Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015397.1 Corchorus olitorius cultivar O-4 contig15430, 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: 50132
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:728 original size:2 final size:2
Alignment explanation
Indices: 723--763 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
713 TTGCCGTACG
723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
764 TGTCTCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1252 original size:30 final size:30
Alignment explanation
Indices: 1218--1279 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1208 TGACAAAGGA
* *
1218 CATTTGGAGGGG-GGGCAATTTGAATAAAAT
1 CATTT-GAGGGGAGGCCAATTTGAACAAAAT
*
1248 CATTTTAGGGGAGGCCAATTTGAACAAAAT
1 CATTTGAGGGGAGGCCAATTTGAACAAAAT
1278 CA
1 CA
1280 AGACATGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.26
Consensus pattern (30 bp):
CATTTGAGGGGAGGCCAATTTGAACAAAAT
Found at i:1683 original size:21 final size:21
Alignment explanation
Indices: 1654--1693 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1644 GTCATTTGGA
*
1654 TAAAAATTGG-TTAAATTTCT
1 TAAAAATTGGATGAAATTTCT
1674 TAAAATATTGGATGAAATTT
1 TAAAA-ATTGGATGAAATTT
1694 ATCGGAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
TAAAAATTGGATGAAATTTCT
Found at i:2867 original size:11 final size:11
Alignment explanation
Indices: 2824--2861 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2814 TTCCTATATA
*
2824 AAATAAATTAT
1 AAATTAATTAT
2835 CAAA-TAATTAT
1 -AAATTAATTAT
2846 AAATTAATTAT
1 AAATTAATTAT
2857 AAATT
1 AAATT
2862 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:4954 original size:328 final size:323
Alignment explanation
Indices: 4049--5003 Score: 1012
Period size: 331 Copynumber: 2.9 Consensus size: 323
4039 GCCATCCCTA
* * * *
4049 AGTACACGATTTCGGTTAAAATTTTGAAAAAATTGACACGAAATATTTCTCCCCAATTTTGGCCA
1 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTAACA-GAAA-ATTTCTCCTCAATTTTGGCCA
* * * * *
4114 AAATACTCATAAAAAATATATAACTCAACGTCAAAAACATTGAAGGGTTTCTCACGCTTCTAATA
64 CAATACTCAT-AAAAATATATAACTCTACGTCAAAAAGATTGAAGGGCTTCTCACGCTTCTTATA
* * * *
4179 TCATTTTTCCTATTTTCCTTCGAATTAGTTTCCAATTAAATCGAAACCAGATTGAGATGCTCGTA
128 TCA-TTTTCCTATTTT-TTTCGAATTAATTTCTAATTAAATCGAAACCAGATTGAGATTCTCGTA
* * *
4244 AAAAAAATCCTTAAAACCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTC
191 AAAAAAATCCTTAAATCCAATGTGGCTAAGATTTC-TTAGATGAATATAGATATTTCAATGA-AC
* * * * ** * * * * *
4309 TTGGCGCAAAAAATCATGCAAAACTA-AACCGTGGCCTCGGAATGCGTTTTTAGTCAAAAACCGT
254 TTAGAGCCAAAAATCATCCAAAAC-AGAGTCGGGGCCTCAGAACGCGTTTCTAGTAAAAAACCG-
4373 GATGATT
317 GATGATT
* * * * *
4380 AGTATACGATTTTGGCTAAAATTTTGCTAAAATTAACCCGAAAGAATTT-TCCTCAATTTTTGGT
1 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTAA-CAG-AA-AATTTCTCCTCAA-TTTTGGC
* * *
4444 CACAATACTCATAAAAATTTATAATTCAATAC--CAAAAAGATTGAAAGGCTAT-TCACGCTTC-
62 CACAATACTCATAAAAATATATAACTC--TACGTCAAAAAGATTGAAGGGCT-TCTCACGCTTCT
* * * * *
4505 TATTATCTATTTTCCTATCTTTTCCGAATTAATTTCTAATTAAATC-AAAACATGATTCACATTC
124 TA-TATC-ATTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACCA-GATTGAGATTC
* * * **
4569 TTGTAAAAATAAATCCTTTAATCCAATGTGGGTAAGATTTGCTTAGATGGGTATAGATATTTCAA
186 TCGTAAAAA-AAATCCTTAAATCCAATGTGGCTAAGATTT-CTTAGATGAATATAGATATTTCAA
* *
4634 TAGAACTTAGAGCCAAAAATCATTCAAAACAGAGTCGGGGCTTCAGAACGCGTTTCTAGTAAAAA
249 T-GAACTTAGAGCCAAAAATCATCCAAAACAGAGTCGGGGCCTCAGAACGCGTTTCTAGTAAAAA
*
4699 ACC-GATGGTT
313 ACCGGATGATT
* * *
4709 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTTATCAGAGAAATTTCACCTCAACTTTGGGCC
1 AGTACACGATTTCGGCTAAAATTTTGCAAAAA-TTAACAGA-AAATTTCTCCTCAA-TTTTGGCC
* *
4774 ACAATACTAATAAAAATATATAACTCTACGTCAAAAAGATCGAAGGGCTTCTCACGCTTCTTATA
63 ACAATACTCATAAAAATATATAACTCTACGTCAAAAAGATTGAAGGGCTTCTCACGCTTCTTATA
* * *
4839 TCATTTTCCTATTTTTTTCGAATTAATTTCTTATTAAATCGAAACCGGAATGAGATTCTCGTAAA
128 TCATTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACCAGATTGAGATTCTCGTAAA
* * * *
4904 AACAAATCCTTAAATCTAATGTGGCTCAGATTTCATTAGACGAATATAGATACTTCAATG-ACTC
193 AA-AAATCCTTAAATCCAATGTGGCTAAGATTTC-TTAGATGAATATAGATATTTCAATGAACT-
* *
4968 TTGACGCCAAAAATCATGCCAAAA-TGAGTCGGGGCC
255 TAGA-GCCAAAAATCAT-CCAAAACAGAGTCGGGGCC
5004 CTGGAACGTG
Statistics
Matches: 515, Mismatches: 83, Indels: 55
0.79 0.13 0.08
Matches are distributed among these distances:
326 3 0.01
327 8 0.02
328 126 0.24
329 116 0.23
330 44 0.09
331 186 0.36
332 29 0.06
333 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (323 bp):
AGTACACGATTTCGGCTAAAATTTTGCAAAAATTAACAGAAAATTTCTCCTCAATTTTGGCCACA
ATACTCATAAAAATATATAACTCTACGTCAAAAAGATTGAAGGGCTTCTCACGCTTCTTATATCA
TTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACCAGATTGAGATTCTCGTAAAAAA
AATCCTTAAATCCAATGTGGCTAAGATTTCTTAGATGAATATAGATATTTCAATGAACTTAGAGC
CAAAAATCATCCAAAACAGAGTCGGGGCCTCAGAACGCGTTTCTAGTAAAAAACCGGATGATT
Found at i:5156 original size:144 final size:145
Alignment explanation
Indices: 4900--5162 Score: 325
Period size: 144 Copynumber: 1.8 Consensus size: 145
4890 GAGATTCTCG
* * *
4900 TAAAAACAAATCCTTAAATCTAATGTGGCTCAGATTTCATTAGACGAATATAGATACTTCAATGA
1 TAAAAACAAATCCTTAAATCCAATGTGGATCAGATTTCATTAGACGAACATAGATACTTCAATGA
* * * * * *
4965 CTCTTGACGCCAAAAATCATGCCAAAATGAGTCGGGGCCCTGGAACGTGTTTTTAGACGAAACAA
66 CTCTTGACGCCAAAAATCATGACAAAAAGAGCCGGAGCCCCGAAACGTGTTTTTAGACGAAACAA
5030 GGTTCAAATGATCAT
131 GGTTCAAATGATCAT
* * * * *
5045 TAAAAA-AAATCCTTAAATCCAATGTGGATGAGATTTGATTAGATGTACATAGATATTTCAA-GA
1 TAAAAACAAATCCTTAAATCCAATGTGGATCAGATTTCATTAGACGAACATAGATACTTCAATG-
* ** *
5108 AGTCTTGGTGCCAAAAATCAT-ACAAAACAGAGCCTGAGCCCCGAAACGTGTTTTT
65 ACTCTTGACGCCAAAAATCATGACAAAA-AGAGCCGGAGCCCCGAAACGTGTTTTT
5163 TGCCAAAAAC
Statistics
Matches: 98, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
143 6 0.06
144 86 0.88
145 6 0.06
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (145 bp):
TAAAAACAAATCCTTAAATCCAATGTGGATCAGATTTCATTAGACGAACATAGATACTTCAATGA
CTCTTGACGCCAAAAATCATGACAAAAAGAGCCGGAGCCCCGAAACGTGTTTTTAGACGAAACAA
GGTTCAAATGATCAT
Found at i:5822 original size:803 final size:802
Alignment explanation
Indices: 4242--5823 Score: 1958
Period size: 803 Copynumber: 2.0 Consensus size: 802
4232 GAGATGCTCG
* *
4242 TAAAAAAAATCCTTAAAACCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAG
1 TAAAAAAAATCCTTAAAACCAATGTGGATGAGATTTCGTTAGATGAACATAGATATTTCAATGAG
* * * * *
4307 TCTTGGCGCAAAAAATCATGCAAAACTAAACCGTGGCCTCGGAATGCGTTTTTAGTCAAAAACCG
66 TCTTGGCGCAAAAAATCATACAAAACTAAACCGTGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
* * *
4372 TGATGATTAGTATACGATTTTGGCTAAAATTTTGCTAAAATTAACCCGAAAGAATTTTCCTCAAT
131 TGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAAGAATTTTCCTCAAT
* *
4437 TTTTGGTCACAATACTCATAAAAATTTATAATTCAATACCAAAAAGATTGAAAGGCTATTCACGC
196 TTCTGGCCACAATACTCATAAAAATTTATAATTCAATACCAAAAAGATTGAAAGGCTATTCACGC
** *
4502 TTCTATTATCTATTTTCCTATCTTTTCCGAATTAATTTCTAATTAAATCAAAACATGATTCACAT
261 TTAGAATATCTATTTTCCTA-CTTTTCCGAATTAATTTCTAATTAAATCAAAACATGATTCACAT
* ** * * * ** * **
4567 TCTTGTAAAAATAAATCCTTTAATCCAATGTGGGTAAGATTTGCTTAGATGGGTATAGATATTTC
325 GCTCATAAAAACAAATCATTAAATCCAATGTAAGTAAGACTTGCTTAGATGAATATAGATATTTC
* * * * *
4632 AATAGAACTTAGAGCCAAAAATCATTCAAAACAGAGTCGGGGCTTCAGAACGCGTTTCTAGTAAA
390 AATAGAACTTAGAGCCAAAAATCATGCAAAACAGAGCCGGGGCCTCAGAACGCGTTTATAGAAAA
* * * *
4697 AAACCGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTATCAGAGAAATTTCACCT
455 AAACCGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATCTACCAGAAAAATTTCACCT
* *
4762 CAACTTTGGGCCACAATACTAATAAAAATATATAACTCTACGTCAAAAAGATCGAAGGGCTTCTC
520 CAACTTTGGGCCACAATACTAATAAAAATATATAACTCAACGCCAAAAAGATCGAAGGGCTTCTC
* * * *
4827 ACGCTTCTTATATCATTTTCCTATTTTTTTCGAATTAATTTCTTATTAAATCGAAACCGGAATGA
585 ACGCTCCTAATATCATTTTCCTATTTTTTCCAAATTAATTTCTTATTAAATCGAAACCGGAATGA
*
4892 GATTCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTCAGATTTCATTAGACGAATATAGATAC
650 GATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTCAGATTTCATTAGACGAATATAGATAC
** **
4957 TTCAATGACTCTTGACGCCAAAAATCATGCCAAAATGAGTCGGGGCCCTGGAACGTGTTTTTAGA
715 TTCAATGACTCTTGACGAAAAAAATCATGCCAAAATGAGTCGGGGCCCTGGAACACGTTTTTAGA
5022 CGAAACAAGGTTCAAATGATCAT
780 CGAAACAAGGTTCAAATGATCAT
* *
5045 TAAAAAAAATCCTTAAATCCAATGTGGATGAGATTT-GATTAGATGTACATAGATATTTCAA-GA
1 TAAAAAAAATCCTTAAAACCAATGTGGATGAGATTTCG-TTAGATGAACATAGATATTTCAATG-
* * * * *
5108 AGTCTTGGTGCCAAAAATCATACAAAAC-AGAGCC-TGAGCCCCGAAACGTGTTTTTTGCCAAAA
64 AGTCTTGGCGCAAAAAATCATACAAAACTA-AACCGTG-GCCCCGAAACGCGTTTTTAGCCAAAA
* * *
5171 ACCGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGAATTTTCCT
127 ACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAAGAATTTTCCT
* * * * * *
5236 CAATTTCTGGCCATAATACTCATAAAAGATTATCTAATTTAATGCCAAAAAGATTGAAAGGTTTT
192 CAATTTCTGGCCACAATACTCATAAAA-ATT-TATAATTCAATACCAAAAAGATTGAAAGGCTAT
* * * *
5301 TCACGCTTAGAATAT-TGTTTTTCCTA-TTTTCTGAATTAATTTCTAATTAAATCGAAATATGAT
255 TCACGCTTAGAATATCT-ATTTTCCTACTTTTCCGAATTAATTTCTAATTAAATCAAAACATGAT
* * * *
5364 TCAGATGCTCATAAAAGCAAATCATTAAATCCAATGTAAGTGAGACTTGGTTAGATGAATATAGA
319 TCACATGCTCATAAAAACAAATCATTAAATCCAATGTAAGTAAGACTTGCTTAGATGAATATAGA
* * ** *
5429 TATTTCAAT-GAGACTTGGCGTTAAAAATCATGCAAAACAGAGCCGCGGAGCCTGA-AACGCGTT
384 TATTTCAATAGA-ACTTAGAGCCAAAAATCATGCAAAACAGAGCCG-GG-GCCTCAGAACGCGTT
* * *
5492 TATAGGAAAAAAACCATGATGGTTGGTACACG-TTTCAGCTAAAA-TTTGCAAAACTCTACCCGA
446 TATA-GAAAAAAACC--GATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATCTACCAGA
* * * * * * *
5555 AAAATTTCTCAC-CAATTTTTGGCCATAATGCTCATAAAAATATATAACTCAACGCCAAAAAGTT
508 AAAATTTCAC-CTCAACTTTGGGCCACAATACTAATAAAAATATATAACTCAACGCCAAAAAGAT
* *
5619 TGAAGGGCTTCTCACTCTCCTAATATCATTTTTCCT-TTTTTTCCAAATTAATTT-TTAATTAAA
572 CGAAGGGCTTCTCACGCTCCTAATATCA-TTTTCCTATTTTTTCCAAATTAATTTCTT-ATTAAA
* * * * *
5682 TCGAAACCGGATTGAGATGCTCGTAAAAA-AATTCGTTAAAT-TCAATGTGGCTGAGATTTCGTT
635 TCGAAACCGGAATGAGATGCTCGTAAAAACAAATCCTTAAATCT-AATGTGGCTCAGATTTCATT
* * * * * * * *
5745 AGATGAATGTATATATTTCAATGAGTCTTGGCGAAAAAAATTATG-CAAAACTGAGTC-GGG-CA
699 AGACGAATATAGATACTTCAATGACTCTTGACGAAAAAAATCATGCCAAAA-TGAGTCGGGGCCC
5807 TCGGAACACGTTTTTAG
763 T-GGAACACGTTTTTAG
5824 TCAAAAACCG
Statistics
Matches: 660, Mismatches: 100, Indels: 38
0.83 0.13 0.05
Matches are distributed among these distances:
802 9 0.01
803 328 0.50
804 89 0.13
805 201 0.30
806 19 0.03
807 14 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (802 bp):
TAAAAAAAATCCTTAAAACCAATGTGGATGAGATTTCGTTAGATGAACATAGATATTTCAATGAG
TCTTGGCGCAAAAAATCATACAAAACTAAACCGTGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
TGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAAGAATTTTCCTCAAT
TTCTGGCCACAATACTCATAAAAATTTATAATTCAATACCAAAAAGATTGAAAGGCTATTCACGC
TTAGAATATCTATTTTCCTACTTTTCCGAATTAATTTCTAATTAAATCAAAACATGATTCACATG
CTCATAAAAACAAATCATTAAATCCAATGTAAGTAAGACTTGCTTAGATGAATATAGATATTTCA
ATAGAACTTAGAGCCAAAAATCATGCAAAACAGAGCCGGGGCCTCAGAACGCGTTTATAGAAAAA
AACCGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATCTACCAGAAAAATTTCACCTC
AACTTTGGGCCACAATACTAATAAAAATATATAACTCAACGCCAAAAAGATCGAAGGGCTTCTCA
CGCTCCTAATATCATTTTCCTATTTTTTCCAAATTAATTTCTTATTAAATCGAAACCGGAATGAG
ATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTCAGATTTCATTAGACGAATATAGATACT
TCAATGACTCTTGACGAAAAAAATCATGCCAAAATGAGTCGGGGCCCTGGAACACGTTTTTAGAC
GAAACAAGGTTCAAATGATCAT
Found at i:6306 original size:661 final size:657
Alignment explanation
Indices: 5045--7305 Score: 2937
Period size: 661 Copynumber: 3.4 Consensus size: 657
5035 AAATGATCAT
* * * * * *
5045 TAAAAAAAATCCTTAAATCCAATGTGGATGAGATTT-GATTAGATGTACATAGATATTTCAA-GA
1 TAAAAAAATTCCTTAAATTCAATGTGGCTGAGATTTCG-TTAGATGAATATATATATTTCAATG-
* * * * * * * * * * *
5108 AGTCTTGGTGCCAAAAATCATACAAAACAGAGCCTGAGCCCCGAAACGTGTTTTTTGCCAAAAAC
64 AGTCTTGGCGACAAAAATTATGCAAAACTGAGTC-G-GGCTCGGAACGCGTTTTTAGCCAAAAAC
* *
5173 CGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGAATTTTCCTCA
127 CGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGAATTTTCCTCA
* * * * * * *
5238 ATTTCTGGCCATAATACTCATAAAAGATTATCTAATTTAATGCCAAAAAGATTGAAAGGTTTTTC
192 ATTTTTGGCCACAATACTCATAAAA-AATATATAATTCAACG-CAAAAAAATTGAAAGGTTTTTC
** * * *
5303 ACGCTTAGAATATTGTTTTTCCTA--TTTTCTGAATTAATTTCTAATTAAATCGAAATATGATTC
255 ACGCTTTTAATATCGGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTC
* ** *
5366 AGATGCTCATAAAAGCAAATCATTAAATCCAATGTAAGTGAGACTTGGTTAGATGAATATAGATA
320 AGATGCTCGTAAAAGCAAATCATTAAATCCAATGTGGGTGAGATTTGGTTAGATGAATATAGATA
**
5431 TTTCAATGAGACTTGGCGTTAAAAATCATGCAAAACAGAGCCGCGGAGCCTGAAACGCGTTTATA
385 TTTCAATGAGACTTGGCGCAAAAAATCATGCAAAACAGAGCCG-GGAGCCTGAAACGCGTTTATA
* * * *
5496 G-GAAAAAAACCATGATGGTTGGTACACG-TTTCAGCTAAAA-TTTGCAAAACTCTACCCGAAAA
449 GTG-AAAAAA-CGTTATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAA-TTTACCCGAAAA
* * *
5558 ATTTCTCACCAATTTTTGGCCATAATGCTCATAAAAATATATAACTCAACGCCAAAAAGTTTGAA
511 ATTTCTCCCCAATTTTTGGCCACAATGCTCATAAAAATATATAACTCAACGCCAAAATGTTTGAA
* * * *
5623 GGGCTTCTC-ACTCTCCTAATATCATTTTTCCTTTTTTTCCAAATTAATTTTTAATTAAATCGAA
576 GGGCTTCTCAAGT-TTCTAATATCATTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAA
*
5687 ACCGGATTGAGATGCTCG
640 ATCGGATTGAGATGCTCG
* *
5705 TAAAAAAATTCGTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATGTATATATTTCAATGAG
1 TAAAAAAATTCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATATATATTTCAATGAG
* * *
5770 TCTTGGCGAAAAAAATTATGCAAAACTGAGTCGGGCATCGGAACACGTTTTTAGTCAAAAACCGT
66 TCTTGGCGACAAAAATTATGCAAAACTGAGTCGGGC-TCGGAACGCGTTTTTAGCCAAAAACCGT
* *
5835 GATGGTTAGTACATGATTTCGGCTAAAATTTTCCAAAAATTTACCCGAAAGAGTTTTCCTCAATT
130 GATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGAATTTTCCTCAATT
* *
5900 TTTGGCCACGATACTCATAAAAAATATATAATTCAACGCAAAAAACATTGAAATGTTTTTCACGC
195 TTTGGCCACAATACTCATAAAAAATATATAATTCAACGCAAAAAA-ATTGAAAGGTTTTTCACGC
*
5965 TTTTAATATCGGTTTTCCTATTTTTTTCCGAATTAATTTCTAACTAAATCGAAATATGATTCAGA
259 TTTTAATATCGGTTTTCCTA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTCAGA
*
6030 TGCTCGTAAAAGCAAATCATTAAATCCAATGTGGGTGAGATTTGGTTAGATAAATATAGATATTT
323 TGCTCGTAAAAGCAAATCATTAAATCCAATGTGGGTGAGATTTGGTTAGATGAATATAGATATTT
* ** ** *
6095 CAATAAGACTTGGCGCCGAAAATCATGCAAAACAGAGCCGGGCCCCCGAAACGCGTTTATAGTGA
388 CAATGAGACTTGGCGCAAAAAATCATGCAAAACAGAGCCGGGAGCCTGAAACGCGTTTATAGTGA
* * *
6160 AAAAGCGTTATGGTTAGTACACGATTTCGGCTAAAATTTTGCGAAAATTTACCCGAAACATTTCT
453 AAAAACGTTATGGTTAGTACACGATTTCAGCTAAAATTTTGC-AAAATTTACCCGAAAAATTTCT
* * *
6225 CCCCTA-TTTTGGCCACAATACTCATAAAAATTAAATAACTCAACGCCAAAATGTTTGAAGGGCT
517 CCCCAATTTTTGGCCACAATGCTCATAAAAA-TATATAACTCAACGCCAAAATGTTTGAAGGGCT
* * *
6289 TCTCAAGTTTTTAATATCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAATCGGA
581 TCTCAAGTTTCTAATATCATTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAATCGGA
6354 TTGAGATGCTCG
646 TTGAGATGCTCG
* * *
6366 TAAATACAAA-TCCTTAAGTTCAATGCGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATG
1 TAAA-A-AAATTCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATATATATTTCAATG
* * * * *
6430 AGTCTTGGCGTCAAAAATCATACAAAACTGAGTCGGGGTGTCGGAACGCGTTTTTAGCTAAAAAC
64 AGTCTTGGCGACAAAAATTATGCAAAACTGAGTC-GGG-CTCGGAACGCGTTTTTAGCCAAAAAC
* * * * *
6495 TGTGATAGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGGAAGAA-TTTCCTCA
127 CGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGAATTTTCCTCA
* *
6559 ATTTTTGGCCACAATACTCATAAAAAATATATAATTCAATGCCAAAAAAAAATTGAAAGGCTTTT
192 ATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACG-C--AAAAAAATTGAAAGGTTTTT
* *
6624 CACG-TTTCTAATATCGGTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCTAAATATGAT
254 CACGCTTT-TAATATCGGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGAT
* * * * *
6688 TCATATGCTCGTAAAAGCAAATCCTTAAATTCAATATGGGTGAGATTTGGTTAGATGAGTATAGA
318 TCAGATGCTCGTAAAAGCAAATCATTAAATCCAATGTGGGTGAGATTTGGTTAGATGAATATAGA
* * *
6753 TATTTAAATGAGACTTGGCGCAAAAAATCATGCAAAACAGAGCCGGGGGTCTGAAACGCGTTTAT
383 TATTTCAATGAGACTTGGCGCAAAAAATCATGCAAAACAGAGCCGGGAGCCTGAAACGCGTTTAT
* * *
6818 AGTAAAAAAACG-TA--G--CGTACACGATTTCAGCT-AAATTTTGCAAAAATTTACCCAAAAAA
448 AGTGAAAAAACGTTATGGTTAGTACACGATTTCAGCTAAAATTTTGC-AAAATTTACCCGAAAAA
*
6877 TTTCTCCCCAATTTTTGACCACAATGCTCATGAAAAATATATAACTCAACGCCAAAATGTTTGAA
512 TTTCTCCCCAATTTTTGGCCACAATGCTCAT-AAAAATATATAACTCAACGCCAAAATGTTTGAA
* * *
6942 GGGCTTCTCACGCTTCTAATATCA-TTTTCATATTTTTTTCCGAATTAATTTCTAATTAAATCGA
576 GGGCTTCTCAAGTTTCTAATATCATTTTTC--CTTTTTTTCCGAATTAATTTCTAATTAAATCGA
7006 AATCGGATTGAGATGCTCG
639 AATCGGATTGAGATGCTCG
* * * *
7025 TAAAAAAATTCCTTAAATTCAATGTGGTTAATATTTCGTTAGATGAATATATATATTCCAATGAG
1 TAAAAAAATTCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATATATATTTCAATGAG
* * * * *
7090 TCTTGGCGACAAAAATTATGCAAAACTGAGCCGAGTCCCGGAACGCGTTTTTAACCAAAAATCGT
66 TCTTGGCGACAAAAATTATGCAAAACTGAGTCG-GGCTCGGAACGCGTTTTTAGCCAAAAACCGT
* * ** *
7155 AATGGTTAGTACATGATTTCGGCGAAAATTTTGCAAAAATTTACCTTAAAGAATTTTTCTCAATT
130 GATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGAATTTTCCTCAATT
* * ** * * *
7220 TTTAGTCATGATACTCATAAAAAATATATAATTCAACACCAAAAAAATTAAAAGG-TTTTCAC-T
195 TTTGGCCACAATACTCATAAAAAATATATAATTCAAC-GCAAAAAAATTGAAAGGTTTTTCACGC
*
7283 TTTTAATATTGGTTTTCCT-TTTT
259 TTTTAATATCGGTTTTCCTATTTT
7306 ATGTGGGTGA
Statistics
Matches: 1403, Mismatches: 168, Indels: 67
0.86 0.10 0.04
Matches are distributed among these distances:
653 3 0.00
654 15 0.01
655 10 0.01
656 14 0.01
657 117 0.08
658 249 0.18
659 177 0.13
660 136 0.10
661 265 0.19
662 135 0.10
663 243 0.17
664 33 0.02
665 6 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (657 bp):
TAAAAAAATTCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATATATATTTCAATGAG
TCTTGGCGACAAAAATTATGCAAAACTGAGTCGGGCTCGGAACGCGTTTTTAGCCAAAAACCGTG
ATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGAATTTTCCTCAATTT
TTGGCCACAATACTCATAAAAAATATATAATTCAACGCAAAAAAATTGAAAGGTTTTTCACGCTT
TTAATATCGGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTCAGATGC
TCGTAAAAGCAAATCATTAAATCCAATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAA
TGAGACTTGGCGCAAAAAATCATGCAAAACAGAGCCGGGAGCCTGAAACGCGTTTATAGTGAAAA
AACGTTATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAATTTACCCGAAAAATTTCTCCCC
AATTTTTGGCCACAATGCTCATAAAAATATATAACTCAACGCCAAAATGTTTGAAGGGCTTCTCA
AGTTTCTAATATCATTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAATCGGATTGAG
ATGCTCG
Found at i:6439 original size:330 final size:328
Alignment explanation
Indices: 5051--7274 Score: 2285
Period size: 330 Copynumber: 6.7 Consensus size: 328
5041 TCATTAAAAA
* * * *
5051 AAATCCTTAAATCCAATGTGGATGAGATTT-GATTAGATGTACATAGATATTTCAA-GAAGTCTT
1 AAATCCTTAAATTCAATGTGGCTGAGATTTCG-TTAGATGAATATAGATATTTCAATG-AGTCTT
* * * * * *
5114 GGTGCCAAAAATCATACAAAACAGAGCCTGAGCCCCGAAACGTGTTTTTTGCCAAAAACCGTGAT
64 GGCGCCAAAAATCATGCAAAACAGAGCC-GGGCCCCGAAACGCGTTTTTAGTCAAAAACCGTGAT
* * *
5179 GGTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGAATTTTCCTCAATTTCT
128 GGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAA-AATTTTCCCCAATTTTT
* * * * * * *
5244 GGCCATAATACTCATAAAAGATTATCTAATTTAATGCCAAAAAGATTGAAAGGTTTTTCACGCTT
192 GGCCACAATACTCATAAAA-A-TATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTT
** * * *
5309 AGAATATTGTTTTTCCTA-TTTTCTGAATTAATTTCTAATTAAATCGAAATATGATTCAGATGCT
255 CTAATATCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAATAGGATTCAGATGCT
*
5373 CATAAAAGC
320 CGTAAAAGC
* * * * * *
5382 AAATCATTAAATCCAATGTAAG-TGAGACTTGGTTAGATGAATATAGATATTTCAATGAGACTTG
1 AAATCCTTAAATTCAATGT-GGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTG
** * * * ** *
5446 GCGTTAAAAATCATGCAAAACAGAGCCGCGGAGCCTGAAACGCGTTTATAGGAAAAAAACCATGA
65 GCGCCAAAAATCATGCAAAACAGAGCCG-GG-CCCCGAAACGCGTTTTTA-GTCAAAAACCGTGA
* * * * *
5511 TGGTTGGTACACG-TTTCAGCTAAAA-TTTGCAAAACTCTACCCGAAAAATTTCTCACCAATTTT
127 TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAAATTT-TCCCCAATTTT
* * * * * *
5574 TGGCCATAATGCTCATAAAAATATATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCACTCTCC
191 TGGCCACAATACTCATAAAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTTC
* * * * ** *
5639 TAATATCATTTTTCCTTTTTTTCCAAATTAATTTTTAATTAAATCGAAACCGGATTGAGATGCTC
256 TAATATCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAATAGGATTCAGATGCTC
5704 GTAAAA--
321 GTAAAAGC
* * *
5710 AAATTCGTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATGTATATATTTCAATGAGTCTTG
1 AAA-TCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTG
** * * * ** * *
5775 GCGAAAAAAATTATGCAAAACTGAGTCGGGCATCGGAACACGTTTTTAGTCAAAAACCGTGATGG
65 GCGCCAAAAATCATGCAAAACAGAGCCGGGCCCCGAAACGCGTTTTTAGTCAAAAACCGTGATGG
* * * *
5840 TTAGTACATGATTTCGGCTAAAATTTTCCAAAAATTTACCCGAAAGAGTTTTCCTCAATTTTTGG
130 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAA-AATTTTCCCCAATTTTTGG
* * * * * * * *
5905 CCACGATACTCATAAAAAATATATAATTCAACGCAAAAAACATTGAAATGTTTTTCACGCTTTTA
194 CCACAATACTCAT-AAAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTA
* * *
5970 ATATCGGTTTTCCTATTTTTTTCCGAATTAATTTCTAACTAAATCGAAATATGATTCAGATGCTC
258 ATATCGTTTTTCCTA--TTTTTCCGAATTAATTTCTAATTAAATCGAAATAGGATTCAGATGCTC
6035 GTAAAAGC
321 GTAAAAGC
* * * * * * *
6043 AAATCATTAAATCCAATGTGGGTGAGATTTGGTTAGATAAATATAGATATTTCAATAAGACTTGG
1 AAATCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGG
* * * * *
6108 CGCCGAAAATCATGCAAAACAGAGCCGGGCCCCCGAAACGCGTTTATAGTGAAAAAGCGTTATGG
66 CGCCAAAAATCATGCAAAACAGAGCCGGG-CCCCGAAACGCGTTTTTAGTCAAAAACCGTGATGG
* * *
6173 TTAGTACACGATTTCGGCTAAAATTTTGCGAAAATTTACCCGAAACATTTCTCCCCTA-TTTTGG
130 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAAATTT-TCCCCAATTTTTGG
* * * * * * *
6237 CCACAATACTCATAAAAATTAAATAACTCAACGCCAAAATGTTTGAAGGGCTTCTCAAGTTTTTA
194 CCACAATACTCATAAAAA-TATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTA
* *
6302 ATATCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAATCGGATTGAGATGCTCGT
258 ATATCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAATAGGATTCAGATGCTCGT
6367 AAATA-C
323 AAA-AGC
* *
6373 AAATCCTTAAGTTCAATGCGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGG
1 AAATCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGG
* * * * *** * * *
6438 CGTCAAAAATCATACAAAACTGAGTCGGGGTGTCGGAACGCGTTTTTAG-CTAAAAACTGTGATA
66 CGCCAAAAATCATGCAAAACAGAG-CCGGGCCCCGAAACGCGTTTTTAGTC-AAAAACCGTGATG
* * * * *
6502 GTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGGAAGAA-TTTCCTCAATTTTTG
129 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCC-GAAAAATTTTCCCCAATTTTTG
* * * * *
6566 GCCACAATACTCATAAAAAATATATAATTCAATGCCAAAAAAAAATTGAAAGGCTTTTCACGTTT
193 GCCACAATACTCAT-AAAAATATATAACTCAACGCC--AAAAAGATTGAAAGGCTTCTCACGCTT
* * * *
6631 CTAATATCGGTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCTAAATATGATTCATATGC
255 CTAATATCGTTTTTCCT-ATTTTTCCGAATTAATTTCTAATTAAATCGAAATAGGATTCAGATGC
6696 TCGTAAAAGC
319 TCGTAAAAGC
* * * * * *
6706 AAATCCTTAAATTCAATATGGGTGAGATTTGGTTAGATGAGTATAGATATTTAAATGAGACTTGG
1 AAATCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGG
* ** * * * *
6771 CGCAAAAAATCATGCAAAACAGAGCCGGGGGTCTGAAACGCGTTTATAGTAAAAAAACGT-A--G
66 CGCCAAAAATCATGCAAAACAGAGCC-GGGCCCCGAAACGCGTTTTTAGTCAAAAACCGTGATGG
* * * *
6833 --CGTACACGATTTCAGCT-AAATTTTGCAAAAATTTACCCAAAAAATTTCTCCCCAATTTTTGA
130 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAAATTT-TCCCCAATTTTTGG
* * * *
6895 CCACAATGCTCATGAAAAATATATAACTCAACGCCAAAATGTTTGAAGGGCTTCTCACGCTTCTA
194 CCACAATACTCAT-AAAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTA
* * * *
6960 ATATC-ATTTTCATATTTTTTTCCGAATTAATTTCTAATTAAATCGAAATCGGATTGAGATGCTC
258 ATATCGTTTTTCCTA--TTTTTCCGAATTAATTTCTAATTAAATCGAAATAGGATTCAGATGCTC
7024 GTAAAA--
321 GTAAAAGC
* * * * *
7030 AAATTCCTTAAATTCAATGTGGTTAATATTTCGTTAGATGAATATATATATTCCAATGAGTCTTG
1 AAA-TCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTG
* * * * * * ** * *
7095 GCGACAAAAATTATGCAAAACTGAGCCGAGTCCCGGAACGCGTTTTTAACCAAAAATCGTAATGG
65 GCGCCAAAAATCATGCAAAACAGAGCCGGGCCCCGAAACGCGTTTTTAGTCAAAAACCGTGATGG
* * ** * * *
7160 TTAGTACATGATTTCGGCGAAAATTTTGCAAAAATTTACCTTAAAGAATTTTTCTCAATTTTTAG
130 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAA-AATTTTCCCCAATTTTTGG
* ** * * * *
7225 TCATGATACTCATAAAAAATATATAATTCAACACCAAAAAAATTAAAAGG
194 CCACAATACTCAT-AAAAATATATAACTCAACGCCAAAAAGATTGAAAGG
7275 TTTTCACTTT
Statistics
Matches: 1553, Mismatches: 295, Indels: 91
0.80 0.15 0.05
Matches are distributed among these distances:
324 27 0.02
325 81 0.05
326 104 0.07
327 45 0.03
328 104 0.07
329 194 0.12
330 345 0.22
331 193 0.12
332 211 0.14
333 249 0.16
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (328 bp):
AAATCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGG
CGCCAAAAATCATGCAAAACAGAGCCGGGCCCCGAAACGCGTTTTTAGTCAAAAACCGTGATGGT
TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAAATTTTCCCCAATTTTTGGCC
ACAATACTCATAAAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTAATA
TCGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAATAGGATTCAGATGCTCGTAAA
AGC
Found at i:7525 original size:261 final size:260
Alignment explanation
Indices: 7057--7525 Score: 654
Period size: 261 Copynumber: 1.8 Consensus size: 260
7047 TGTGGTTAAT
* * *
7057 ATTTCGTTAGATGAATATATATATTCCAATGAGTCTTGGCGACAAAAATTATGCAAAACTGAGCC
1 ATTTCGTTAGATGAATATAGATATTCCAATGAGTCTTGGCGACAAAAATCATGCAAAACAGAGCC
* * * *
7122 GAGTCCCGGAACGCGTTTTTAACCAAAAATCGTAATGGTTAGTACATGATTTCGGCGAAAATTTT
66 GAGCCCCGGAACGCGTTTATAACCAAAAACCGTAATGGTTAGTACACGATTTCGGCGAAAATTTT
** * * * * * *
7187 GCAAAAATTTACCTTAAAGAATTTTTCTCAATTTTTAGTCATGATACTCATAAAAAATATATAAT
131 GCAAAAATTTACCCGAAAGAATTTTCCCCAATTTTTAGCCATAATACTCATAAAAAATAAATAAC
7252 TCAACACCAAAAAAATTAAAAGGTTTTCACTTTTTAATATTGGTTTTCCTTTTTATGTGGGTGAG
196 TCAACACCAAAAAAATTAAAAGGTTTTCACTTTTTAATATTGGTTTTCCTTTTTATGTGGGTGAG
* * *
7317 ATTTGGTTAGATGAATATAGATATTTCAATGA-TGCTTGGCGCCAAAAATCATGCAAAACAGAGC
1 ATTTCGTTAGATGAATATAGATATTCCAATGAGT-CTTGGCGACAAAAATCATGCAAAACAGAGC
** * *
7381 CGGAGCCCCGGAACGCGTTTATAATGAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATT
65 C-GAGCCCCGGAACGCGTTTATAACCAAAAACCGTAATGGTTAGTACACGATTTCGGCGAAAATT
** * *
7446 TTGTGAAAATTTACCCGAAA-AATTTCTCCCCTATTTTTGGCCATAATACTCATAAAAAATAAAT
129 TTGCAAAAATTTACCCGAAAGAATTT-TCCCCAATTTTTAGCCATAATACTCATAAAAAATAAAT
*
7510 AACTCAACGCCAAAAA
193 AACTCAACACCAAAAA
7526 GTTTGAAGGG
Statistics
Matches: 179, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
259 1 0.01
260 62 0.35
261 116 0.65
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (260 bp):
ATTTCGTTAGATGAATATAGATATTCCAATGAGTCTTGGCGACAAAAATCATGCAAAACAGAGCC
GAGCCCCGGAACGCGTTTATAACCAAAAACCGTAATGGTTAGTACACGATTTCGGCGAAAATTTT
GCAAAAATTTACCCGAAAGAATTTTCCCCAATTTTTAGCCATAATACTCATAAAAAATAAATAAC
TCAACACCAAAAAAATTAAAAGGTTTTCACTTTTTAATATTGGTTTTCCTTTTTATGTGGGTGAG
Found at i:7845 original size:595 final size:586
Alignment explanation
Indices: 6724--7877 Score: 1539
Period size: 595 Copynumber: 2.0 Consensus size: 586
6714 AAATTCAATA
*
6724 TGGGTGAGATTTGGTTAGATGAGTATAGATATTTAAATGAGACTTGGCGCAAAAAATCATGCAAA
1 TGGGTGAGATTTGGTTAGATGAATATAGATATTTAAATGAGACTTGGCGCAAAAAATCATGCAAA
* ** * * *
6789 ACAGAGCCGGGGGTCTGAAACGCGTTTATAGTAAAAAAACGTAGCGTACACGATTTCAGCTAAAT
66 ACAGAGCCGGAGCCCCGAAACGCGTTTATAATAAAAAAACGTAGAGTACACGATTTCAGCTAAAT
* * *
6854 TTTGCAAAAATTTACCCAAAAAATTTCTCCCCAATTTTTGACCACAATGCTCATGAAAAATATAT
131 TTTGCAAAAATTTACCCAAAAAATTTCTCCCCAATTTTTGACCACAATACTCATAAAAAATAAAT
* *
6919 AACTCAACGCCAAAATGTTTGAAGGGCTTCTCACGCTTCTAATATCATTTTCATATTTTTTTCCG
196 AACTCAACGCCAAAAAGTTTGAAGGGCTTCTCAAGCTTCTAATATCATTTTCATATTTTTTTCCG
* * * * *
6984 AATTAATTTCTAATTAAATCGAAATCGGATTGAGATGCTCGTAAAAAAATTCCTTAAATTCAATG
261 AATTAATTTCTAATCAAATCGAAACCAGATTGAAATGCTCATAAAAAAATTCCTTAAATTCAATG
* * * * * *
7049 TGGTTAATATTTCGTTAGATGAATATATATATTCCAATGAGTCTTGGCGACAAAAATTATGCAAA
326 TGGCTAAGATTTCGTTAGATGAATATAGATATTCCAATGAGTCTTGACGACAAAAATCATACAAA
* * * *
7114 ACTGAGCCGAGTCCCGGAACGCGTTTTTAACCAAAAATCGTAATGGTTAGTACATGATTTCGGCG
391 ACTAAGCCGAGTCCCGGAACGCGTTTTTAACCAAAAATCGTAATAGTTAGTACACGATTTCGGCA
* * ** * * *
7179 AAAATTTTGCAAAAATTTACCTTAAAGAATTTTTCTCAATTTTTAGTCATGATACTCATAAAAAA
456 AAAATTTTACAAAAATTGACCCGAAAGAATTTTCCTCAATTTTTAGCCACGATACTCATAAAAAA
7244 TATATAATTCAACACCAAAAAAATTAAAAGG-TTTTCACTTTTTAATATTGGTTTTCCTTTTTAT
521 TATATAATTCAACACCAAAAAAATTAAAAGGCTTTTCACTTTTTAATATTGGTTTTCCTTTTTAT
7308 G
586 G
* *
7309 TGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGATG-CTTGGCGCCAAAAATCATGCAA
1 TGGGTGAGATTTGGTTAGATGAATATAGATATTTAAATGA-GACTTGGCGCAAAAAATCATGCAA
* * * *
7373 AACAGAGCCGGAGCCCCGGAACGCGTTTATAATGAAAAACCGTGATGGTTAGTACACGATTTCGG
65 AACAGAGCCGGAGCCCCGAAACGCGTTTATAATAAAAAAACGT-A--G--AGTACACGATTTCAG
** * * * *
7438 CTAAAATTTTGTGAAAATTTACCCGAAAAATTTCTCCCCTATTTTTGGCCATAATACTCATAAAA
125 CT-AAATTTTGCAAAAATTTACCCAAAAAATTTCTCCCCAATTTTTGACCACAATACTCATAAAA
* * * *
7503 AATAAATAACTCAACGCCAAAAAGTTTGAAGGGGTTCTCAAGTTTTTAATATCATTTTTTCTTAT
189 AATAAATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCAAGCTTCTAATATCA--TTTTCATAT
7568 GTTTTTTCCGAATTAATTTCTAATCAAATCGAAACCAGATTGAAATGCTCATAAATACAAA-TCC
252 -TTTTTTCCGAATTAATTTCTAATCAAATCGAAACCAGATTGAAATGCTCATAAA-A-AAATTCC
* * *
7632 TTAAGTTCAATGTGGCTGAGA-TTCGTTAGATGAATATAGATATTTCAATGAGTCTTGACG-CAA
314 TTAAATTCAATGTGGCTAAGATTTCGTTAGATGAATATAGATATTCCAATGAGTCTTGACGAC-A
* * * * *
7695 AAAATCATACAAAACTAAGCTGGGGTCTCGGAACGCGTTTTTAGCCAAAAA-CTGTGATAGTTAG
378 AAAATCATACAAAACTAAGC-CGAGTCCCGGAACGCGTTTTTAACCAAAAATC-GTAATAGTTAG
* *
7759 TACACGAATTT-GGCAAAAATTTTACAAAAATTGACCCGGAAGAATTTTCCTCAATTTTTGGCCA
441 TACACG-ATTTCGGCAAAAATTTTACAAAAATTGACCCGAAAGAATTTTCCTCAATTTTTAGCCA
** * *
7823 CGATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCAC
505 CGATACTCATAAAAAATATATAATTCAACACCAAAAAAATTAAAAGGCTTTTCAC
7878 GTTTCCAATA
Statistics
Matches: 488, Mismatches: 64, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
585 94 0.19
586 2 0.00
588 1 0.00
590 15 0.03
591 102 0.21
593 9 0.02
594 104 0.21
595 147 0.30
596 14 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (586 bp):
TGGGTGAGATTTGGTTAGATGAATATAGATATTTAAATGAGACTTGGCGCAAAAAATCATGCAAA
ACAGAGCCGGAGCCCCGAAACGCGTTTATAATAAAAAAACGTAGAGTACACGATTTCAGCTAAAT
TTTGCAAAAATTTACCCAAAAAATTTCTCCCCAATTTTTGACCACAATACTCATAAAAAATAAAT
AACTCAACGCCAAAAAGTTTGAAGGGCTTCTCAAGCTTCTAATATCATTTTCATATTTTTTTCCG
AATTAATTTCTAATCAAATCGAAACCAGATTGAAATGCTCATAAAAAAATTCCTTAAATTCAATG
TGGCTAAGATTTCGTTAGATGAATATAGATATTCCAATGAGTCTTGACGACAAAAATCATACAAA
ACTAAGCCGAGTCCCGGAACGCGTTTTTAACCAAAAATCGTAATAGTTAGTACACGATTTCGGCA
AAAATTTTACAAAAATTGACCCGAAAGAATTTTCCTCAATTTTTAGCCACGATACTCATAAAAAA
TATATAATTCAACACCAAAAAAATTAAAAGGCTTTTCACTTTTTAATATTGGTTTTCCTTTTTAT
G
Found at i:8286 original size:334 final size:324
Alignment explanation
Indices: 7306--10165 Score: 1272
Period size: 334 Copynumber: 8.7 Consensus size: 324
7296 TTTCCTTTTT
7306 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGATGCTTGGCGCCAAAAATCATGC
1 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGA-GCTTGGCGCCAAAAATCATGC
* * * *
7371 AAAACAGAGCCGGAGCCCCGGAACGCGTTTATAATGAAAAACCGTGATGGTTAGTACACGATTTC
65 AAAACAGAG-CGGGGCCCTGGAACGCGTTTATAGTCAAAAACCGTGATGGTTAGTACACGATTTC
* * *
7436 GGCTAAAATTTTGTGAAAATTTACCCGAAAAATTTCTCCCCTA-TTTTTGGCCATAATACTCATA
129 GGCTAAAATTTTGCGAAAATTTGCCCGAAAAATTTCTCCCCAATTTTTTGGCC--AATACTCATA
* * * * *
7500 AAAAATAAATAACTCAACGCCAAAAAGTTTGAAGGGGTTCTCAAGTTTTTAATATCATTTTTTCT
192 AAAAATATATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCACG-TTTTAATATC-GTTTTTCC
* * * *
7565 TATGTTTTTTCCGAATTAATTTCTAATCAAATCGAAACCAGATTGAAATGCTCATAAATACAAAT
255 TA--TTTTTT-CGAATTAATTTCTAATTAAA-CGAAATCAGATTGAGATGCTCGTAAA-ACAAAT
7630 CCTTAAGTTCA
315 CCTTAA-TTCA
* * * * *
7641 ATGTGGCTGAGA-TTCGTTAGATGAATATAGATATTTCAATGAGTCTTGACGCAAAAAATCATAC
1 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGAG-CTTGGCGCCAAAAATCATGC
* * * * *
7705 AAAACTA-AGCTGGGG-TCTCGGAACGCGTTTTTAGCCAAAAACTGTGATAGTTAGTACACGAAT
65 AAAAC-AGAGC-GGGGCCCT-GGAACGCGTTTATAGTCAAAAACCGTGATGGTTAGTACACG-AT
* * * * *
7768 TT-GGCAAAAATTTTAC-AAAAATTGACCCGGAAGAATTT-TCCTCAA-TTTTTGGCCACGATAC
126 TTCGGCTAAAATTTTGCGAAAATTTG-CCC-GAAAAATTTCTCCCCAATTTTTTGGCCA--ATAC
* * * * * * *
7829 TCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGTTTCCAATATCGATT
187 TCATAAAAAATATATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCACGTTT-TAATATCGTTT
* * *
7894 TTCCTATTTTTTCTGAATTAATTTCTAATTAAGTCGAAATAAGAGTT-AGATACTCGTAAAAGCA
251 TTCCTATTTTTTC-GAATTAATTTCTAATTAA-ACGAAATCAGA-TTGAGATGCTCGTAAAA-CA
*
7958 AATCCTTACATCCA
312 AATCCTTA-ATTCA
* *
7972 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGACGTGGCGCCAGAAATCATGC
1 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGAG-CTTGGCGCCAAAAATCATGC
* ** * *
8037 AAAACAGAGTCGGGGCCCTTGAATACGTTTATAGTTAAAAACCGTGGTGGTTAGTACACGATTTC
65 AAAACAGAG-CGGGGCCCTGGAACGCGTTTATAGTCAAAAACCGTGATGGTTAGTACACGATTTC
* * *
8102 GGCTAAAAGTTTGCGAAAATTTGCCCAAAAAAATTTCTCCCCAATTTTTTTGGCGCAATAATCAT
129 GGCTAAAATTTTGCGAAAATTTGCCC-GAAAAATTTCTCCCCAA-TTTTTTGGC-CAATACTCAT
* *
8167 AAAAAATATATAACTCAACGCTAAAAAGTTTGAAGGGCTTCTCACGCTTTTAATCTCGTTTTTCC
191 AAAAAATATATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCACG-TTTTAATATCGTTTTTCC
*
8232 TATTTTTTGCGAACTAATTTCTAATTAACACGAAATCAGATTGAGATGCTCGTAAAAACAAATCC
255 TATTTTTT-CGAATTAATTTCTAATTAA-ACGAAATCAGATTGAGATGCTCGT-AAAACAAATCC
8297 TTAAATTCA
317 TT-AATTCA
* * * * * * * * **
8306 ATGTGGCTCTGACAAAAAAAAAAATTCAATGTGGCTGAGATTTCGTTACATAAATA-TTGATTTT
1 ATGTGG--GTG----------AGA-T---T-TGG-TTAGA--T-G-AATATAGATATTTCAATGA
* * * * * *
8370 TCAATGAGTCATGTCGCCAAAAATCATACAAAACTA-AGCCAGAGCCC-GGAACGCGTTTTTTAG
44 GC-TTG-G-C-----GCCAAAAATCATGCAAAAC-AGAG-CGGGGCCCTGGAACGCG-TTTATAG
* * * ** * *
8433 CCAAAAACTGTAATACTTAGTACACGATTTCGGCTAAAATTTTTC-AAAAATTGACCCGAAAGAA
98 TCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCGAAAATTTG-CCCGAAA-AA
* * * *
8497 TTT-TCCTC-ATTTTTTGGCCACGATACTGATAAAAAAATATATAATTCAACGCCAAAAAGTATG
161 TTTCTCCCCAATTTTTTGGCCA--ATACTCAT-AAAAAATATATAACTCAACGCCAAAAAGTTTG
* * * * * * *
8560 AATGGCTTTTCGCGCTTCTAATATCGATTTTCCTAGTTTATCCGAATTAATTTCTAATTAAACCG
223 AAGGGCTTCTCACG-TTTTAATATCGTTTTTCCTA-TTTTTTCGAATTAATTTCTAATTAAA-CG
*
8625 AAAT-ATGATTTAGATGCTCGTAAAAGCAAATCCTTAAATTCA
285 AAATCA-GATTGAGATGCTCGTAAAA-CAAATCCTT-AATTCA
* * * * *
8667 ATGTGAGTGAGATTTGATTAGATGGATATAGATATTTCAATGAGAGTTGGTGCCAAAAATCATGC
1 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGAG-CTTGGCGCCAAAAATCATGC
* * * * * * ** ** *
8732 -AAACAGAGCCGTG--ATGGTACACGATTT-CAGT--AAAA---TTTTACTTAG-ATA-GAATTT
65 AAAACAGAGCGGGGCCCTGGAACGCG-TTTATAGTCAAAAACCGTGATGGTTAGTACACG-A-TT
* * * * * *** * * **** * *
8786 TC--CTCAATTTTTGACCACGACA-CT-CATAAAAAAATATAT----AA-TTCAACGTCAA-AAT
127 TCGGCTAAAATTTTG-CGA--AAATTTGC-CCGAAAAATTTCTCCCCAATTTTTTGGCCAATACT
* ** *** * * * * ** * ** ***
8841 GATTGAAAGGCT-TTA--C-ACGCTTCTAATA-TATG-A--TTTTCT-A-TTTTTTTTAGAATTA
188 CATAAAAAATATATAACTCAACGC--CAAAAAGTTTGAAGGGCTTCTCACGTTTTAATATCGTT-
*** *
8896 ATTT-CTAATTAAATCG-A--AA------------C---A-C-GATTCAGATGCTCGTAAAAACA
250 -TTTCCT-ATTTTTTCGAATTAATTTCTAATTAAACGAAATCAGATTGAGATGCTCGT-AAAACA
*
8940 AATCCTTAAATCCA
312 AATCCTT-AATTCA
* * * *
8954 ATGTGGGTGAGATTTGGTTTGATGGATATACATATTTCAATGAGACTTGGTGCCAAAAATCATTG
1 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGAG-CTTGGCGCCAAAAATCA-TG
** * *
9019 -AAAACAGAGTCGGGGCCCAAGAACGCGTTTTTAGTCAAAAACCGTGATGGTTGGTATACGATTT
64 CAAAACAGAG-CGGGGCCCTGGAACGCGTTTATAGTCAAAAACCGTGATGGTTAG--TAC-A---
* * * ** * *
9083 CGGGTTTCGGCTAAAATTTTGC-AAAAATTGACAAAAAAATTT-TCCTCAATTTTTGGGCACAAT
122 C-GATTTCGGCTAAAATTTTGCGAAAATTTGCCCGAAAAATTTCTCCCCAATTTTTTGGC-CAAT
* * * * * *
9146 ACTCATAAAAAATATATAACTCAACGACAAAATGATTGACGGGCTTCTCACGCTTCTAATATCCT
185 ACTCATAAAAAATATATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCACG-TTTTAATAT-CG
* *
9211 TTTTTCCTAATTTTTTCCGAATTAGTTTCTAATTAAATCGAAA-CTGGATTGAGATGCTCGTAAA
248 TTTTTCCT-ATTTTTT-CGAATTAATTTCTAATTAAA-CGAAATC-AGATTGAGATGCTCGT-AA
*
9275 AACAAAT-CTTGAAATCCA
308 AACAAATCCTT--AATTCA
* * * * * * *
9293 ATGTGGCAT-AGATTTCGTTAGGTGAATAGAGAT-TTTGAATGAGTCTTGACGCCAAAAATCATA
1 ATGTGG-GTGAGATTTGGTTAGATGAATATAGATATTTCAATGAG-CTTGGCGCCAAAAATCATG
* * * * * * * *
9356 CAAAACTGTGTCGGGATCCC-AGAACGCGTTTTTA-ACAAAAAACCGTGATGGTAAATACACGAT
64 CAAAACAGAG-CGGG-GCCCTGGAACGCGTTTATAGTC-AAAAACCGTGATGGTTAGTACACGAT
* * *
9419 TTCGG---------T-----AA-----CCG-AAAGTTTCTCCCTCAATTTTTAGCCACAATACTC
126 TTCGGCTAAAATTTTGCGAAAATTTGCCCGAAAAATTTCTCCC-CAATTTTTTGGC-CAATACTC
* * * * * * *
9464 ATAAAATATATATAAATCAACGCCAAAAAGATTGAACGGCTTTTCACGCTTCTAATATCATTTTT
189 ATAAAAAATATATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCACG-TTTTAATATCGTTTTT
* * * *
9529 CATATTTTTTTTTCGAATTAATTTCTAATTAAATCGAAA-CAAGATTCAAATACTCGTAAAAACA
253 CCTA---TTTTTTCGAATTAATTTCTAATTAAA-CGAAATC-AGATTGAGATGCTCGT-AAAACA
*
9593 AATCCTTAAATCCA
312 AATCCTT-AATTCA
* * * *
9607 ATGTGGATGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATTATGC
1 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGAG-CTTGGCGCCAAAAATCATGC
** * * * * * * * *
9672 AAAATTGAGCTTGGG-CCTCGGAACGTGTTTTTAGCCAACAATCGTGATAGTTAGCACACGATTT
65 AAAACAGAGC-GGGGCCCT-GGAACGCGTTTATAGTCAAAAACCGTGATGGTTAGTACACGATTT
* * ** * * * *
9736 CGGCTAAAATTTTACAAAAATTTATCTGAATGAATTT-TCCTCAA--TTTTGACCATGATACTCA
128 CGGCTAAAATTTTGCGAAAATTTGCCCGAA-AAATTTCTCCCCAATTTTTTGGCCA--ATACTCA
* * * * * *
9798 TAAAAAATATATAATTCAACGCTAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTC
190 TAAAAAATATATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCACG-TTTTAATATCGTTTTTC
* *
9863 CTATTTTTTCTGAATTAATTTCTAATTGAATCGAAA-CATGATTCAGATGCTCGTAAAAACAAAT
254 CTATTTTTTC-GAATTAATTTCTAATT-AAACGAAATCA-GATTGAGATGCTCGT-AAAACAAAT
*
9927 CCTTAAATCCA
315 CCTT-AATTCA
* * * *
9938 GTATGAGTGAGATTTGGTTAGATGGATATAGATATTTCAATGAGACTTGGTTGGCGCCAAAAATC
1 ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGAG-C----TTGGCGCCAAAAATC
* ** * *** * * * * *
10003 ATGCAAAAGAGAGCCAAGTCCCCAAAATGCGTTTTTAGTCAGAAACCATGAT-GTAACGTACACG
61 ATGCAAAACAGAG-CGGGGCCCTGGAACGCGTTTATAGTCAAAAACCGTGATGGTTA-GTACACG
* * * * * *
10067 ATTTCGGTTGAAATTTT-C-AAAAATTGACCCGAAAAATTTGTCCTCAA-TATTTGGTCACATCA
124 ATTTCGGCTAAAATTTTGCGAAAATTTG-CCCGAAAAATTTCTCCCCAATTTTTTGG---C--CA
*
10129 CATTACTCATAAAAAATGTATAACTCAACGCCAAAAA
183 -A-TACTCATAAAAAATATATAACTCAACGCCAAAAA
10166 TATTTTGGAA
Statistics
Matches: 1931, Mismatches: 378, Indels: 427
0.71 0.14 0.16
Matches are distributed among these distances:
287 86 0.04
288 14 0.01
289 4 0.00
290 3 0.00
291 8 0.00
292 1 0.00
293 4 0.00
296 5 0.00
299 1 0.00
300 1 0.00
301 3 0.00
302 10 0.01
303 5 0.00
304 1 0.00
305 14 0.01
306 3 0.00
307 10 0.01
308 15 0.01
309 6 0.00
310 6 0.00
311 3 0.00
312 15 0.01
313 21 0.01
314 160 0.08
315 84 0.04
316 8 0.00
317 17 0.01
318 7 0.00
319 1 0.00
320 5 0.00
321 2 0.00
322 10 0.01
323 9 0.00
324 18 0.01
325 1 0.00
326 2 0.00
327 4 0.00
329 4 0.00
330 19 0.01
331 177 0.09
332 127 0.07
333 130 0.07
334 313 0.16
335 117 0.06
336 14 0.01
337 4 0.00
338 69 0.04
339 67 0.03
340 41 0.02
341 1 0.00
343 4 0.00
344 2 0.00
345 1 0.00
346 2 0.00
347 1 0.00
348 1 0.00
349 2 0.00
350 1 0.00
351 3 0.00
352 4 0.00
354 2 0.00
355 7 0.00
356 8 0.00
357 1 0.00
358 2 0.00
359 11 0.01
360 13 0.01
361 136 0.07
362 79 0.04
363 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (324 bp):
ATGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGCTTGGCGCCAAAAATCATGCA
AAACAGAGCGGGGCCCTGGAACGCGTTTATAGTCAAAAACCGTGATGGTTAGTACACGATTTCGG
CTAAAATTTTGCGAAAATTTGCCCGAAAAATTTCTCCCCAATTTTTTGGCCAATACTCATAAAAA
ATATATAACTCAACGCCAAAAAGTTTGAAGGGCTTCTCACGTTTTAATATCGTTTTTCCTATTTT
TTCGAATTAATTTCTAATTAAACGAAATCAGATTGAGATGCTCGTAAAACAAATCCTTAATTCA
Found at i:8958 original size:287 final size:287
Alignment explanation
Indices: 8493--9027 Score: 788
Period size: 287 Copynumber: 1.9 Consensus size: 287
8483 TTGACCCGAA
* * * *
8493 AGAATTTTCCTCATTTTTTGGCCACGATACTGATAAAAAAATATATAATTCAACGCCAAAAAGTA
1 AGAATTTTCCTCAATTTTTGACCACGACACTCATAAAAAAATATATAATTCAACGCCAAAAAGTA
* * * *
8558 TGAATGGCTTTTCGCGCTTCTAATATCGATTTTCCTAGTTTATCCGAATTAATTTCTAATTAAAC
66 TGAAAGGCTTTACACGCTTCTAATATCGATTTTCCTAGTTTATCAGAATTAATTTCTAATTAAAC
* * * * *
8623 CGAAATATGATTTAGATGCTCGTAAAAGCAAATCCTTAAATTCAATGTGAGTGAGATTTGATTAG
131 CGAAACACGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGAGTGAGATTTGATTAG
* * *
8688 ATGGATATAGATATTTCAATGAGAGTTGGTGCCAAAAATCA-TGCAAACAGAGCCGTGATGGTAC
196 ATGGATATACATATTTCAATGAGACTTGGTGCCAAAAATCATTGAAAACAGAGCCGTGATGGTAC
8752 ACGATTTCAGTAAAATTTTACTTAGAT
261 ACGATTTCAGTAAAATTTTACTTAGAT
* *
8779 AGAATTTTCCTCAATTTTTGACCACGACACTCATAAAAAAATATATAATTCAACGTCAAAATG-A
1 AGAATTTTCCTCAATTTTTGACCACGACACTCATAAAAAAATATATAATTCAACGCCAAAAAGTA
* * * *
8843 TTGAAAGGCTTTACACGCTTCTAATATATGATTTT-CTATTTTTTTTAGAATTAATTTCTAATTA
66 -TGAAAGGCTTTACACGCTTCTAATAT-CGATTTTCCTA-GTTTATCAGAATTAATTTCTAATTA
* * *
8907 AATCGAAACACGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGT
128 AACCGAAACACGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGAGTGAGATTTGAT
*
8972 TTGATGGATATACATATTTCAATGAGACTTGGTGCCAAAAATCATTGAAAACAGAG
193 TAGATGGATATACATATTTCAATGAGACTTGGTGCCAAAAATCATTGAAAACAGAG
9028 TCGGGGCCCA
Statistics
Matches: 219, Mismatches: 26, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
285 1 0.00
286 83 0.38
287 125 0.57
288 10 0.05
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (287 bp):
AGAATTTTCCTCAATTTTTGACCACGACACTCATAAAAAAATATATAATTCAACGCCAAAAAGTA
TGAAAGGCTTTACACGCTTCTAATATCGATTTTCCTAGTTTATCAGAATTAATTTCTAATTAAAC
CGAAACACGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGAGTGAGATTTGATTAG
ATGGATATACATATTTCAATGAGACTTGGTGCCAAAAATCATTGAAAACAGAGCCGTGATGGTAC
ACGATTTCAGTAAAATTTTACTTAGAT
Found at i:9420 original size:338 final size:339
Alignment explanation
Indices: 8781--9423 Score: 825
Period size: 338 Copynumber: 1.9 Consensus size: 339
8771 ACTTAGATAG
* * *
8781 AATTTTCCTCAATTTTTGACCACGACACTCATAAAAAAATATATAATTCAACGTCAAAATGATTG
1 AATTTTCCTCAATTTTTGACCACAACACTCATAAAAAAATATATAACTCAACGACAAAATGATTG
* *
8846 AAAGGCTTTACACGCTTCTAATATATGATTTTCTATTTTTTTTAGAATTAATTTCTAATTAAATC
66 AAAGGCTTTACACGCTTCTAATATATGATTTTCTAATTTTTTCAGAATTAATTTCTAATTAAATC
* * *
8911 GAAACACGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGAGATTTGGTTTGA
131 GAAACACGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTCGTTAGA
* * ** **
8976 TGGATATACATATTTCAATGAGACTTGGTGCCAAAAATCATTGAAAACAGAGTCGGGGCCCAAGA
196 TGAATAGACATATTTCAATGAGACTTGACGCCAAAAATCATACAAAACAGAGTCGGGGCCCAAGA
* *** *
9041 ACGCGTTTTTAGTCAAAAACCGTGATGGTTGGTATACGATTTCGGGTTTCGGCTAAAATTTTGCA
261 ACGCGTTTTTAGACAAAAACCGTGATGGTAAATACACGATTTCGGGTTTCGGCTAAAATTTTGCA
9106 AAAATTGACAAAAA
326 AAAATTGACAAAAA
** *
9120 AATTTTCCTCAATTTTTGGGCACAATACTCAT-AAAAAATATATAACTCAACGACAAAATGATTG
1 AATTTTCCTCAATTTTTGACCACAACACTCATAAAAAAATATATAACTCAACGACAAAATGATTG
** * * * *
9184 ACGGGCTTCT-CACGCTTCTAATATCCT-TTTTTCCTAATTTTTTCCGAATTAGTTTCTAATTAA
66 AAAGGCTT-TACACGCTTCTAATAT-ATGATTTT-CTAATTTTTTCAGAATTAATTTCTAATTAA
** *
9247 ATCGAAACTGGATTGAGATGCTCGTAAAAACAAAT-CTTGAAATCCAATGTGGCAT-AGATTTCG
128 ATCGAAACACGATTCAGATGCTCGTAAAAACAAATCCTT-AAATCCAATGTGG-ATGAGATTTCG
* * * * * * *
9310 TTAGGTGAATAGAGAT-TTTGAATGAGTCTTGACGCCAAAAATCATACAAAACTGTGTCGGGATC
191 TTAGATGAATAGACATATTTCAATGAGACTTGACGCCAAAAATCATACAAAACAGAGTCGGG-GC
9374 CC-AGAACGCGTTTTTA-ACAAAAAACCGTGATGGTAAATACACGATTTCGG
255 CCAAGAACGCGTTTTTAGAC-AAAAACCGTGATGGTAAATACACGATTTCGG
9424 TAACCGAAAG
Statistics
Matches: 259, Mismatches: 38, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
337 1 0.00
338 135 0.52
339 122 0.47
340 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (339 bp):
AATTTTCCTCAATTTTTGACCACAACACTCATAAAAAAATATATAACTCAACGACAAAATGATTG
AAAGGCTTTACACGCTTCTAATATATGATTTTCTAATTTTTTCAGAATTAATTTCTAATTAAATC
GAAACACGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTCGTTAGA
TGAATAGACATATTTCAATGAGACTTGACGCCAAAAATCATACAAAACAGAGTCGGGGCCCAAGA
ACGCGTTTTTAGACAAAAACCGTGATGGTAAATACACGATTTCGGGTTTCGGCTAAAATTTTGCA
AAAATTGACAAAAA
Found at i:10385 original size:27 final size:27
Alignment explanation
Indices: 10275--10392 Score: 68
Period size: 27 Copynumber: 4.4 Consensus size: 27
10265 TATTTTGTAA
*
10275 AAATAATATTTAAATAAT-ATGAATTTAG
1 AAAT-ATATTTTAATAATAAT-AATTTAG
* ** *
10303 AAATATATTTGAA-AA-AA-AATACACA
1 AAATATATTTTAATAATAATAATTTA-G
* *
10328 AAATTATATTTTAATAATGGCAT-AGTT-G
1 AAA-TATATTTTAATAAT--AATAATTTAG
10356 AAATATATTTTAATAATAATAATTTAG
1 AAATATATTTTAATAATAATAATTTAG
*
10383 AAATGTATTT
1 AAATATATTT
10393 GTAAAAAAGG
Statistics
Matches: 67, Mismatches: 13, Indels: 21
0.66 0.13 0.21
Matches are distributed among these distances:
24 4 0.06
25 5 0.07
26 15 0.22
27 34 0.51
28 7 0.10
30 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.39
Consensus pattern (27 bp):
AAATATATTTTAATAATAATAATTTAG
Found at i:21895 original size:23 final size:25
Alignment explanation
Indices: 21865--21920 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
21855 TATATTCTTT
*
21865 TATTATTTT-CTTT-ATTTGAAAAA
1 TATTATTTTGATTTAATTTGAAAAA
21888 TATTATTTTTGATTTAATTTGAAAAA
1 TATTA-TTTTGATTTAATTTGAAAAA
21914 TATTATT
1 TATTATT
21921 AGTACGGCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.17
24 4 0.14
25 5 0.17
26 15 0.52
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (25 bp):
TATTATTTTGATTTAATTTGAAAAA
Found at i:26303 original size:14 final size:14
Alignment explanation
Indices: 26284--26310 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26274 TTTAAAGGTT
26284 GTATATATATATAA
1 GTATATATATATAA
26298 GTATATATATATA
1 GTATATATATATA
26311 TATATAACTA
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:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
GTATATATATATAA
Found at i:39158 original size:108 final size:108
Alignment explanation
Indices: 38888--39213 Score: 490
Period size: 108 Copynumber: 3.0 Consensus size: 108
38878 TCTGCTTTTA
* ** * *
38888 AGCTTGTCCTGTTTTAAAACTAAATTGTGATTTTGAAATAAACCATTTGTAAAGAACTCTGCATG
1 AGCTTGTCCTGTTTGAAAACTAAATTGTGATAGTGAAATAAACTATTTTTAAAGAACTCTGCATG
* *
38953 AAGCATGCTTTCTCACAAAGACATTTCGTAGTTCTAGTTTTTCTT
66 AAGCATGCTTTCTCACAAAGAAATTTAGTAGTTCTAG-TTTTC-T
* *
38998 AGCTTGTCCTGTTTGAAAACTAAATTGTGATAGTGAAACAAACTATATTTAAAGAACTCTGCATG
1 AGCTTGTCCTGTTTGAAAACTAAATTGTGATAGTGAAATAAACTATTTTTAAAGAACTCTGCATG
39063 AAGCATGCTTTCTCACAAAGAAATTTAGTAGTTCTAGTTTTCT
66 AAGCATGCTTTCTCACAAAGAAATTTAGTAGTTCTAGTTTTCT
* **
39106 AGCTTGTCCTGTTTGAAAACTAAATTGTGAAAGTGAAATAAACTATTTTTAAAGAACTCTTAATG
1 AGCTTGTCCTGTTTGAAAACTAAATTGTGATAGTGAAATAAACTATTTTTAAAGAACTCTGCATG
* * * *
39171 AAGCATGCTTTCTCACCAAGATATTTTGAAGTTCTAGTTTTCT
66 AAGCATGCTTTCTCACAAAGAAATTTAGTAGTTCTAGTTTTCT
39214 TTCTTTTTGT
Statistics
Matches: 198, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
108 100 0.51
109 5 0.03
110 93 0.47
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (108 bp):
AGCTTGTCCTGTTTGAAAACTAAATTGTGATAGTGAAATAAACTATTTTTAAAGAACTCTGCATG
AAGCATGCTTTCTCACAAAGAAATTTAGTAGTTCTAGTTTTCT
Found at i:41769 original size:31 final size:31
Alignment explanation
Indices: 41723--41883 Score: 187
Period size: 31 Copynumber: 5.2 Consensus size: 31
41713 CGTGACATGG
* ** *
41723 CACGTGCCACTTTTTTGAAACACATGGCATGC
1 CACGTGTCAC-TTTTTGGTACACATGGCGTGC
* *
41755 CATGTGTCACTTTTTGGTACACATGGCGTGA
1 CACGTGTCACTTTTTGGTACACATGGCGTGC
* *
41786 TACGTGTCACTTTTTGGTACACATGGCGTGA
1 CACGTGTCACTTTTTGGTACACATGGCGTGC
* *
41817 TACGTGTCACTTTTTGGTACACGTGGCGTGC
1 CACGTGTCACTTTTTGGTACACATGGCGTGC
* * * *
41848 CACATGTCGCTTTTTGGTACACGTGGCATGC
1 CACGTGTCACTTTTTGGTACACATGGCGTGC
41879 CACGT
1 CACGT
41884 CAGACACCGT
Statistics
Matches: 114, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
31 106 0.93
32 8 0.07
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.33
Consensus pattern (31 bp):
CACGTGTCACTTTTTGGTACACATGGCGTGC
Found at i:46588 original size:14 final size:15
Alignment explanation
Indices: 46569--46602 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46559 TCAAATACCT
46569 AAAAAA-AAAAAAAG
1 AAAAAAGAAAAAAAG
*
46583 AAAAAAGAAAAAAGG
1 AAAAAAGAAAAAAAG
46598 AAAAA
1 AAAAA
46603 CCACGTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:46600 original size:8 final size:7
Alignment explanation
Indices: 46569--46602 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
46559 TCAAATACCT
*
46569 AAAAAAA
1 AAAAAAG
46576 AAAAAAG
1 AAAAAAG
46583 AAAAAAG
1 AAAAAAG
46590 AAAAAAGG
1 AAAAAA-G
46598 AAAAA
1 AAAAA
46603 CCACGTATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Done.