAAACCATTGAAACTA
CTCTCCATGGAATTTAATTGTTACTTTCCCTAGAGTTACTTTCCCTGAAATCACTCTCCCAAAAA
TCACTCTCCTATGGAGAGTTATTCCATGAAAAGCAACAAACCACC
Found at i:26959 original size:18 final size:19
Alignment explanation
Indices: 26936--26973 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
26926 GTGCATGGGC
*
26936 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
26954 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
26973 T
1 T
26974 AACTATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:28518 original size:18 final size:19
Alignment explanation
Indices: 28495--28532 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28485 GTGCATGGGC
*
28495 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
28513 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
28532 T
1 T
28533 AACGATGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:30001 original size:30 final size:30
Alignment explanation
Indices: 29960--30022 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
29950 TCTTCAAGGG
*
29960 GGAGGGAATGATGCGCCCAAGG-CTTACCAT
1 GGAGAGAATGATGCG-CCAAGGACTTACCAT
* *
29990 GGAGAGAATGATGCGTCAAGGACTTATCAT
1 GGAGAGAATGATGCGCCAAGGACTTACCAT
30020 GGA
1 GGA
30023 CTTGAAGACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGAGAATGATGCGCCAAGGACTTACCAT
Found at i:30089 original size:18 final size:19
Alignment explanation
Indices: 30066--30103 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
30056 GTGCATGGGC
*
30066 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
30084 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
30103 T
1 T
30104 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Done.