Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010516.1 Corchorus capsularis cultivar CVL-1 contig10537, 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: 53546
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:2191 original size:12 final size:11
Alignment explanation
Indices: 2171--2203 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
2161 TGTTGTACAA
2171 TTCTTTTTTTT
1 TTCTTTTTTTT
2182 TTCTTTTTTTT
1 TTCTTTTTTTT
2193 TTCTTTATTTT
1 TTCTTT-TTTT
2204 CCATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:23211 original size:1 final size:1
Alignment explanation
Indices: 23165--23196 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
23155 TAATTCACTG
23165 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23197 AACTTTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42306 original size:1 final size:1
Alignment explanation
Indices: 42300--42329 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
42290 TCTCCTTCGG
42300 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42330 AATTTCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:43795 original size:95 final size:95
Alignment explanation
Indices: 43681--43870 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
43671 GTTCTCCATG
43681 AATGCATCCTTTAAATATTAGGCAAAGCCAAAGCTGAAAACTCATGGGTATTTCTATCGTGAATG
1 AATGCATCCTTTAAATATTAGGCAAAGCCAAAGCTGAAAACTCATGGGTATTTCTATCGTGAATG
43746 GAATCTAGGGTACTTTTTCTGCCATTTCTT
66 GAATCTAGGGTACTTTTTCTGCCATTTCTT
43776 AATGCATCCTTTAAATATTAGGCAAAGCCAAAGCTGAAAACTCATGGGTATTTCTATCGTGAATG
1 AATGCATCCTTTAAATATTAGGCAAAGCCAAAGCTGAAAACTCATGGGTATTTCTATCGTGAATG
43841 GAATCTAGGGTACTTTTTCTGCCATTTCTT
66 GAATCTAGGGTACTTTTTCTGCCATTTCTT
43871 CATGAATATT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (95 bp):
AATGCATCCTTTAAATATTAGGCAAAGCCAAAGCTGAAAACTCATGGGTATTTCTATCGTGAATG
GAATCTAGGGTACTTTTTCTGCCATTTCTT
Found at i:44975 original size:45 final size:45
Alignment explanation
Indices: 44894--44980 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
44884 GGATAGTTTG
* * *
44894 AGCACTCGGCAATCATGGAGCCAAAGCTCTCTTTGATTTCCTTAA
1 AGCACTCGGCAATAATGGAGCCAAAGCTCTCCTTGATCTCCTTAA
* * * * *
44939 AGCATTCGGCAATAATGGATCCTAGGCTTTCCTTGATCTCCT
1 AGCACTCGGCAATAATGGAGCCAAAGCTCTCCTTGATCTCCT
44981 GCACGTTGTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (45 bp):
AGCACTCGGCAATAATGGAGCCAAAGCTCTCCTTGATCTCCTTAA
Found at i:45489 original size:24 final size:24
Alignment explanation
Indices: 45459--45507 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
45449 GGAGTACCAC
*
45459 TGTGTCTTCTCGTGTACCTTCGTG
1 TGTGTCTTCTCGTCTACCTTCGTG
45483 TGTGTCTTCTCGTCTACCTTCGTG
1 TGTGTCTTCTCGTCTACCTTCGTG
45507 T
1 T
45508 CTGGCCTCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.27, G:0.22, T:0.47
Consensus pattern (24 bp):
TGTGTCTTCTCGTCTACCTTCGTG
Found at i:45516 original size:22 final size:23
Alignment explanation
Indices: 45466--45516 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
45456 CACTGTGTCT
* * *
45466 TCTCGTGTACCTTCGTGTGTGTC
1 TCTCGTCTACCTTCGTGTCTGGC
45489 TTCTCGTCTACCTTCGTGTCTGGC
1 -TCTCGTCTACCTTCGTGTCTGGC
45513 -CTCG
1 TCTCG
45517 GCTCACTGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.17
24 20 0.83
ACGTcount: A:0.04, C:0.31, G:0.24, T:0.41
Consensus pattern (23 bp):
TCTCGTCTACCTTCGTGTCTGGC
Found at i:45568 original size:35 final size:35
Alignment explanation
Indices: 45522--45588 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
45512 CCTCGGCTCA
*
45522 CTGCGGAGGCCTCTGTCTTCTCGTGTAACTTCGTG
1 CTGCGCAGGCCTCTGTCTTCTCGTGTAACTTCGTG
*
45557 CTGCGCAGGCCTCTGTCTTCTCGTGTACCTTC
1 CTGCGCAGGCCTCTGTCTTCTCGTGTAACTTC
45589 CTTTCTGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.07, C:0.33, G:0.25, T:0.34
Consensus pattern (35 bp):
CTGCGCAGGCCTCTGTCTTCTCGTGTAACTTCGTG
Found at i:45621 original size:50 final size:50
Alignment explanation
Indices: 45557--45887 Score: 462
Period size: 50 Copynumber: 6.8 Consensus size: 50
45547 TAACTTCGTG
* * *
45557 CTGCGCAGGCCTCTGTCTTCTCGTGTACCTTCCTTTCTGGCCTCGCCTCA
1 CTGCGGAGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCA
*
45607 CTACGGAGGCCTCTGTCTTCTCGTGTATCCTT--T-T-TGGCCTCGCCTCA
1 CTGCGGAGGCCTCTGTCTTCTCGTGTA-CCTTCGTGTCTGGCCTCGCCTCA
** *
45654 CTGCGGAGG-C-CTGTCTTCTCGTGTAATTTTGTGTCTGGCCTCGCCTCA
1 CTGCGGAGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCA
45702 CTGCGGAGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCA
1 CTGCGGAGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCA
* * **
45752 CTGCAGAGGTCTCTGTCTTCTCGTGTAATTTCGTGTCTGGCCTCGCCTCA
1 CTGCGGAGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCA
* *
45802 CTGCGGAGG-C-CTGTCTTCTCGTGTACCTTCATGTCTGGTCTCGCCTCA
1 CTGCGGAGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCA
* *
45850 CTGCAGAGGCCTCTGTCTTCTCGTGTACCTTTGTGTCT
1 CTGCGGAGGCCTCTGTCTTCTCGTGTACCTTCGTGTCT
45888 TCGCGTGTTG
Statistics
Matches: 252, Mismatches: 20, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
44 2 0.01
45 15 0.06
46 2 0.01
47 22 0.09
48 65 0.26
49 4 0.02
50 138 0.55
51 4 0.02
ACGTcount: A:0.08, C:0.33, G:0.24, T:0.35
Consensus pattern (50 bp):
CTGCGGAGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCA
Found at i:45859 original size:148 final size:145
Alignment explanation
Indices: 45563--45887 Score: 488
Period size: 148 Copynumber: 2.2 Consensus size: 145
45553 CGTGCTGCGC
* * *
45563 AGGCCTCTGTCTTCTCGTGTACCTTCCTTTCTGGCCTCGCCTCACTACGGAGGCCTCTGTCTTCT
1 AGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCACTACAGAGGCCTCTGTCTTCT
* * * **
45628 CGTGTATCCTTTTTGGCCTCGCCTCACTGCGGAGGCCTGTCTTCTCGTGTAATTTTGTGTCTGGC
66 CGTGTATCCTGTCTGGCCTCGCCTCACTGCGGAGGCCTGTCTTCTCGTGTAACTTCATGTCTGGC
*
45693 CTCGCCTCACTGCGG
131 CTCGCCTCACTGCAG
* *
45708 AGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCACTGCAGAGGTCTCTGTCTTCT
1 AGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCACTACAGAGGCCTCTGTCTTCT
* *
45773 CGTGTAATTTCGTGTCTGGCCTCGCCTCACTGCGGAGGCCTGTCTTCTCGTGTACCTTCATGTCT
66 CGTGT-A--TCCTGTCTGGCCTCGCCTCACTGCGGAGGCCTGTCTTCTCGTGTAACTTCATGTCT
*
45838 GGTCTCGCCTCACTGCAG
128 GGCCTCGCCTCACTGCAG
*
45856 AGGCCTCTGTCTTCTCGTGTACCTTTGTGTCT
1 AGGCCTCTGTCTTCTCGTGTACCTTCGTGTCT
45888 TCGCGTGTTG
Statistics
Matches: 162, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
145 65 0.40
146 1 0.01
148 96 0.59
ACGTcount: A:0.08, C:0.33, G:0.24, T:0.35
Consensus pattern (145 bp):
AGGCCTCTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCACTACAGAGGCCTCTGTCTTCT
CGTGTATCCTGTCTGGCCTCGCCTCACTGCGGAGGCCTGTCTTCTCGTGTAACTTCATGTCTGGC
CTCGCCTCACTGCAG
Found at i:45886 original size:98 final size:99
Alignment explanation
Indices: 45563--45887 Score: 468
Period size: 98 Copynumber: 3.3 Consensus size: 99
45553 CGTGCTGCGC
** * *
45563 AGGCCTCTGTCTTCTCGTGTACCTTCCTTTCTGGCCTCGCCTCACTACGGAGGCCTCTGTCTTCT
1 AGGCCTCTGTCTTCTCGTGTACCTTTGTGTCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCT
*
45628 CGTGTATCCTT-T-T-TGGCCTCGCCTCACTGCGG
66 CGTGTA-CCTTCTGTCTGGCCTCGCCTCACTGCAG
**
45660 AGG-C-CTGTCTTCTCGTGTAATTTTGTGTCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCT
1 AGGCCTCTGTCTTCTCGTGTACCTTTGTGTCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCT
45723 CGTGTACCTTCGTGTCTGGCCTCGCCTCACTGCAG
66 CGTGTACCTTC-TGTCTGGCCTCGCCTCACTGCAG
* *
45758 AGGTCTCTGTCTTCTCGTGTA-ATTTCGTGTCTGGCCTCGCCTCACTGCGGAGG-C-CTGTCTTC
1 AGGCCTCTGTCTTCTCGTGTACCTTT-GTGTCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTC
*
45820 TCGTGTACCTTCATGTCTGGTCTCGCCTCACTGCAG
65 TCGTGTACCTTC-TGTCTGGCCTCGCCTCACTGCAG
45856 AGGCCTCTGTCTTCTCGTGTACCTTTGTGTCT
1 AGGCCTCTGTCTTCTCGTGTACCTTTGTGTCT
45888 TCGCGTGTTG
Statistics
Matches: 208, Mismatches: 12, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
94 4 0.02
95 59 0.28
96 2 0.01
97 4 0.02
98 89 0.43
99 8 0.04
100 42 0.20
ACGTcount: A:0.08, C:0.33, G:0.24, T:0.35
Consensus pattern (99 bp):
AGGCCTCTGTCTTCTCGTGTACCTTTGTGTCTGGCCTCGCCTCACTGCGGAGGCCTCTGTCTTCT
CGTGTACCTTCTGTCTGGCCTCGCCTCACTGCAG
Found at i:47817 original size:2 final size:2
Alignment explanation
Indices: 47810--47841 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47800 GGTTAGATAA
47810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47842 TTCAAGAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49133 original size:323 final size:323
Alignment explanation
Indices: 47107--49417 Score: 2734
Period size: 325 Copynumber: 7.1 Consensus size: 323
47097 CAATTTTTTT
* * * *
47107 TTCAGATGCTCGTAAAAACAAAT-CTTGCTA-TCTAATGTGATTGAAATTTGATTCGATAAATAT
1 TTCAGATGCTCGTAAAAACAAATCCTT-ATATTCTAATGTGGTTGACATTTGGTTCGATAAATAT
* * * *** * * *
47170 AAATATTTCAAGGAGCATTTGTATCAAAAATCATGCAAAATTGAATTGGCGCTCCGGAATGTGTT
65 AGATATTTCAAGGAGCATTTGTACCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTT
* * * *
47235 TTTAGCAAAAAACCGTGATGGTTA-TCATACAATTTCGGTTAAAAACTGACCCGAAAAGTTTTTT
130 TTTAGCCAAAAACCGTGATGGTTAGT-ACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTT
* * * * * * * *
47299 CACAATTTTTTGCTATAATACTCCGAGAAAATATATAATTTAATGCTAAAAAGATTGACAGACTT
194 CTCAATTTTTTGCCA-AATACTCCGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
* * * * * *
47364 TTTACACTTATAATATCGTATTTTCATTTTTTTTTTCGAATTAATTACGAATTAAATCGAAACAA
258 TTCACGCTTATAATATCGTTTTTTCATTTTTTTTCT-GAATTAATTTCTAATTAAATCGAAACAA
47429 GA
322 GA
* * * *
47431 TTCAAATGCTCGTAAAAATAAATCTTTATA-TCTAATGTGGTTGGCATTTGGTTCGATAAATATA
1 TTCAGATGCTCGTAAAAACAAATCCTTATATTCTAATGTGGTTGACATTTGGTTCGATAAATATA
* * * * * *
47495 GATATTTCATGAACCATTTGTACCAAAAAACAAGCAAAATTGAGTCGGGGCACCGGAACGCGTTT
66 GATATTTCAAGGAGCATTTGTACCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTT
** *** * *
47560 TTAGTAAAAAACCGTGAT-AACA-TACATGATTTCGGCTAAAAACTAACCCGAAAAGTTTTTTCT
131 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCT
* *
47623 CAATTTTTTGCCAAAATACTCCTAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTT
196 CAATTTTTTGCC-AAATACTCCGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTT
* *
47688 CACGCTTATAATACCGTTTTTTCA-TTTTTTTCTGAATTAATTTCTAATTATATCGAAACAAGA
260 CACGCTTATAATATCGTTTTTTCATTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA
* * *
47751 TTCATATGCTCGTAAAAACAAATCTTTATA-TCTAATGTGGTTGACATTTGGTTAGATAAATATA
1 TTCAGATGCTCGTAAAAACAAATCCTTATATTCTAATGTGGTTGACATTTGGTTCG---------
* * * *
47815 TATATATATATATATATATATATATATTTCAAGAACCATTTATACCAAAAATCAAGCAAAATTGA
57 -----------ATA-A-ATATAGATATTTCAAGGAGCATTTGTACCAAAAATCAAGCAAAATTGA
* *
47880 GCCGAGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAA
109 GCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
** * * *
47945 TTTGACCCGAAAAG-TTTTTCTCAATATTTTGACACAATACTCCGAAAAAATATATATTTCAACG
174 ACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCA-AATACTCCGAAAAAATATATAATTCAACG
* *
48009 CCAAAAAAATTGACGGGTTTTTCACGCTTATAATATCGTTTTTTTCATTTTATTTTCTGAATTAA
238 CCAAAAAGATTGACGGGCTTTTCACGCTTATAATATCG-TTTTTTCATTTT-TTTTCTGAATTAA
*
48074 TTACTAATTAAATCGAAACAAGA
301 TTTCTAATTAAATCGAAACAAGA
*
48097 TTCAGATGCTCGTAAAAACAAATCCTTAATATTC-AATGTGGCTGACATTTGGTTCGATAAATAT
1 TTCAGATGCTCGTAAAAACAAATCCTT-ATATTCTAATGTGGTTGACATTTGGTTCGATAAATAT
* * * * *
48161 AGATATTTCAAGGAGTATTTGTGCCAAAAATCAAGCAAAATTGAGCCAGGGCTCCGAAACACGTT
65 AGATATTTCAAGGAGCATTTGTACCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTT
* * *
48226 TTTAGCCATAAACC------G-T-G--CACTATTTCAGCTAAAAACTGACCCGAAAAGTTTTTTA
130 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTT-
* ** * * * *
48281 CT-AAATTTTCACCACAATACTCCGAAAAAAATATATAATTCAACACCAAAATGATTGACGGACA
194 CTCAATTTTTTGCCA-AATACTCCG-AAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCT
* * * * *
48345 TTTCACGCTTATAATATTGTTTTTT--TTTTTTATATATGAATGAATTTCTAATGAAATCAAAAC
257 TTTCACGCTTATAATATCGTTTTTTCATTTTTT-T-TCTGAATTAATTTCTAATTAAATCGAAAC
48408 AAGA
320 AAGA
* * *
48412 TTCAGATGCTCGTAAAAACAAGTCTTTATA-TCTAATGTGGTTGAAATTTGGTTCGATAAATATA
1 TTCAGATGCTCGTAAAAACAAATCCTTATATTCTAATGTGGTTGACATTTGGTTCGATAAATATA
* * *
48476 GATATTTCAAGGAGCATTTGTACCAAAAATCATGCAAAATTGAGTCGGGGCTCAGGAACGCGTTT
66 GATATTTCAAGGAGCATTTGTACCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTT
* * *
48541 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTTACTCGAAATGTTTTTTTT
131 TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAG--TTTTTT
* * * *
48606 CTCAATTTTTTGCCACAATACTCCGGAAAAGTATATAATTCAACGCCAAAAATATTGACGGGCAT
194 CTCAATTTTTTGCCA-AATACTCCGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
* * * *
48671 TTCACTCTTAAAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATGAAATCGAAACAAG
258 TTCACGCTTATAATATCGTTTTTTCATTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAG
48736 A
323 A
*
48737 TTCAGATGCTCGTAAAAAC-AAGCCTT-TATATCTAATGTGGTTGACATTTGGTTCGATAAATAT
1 TTCAGATGCTCGTAAAAACAAATCCTTATAT-TCTAATGTGGTTGACATTTGGTTCGATAAATAT
* *
48800 AGATATTTCAAGGAGCATTTGTACCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGTGTT
65 AGATATTTCAAGGAGCATTTGTACCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTT
* *
48865 TTTAGCCAAACACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCTGAAAAGTTTTTTC
130 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTC
* * * *
48930 TCAATTTTTTGCCAATTTACTCCTAAAAAATATATAATTTAACACCAAAAAGATTGACGGGCTTT
195 TCAATTTTTTGCCAA-ATACTCCGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTT
* *
48995 TCACGCTTATAATATTGTTTTTTCATTTTTTTTCTGAATTAATTACTAATTAAATCGAAACAAGA
259 TCACGCTTATAATATCGTTTTTTCATTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA
* ** * * *
49060 -TCTAGATGCTTGTAAAAACAAATCCTTATATTC-AACATGGCTGACATTTGGTTCAATAGATAT
1 TTC-AGATGCTCGTAAAAACAAATCCTTATATTCTAATGTGGTTGACATTTGGTTCGATAAATAT
* * *
49123 AGTTATTTCAAGAAGCATTTGTATCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTT
65 AGATATTTCAAGGAGCATTTGTACCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTT
* * * * *
49188 TTTAGCCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAAACACTTACTCGAAACGTTTTTTT
130 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAG-TTTTTT
* * * * *
49253 CTCAATTTTTTGCCACAATACTCCGGAAAAGTATATAATTCAAGGCCAAAAAGATTGACGTGCAT
194 CTCAATTTTTTGCCA-AATACTCCGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
* * *
49318 TTCACGCTTATAATATCGTTTTTTCATTTTTTTTTTCCGAATAAATTTCTAATGAAATCGAAACA
258 TTCACGCTTATAATATCGTTTTTTCA--TTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
49383 AGA
321 AGA
* *
49386 TTCAGATGCTCGTATAAACAAGTCCTTATATT
1 TTCAGATGCTCGTAAAAACAAATCCTTATATT
49418 GAGCCGGGGC
Statistics
Matches: 1714, Mismatches: 209, Indels: 126
0.84 0.10 0.06
Matches are distributed among these distances:
313 4 0.00
314 106 0.06
315 80 0.05
316 28 0.02
317 53 0.03
318 1 0.00
320 79 0.05
321 9 0.01
322 114 0.07
323 277 0.16
324 245 0.14
325 330 0.19
326 89 0.05
327 11 0.01
340 3 0.00
341 1 0.00
342 80 0.05
343 80 0.05
344 37 0.02
345 3 0.00
346 59 0.03
347 23 0.01
348 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (323 bp):
TTCAGATGCTCGTAAAAACAAATCCTTATATTCTAATGTGGTTGACATTTGGTTCGATAAATATA
GATATTTCAAGGAGCATTTGTACCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTT
TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCT
CAATTTTTTGCCAAATACTCCGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTC
ACGCTTATAATATCGTTTTTTCATTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA
Found at i:50587 original size:324 final size:323
Alignment explanation
Indices: 49415--50947 Score: 2183
Period size: 324 Copynumber: 4.8 Consensus size: 323
49405 AAGTCCTTAT
* * * **
49415 ATTGAGCCGGGGCTCCGGAACGTGTCTTTAGCCAAACACCGTGATAATTAGTACACGATTTCGGC
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
* *
49480 TAAAAACTGACCTGAAAAG-TTTTTTCTCAATTTTTTGCCA-ATTTACTCCTAAAAAATATATAA
66 TAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCACA-ATACTCCTAAAAAATATATAA
* *
49543 TTCAACACCAAAAAGAATGACGGGCTTTTCACGCTTAT-ATATTGTTTTTTCATTTTTTTTCCGA
130 TTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTTCCGA
*
49607 ATTAATTTCTAATTATATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCTTTATATCTAATG
195 ATTAATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCTAATG
* * *
49672 TCGTTGACATTTGGTTAGATAAATATAGATATTTCAAGAAGCATTTGT------A-C---CAAA
260 TGGTTGACATTTGGTTCGATAAATATATATATTTCAAGAAGCATTTGTACCAAAATCAAGCAAA
* * *
49726 ATTGAGCCGGGGCTCCGGAACGCCTTTTTACCCAAAACCCGTGATGGTTAGTACACGATTTCGGC
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
49791 TAAAAACTGACCCGAAAAG-TTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAAT
66 TAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAAT
* * * ** *
49855 TCAACGCCAAATAGATTCATGACCTTTTCACGCTTATAAAATTGTTTTTTCA-TTTTTTTCCGAA
131 TCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTTCCGAA
* * *
49919 TTAATTTCTAATTATATCGAAACAAAATTCAGATACTCGTAAAAACAAATATTTATATCTAATGT
196 TTAATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCTAATGT
*
49984 GGTTGACATTTGGTTCGATAAATACAGT-TATTTCAAGAAGCATTTGTACCAAAATCAAGCAAA
261 GGTTGACATTTGGTTCGATAAATATA-TATATTTCAAGAAGCATTTGTACCAAAATCAAGCAAA
* *
50047 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGGA
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
** * * * * *
50112 TAAAAGTTTATCCGAAAA-TTTTTTTCTCAATATTTTGCCACAATACTCCGAAAAAATATATATT
66 TAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAAT
* * *
50176 TCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTATAATATCGTTTTTTCATTTTTTTTCAGAA
131 TCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTTCCG-A
* *
50241 ATTTATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATATAATG
195 ATTAATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCTAATG
*
50306 TGGTTGACATTTGGTTCGA-AGAATATATATATTTCAAGAACCATTTGTACCAAAAATCAAGCAA
260 TGGTTGACATTTGGTTCGATA-AATATATATATTTCAAGAAGCATTTGTACC-AAAATCAAGCAA
50370 A
323 A
**
50371 ATTGAGCCGGGGCTCCGGAATACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
** *
50436 TAAAATTTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCA-ATTTACTCCTAAAAAATATATAA
66 TAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCACA-ATACTCCTAAAAAATATATAA
* *
50500 TTCAACGCCAAAAAGGTTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCCGA
130 TTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTTCCGA
* * * * *
50565 ATTAATTACTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCTTATAT-TCAAC
195 ATTAATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCT-AAT
* * *
50629 ATGGCTGACATTTGGTTCAATAAATATAGT-TATTTCAAGAAGCATTTGTACCAAAAATCAAGCA
259 GTGGTTGACATTTGGTTCGATAAATATA-TATATTTCAAGAAGCATTTGTACC-AAAATCAAGCA
50693 AA
322 AA
*
50695 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTATACGATTTCGGC
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
* * * ** *
50760 TAAACACTGACTCGAAACGTTTTTTTCTCAATTTTTTGCCACAATACTCCGGAAAAGTATATAAT
66 TAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAAT
* * * *
50825 TCAAGGCCAAAAAGATTGACGTGCATTTCACGCTTATAATATCGTTTTTTCATTTTTTTTCCG-A
131 TCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTTCCGAA
* * * *
50889 TTAAATTTCTAATGAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAGTCCTTATAT
196 TT-AATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATAT
50948 TGAGCCGGGG
Statistics
Matches: 1096, Mismatches: 100, Indels: 39
0.89 0.08 0.03
Matches are distributed among these distances:
311 264 0.24
312 14 0.01
317 1 0.00
318 1 0.00
321 164 0.15
322 11 0.01
323 110 0.10
324 430 0.39
325 101 0.09
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (323 bp):
ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
TAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAAT
TCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTTCCGAA
TTAATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCTAATGT
GGTTGACATTTGGTTCGATAAATATATATATTTCAAGAAGCATTTGTACCAAAATCAAGCAAA
Found at i:51473 original size:575 final size:575
Alignment explanation
Indices: 50371--51523 Score: 1743
Period size: 575 Copynumber: 2.0 Consensus size: 575
50361 ATCAAGCAAA
*
50371 ATTGAGCCGGGGCTCCGGAATACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
1 ATTGAGCCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
**
50436 TAAAATTTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCAATTTACTCCTAAAAAATATATAAT
66 TAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCAATTTACTCCTAAAAAATATATAAT
* ***
50501 TCAACGCCAAAAAGGTTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCCGAA
131 TCAACGACAAAAACAATGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCCGAA
*
50566 TTAATTACTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCTTATATTCAACAT
196 TTAATTACTAATTAAATCGAAACAAAATCCAGATGCTCGTAAAAACAAATCCTTATATTCAACAT
* * *
50631 GGCTGACATTTGGTTCAATAAATATAGTTATTTCAAGAAGCATTTGTACCAAAAATCAAGCAAAA
261 GGCTGACATTTGGTTCAATAAATATAGATATTTCAAAAAGCATTTGTACCAAAAATCAACCAAAA
* * *
50696 TTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTATACGATTTCGGCT
326 TTGAGCCGGGGCTCCAGAACGCCTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
* * *
50761 AAACACTGACTCGAAACGTTTTTTTCTCAATTTTTTGCCACAATACTCCGGAAAAGTATATAATT
391 AAAAACTGACCCGAAACGTTTTTTTCTCAATTTTTTGCCACAATACTCCGGAAAAATATATAATT
*
50826 CAAGGCCAAAAAGATTGACGTGCATTTCACGCTTATAATATCGTTTTTTCATTTTTTTTCCGATT
456 CAAAGCCAAAAAGATTGACGTGCATTTCACGCTTATAATATCGTTTTTTCATTTTTTTTCCGATT
* *
50891 AAATTTCTAATGAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAGTCCTTAT
521 AAATTTCTAATGAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAT
** *
50946 ATTGAGCCGGGGCTCCGGAACGTGTTTTTAGCCAAACACCGTGATGGTTAGTACACGATTTCGGC
1 ATTGAGCCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
*
51011 TAAAAACTGACCTGAAAAGTTTTTTTTCTCAATTTTTCT-CCAATTTACTCCTAAAAAATATATA
66 TAAAAACTGACCCGAAAAG-TTTTTTTCTCAATTTTT-TGCCAATTTACTCCTAAAAAATATATA
*
51075 ATTCAACGACAAAAACAATGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTT-TCG
129 ATTCAACGACAAAAACAATGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCCG
* * * * *
51139 AATTAATTTCTAATTATATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCTTTATA-TCTA-
194 AATTAATTACTAATTAAATCGAAACAAAATCCAGATGCTCGTAAAAACAAATCCTTATATTCAAC
* *
51202 ATGTCGTTGACATTTGGTT-AGATAAATATAGATATTTCAAAAAGTATTTGTACCAAAAATCAAC
259 ATG--GCTGACATTTGGTTCA-ATAAATATAGATATTTCAAAAAGCATTTGTACCAAAAATCAAC
*
51266 CAAAATTGAGCCGGGGCTCCAGAACGCCTTTTTA-CCCAAAACTCGTGATGGTTAGTACACGATT
321 CAAAATTGAGCCGGGGCTCCAGAACGCCTTTTTAGCCAAAAAC-CGTGATGGTTAGTACACGATT
* * ** *
51330 TCGGCTAAAAACTGACCCGAAATG-TTTTTTCTCAGTTTTTTGCCGTAATACT-CTGAACAAATA
385 TCGGCTAAAAACTGACCCGAAACGTTTTTTTCTCAATTTTTTGCCACAATACTCCGGAA-AAATA
* * *
51393 TATTATTCAAAGCCTAAAAGATTGACG-GACTTTTCACGCTTATAA-ATCGTTTTTTCATTCTTT
449 TATAATTCAAAGCCAAAAAGATTGACGTG-CATTTCACGCTTATAATATCGTTTTTTCATT-TTT
* *
51456 TTTCCCGAATT-AATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTA
512 TTT-CCG-ATTAAATTTCTAATGAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTA
51520 T
575 T
51521 ATT
1 ATT
51524 CAACGTGGCT
Statistics
Matches: 524, Mismatches: 43, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
573 22 0.04
574 85 0.16
575 314 0.60
576 102 0.19
577 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (575 bp):
ATTGAGCCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
TAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCCAATTTACTCCTAAAAAATATATAAT
TCAACGACAAAAACAATGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCCGAA
TTAATTACTAATTAAATCGAAACAAAATCCAGATGCTCGTAAAAACAAATCCTTATATTCAACAT
GGCTGACATTTGGTTCAATAAATATAGATATTTCAAAAAGCATTTGTACCAAAAATCAACCAAAA
TTGAGCCGGGGCTCCAGAACGCCTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
AAAAACTGACCCGAAACGTTTTTTTCTCAATTTTTTGCCACAATACTCCGGAAAAATATATAATT
CAAAGCCAAAAAGATTGACGTGCATTTCACGCTTATAATATCGTTTTTTCATTTTTTTTCCGATT
AAATTTCTAATGAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAT
Found at i:51971 original size:321 final size:317
Alignment explanation
Indices: 50946--52266 Score: 1580
Period size: 323 Copynumber: 4.1 Consensus size: 317
50936 AAGTCCTTAT
*
50946 ATTGAGCCGGGGCTCCGGAACGTGTTTTTAGCC-AAACACCGTGATGGTTAGTACACGATTTCGG
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAC-CCGTGATGGTTAGTACACGATTTCGG
* * *
51010 CTAAAAACTGACCTGAAAAGTTTTTTTTCTCAATTTTTCT-CCAATTTACTCCTAAAAAATATAT
65 CTAAAAACTGACCCGAAAAG--TTTTTTCTCAATTTTT-TGCCAA-ATACTCCGAAAAAATATAT
* * * *
51074 AATTCAACGACAAAAACAATGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTTCG
126 AATTCAACGCCAAAAAGATTGACGGG-TTTTCACG--T-TAATATTGTTTTTTCATTTTTTTCCG
* * *
51139 AATTAATTTCTAATTATATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCTTTATATCTAAT
187 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTAAT
* * * * * *
51204 GTCGTTGACATTTGGTTAGATAAATATAGATATTTCAAAAAGTATTTGTACCAAAAATCAACCAA
252 GTGGCTGACATTTGGTTCGATAAATATAGATATTTCAAGAAGCATTTGTACCAAAAATCAAGCAA
51269 A
317 A
* * * *
51270 ATTGAGCCGGGGCTCCAGAACGCCTTTTTACCCAAAACTCGTGATGGTTAGTACACGATTTCGGC
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAACCCGTGATGGTTAGTACACGATTTCGGC
* * * * * *
51335 TAAAAACTGACCCGAAATGTTTTTTCTCAGTTTTTTGCCGTAATACTCTGAACAAATATATTATT
66 TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCC-AAATACTCCGAAAAAATATATAATT
* * * * *
51400 CAAAGCCTAAAAGATTGACGGACTTTTCACGCTTATAAATCGTTTTTTCATTCTTTTTTCCCGAA
130 CAACGCCAAAAAGATTGACGG-GTTTTCACG-TTA-ATATTGTTTTTTCA-T-TTTTTT-CCGAA
* * *
51465 TTAATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTATAT-TCAACG
189 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCT-AATG
*
51529 TGGCTGACATTTGGTTCGATAAATATAGATATTTCAAG--GTTATTTGTACCAAAAATCAAGCAA
253 TGGCTGACATTTGGTTCGATAAATATAGATATTTCAAGAAG-CATTTGTACCAAAAATCAAGCAA
51592 A
317 A
* * * *
51593 ATTGAGCAGGGGCTCCGAAACGCGTTTTTAGCCATAAA-CCGTGATTGTTAGTACACGATTTCAG
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCA-AAACCCGTGATGGTTAGTACACGATTTCGG
** *
51657 CTAAAAACTGACCCGAAAAGACTTTTCTCAGTTTTTTGCCATAATACTCCGAAAAAATATATAAT
65 CTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCA-AATACTCCGAAAAAATATATAAT
* * * *
51722 TCAACGCCAAAAAGATTGACAGGGTTTTAACAG-TACTATCGTTTTTTAATTTTTTTTTCCGAAT
129 TCAACGCCAAAAAGATTGAC-GGGTTTTCAC-GTTAATATTGTTTTTTCA--TTTTTTTCCGAAT
* * * * * *
51786 GAATTTTTAATCACATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTATATCCAATGTG
190 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTAATGTG
* * * **
51851 GCCGAAATTTGGTTCGATAAATATAGATAGTTCAAGGAA-CATTTGTACCAAAAATCTTGCAAA
255 GCTGACATTTGGTTCGATAAATATAGATATTTCAA-GAAGCATTTGTACCAAAAATCAAGCAAA
* *
51914 ATTGAGCCGGGGCTCCGGAACGTGTTTTTAGCCAAAACCCGTGATGGTTATTACACGATTTCGGC
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAACCCGTGATGGTTAGTACACGATTTCGGC
** * * * *
51979 TAAAATTTGACCTGAAAGGTTTTTTTCTCAATTTTTTGCCAATTTACTCCTAAAAAATATATAAT
66 TAAAAACTGACCCGAAAAG-TTTTTTCTCAATTTTTTGCCAA-ATACTCCGAAAAAATATATAAT
52044 TCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCGAAT
129 TCAACGCCAAAAAGATTGACGGG-TTTTCACG--T-TAATATTGTTTTTTCATTTTTTTCCGAAT
* * * * * * * *
52109 TAATTACTTATTATATCGAAACAAAATTCAGATACTTGTATAAAAC-AGTCTTTATATCTAATGT
190 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAAACAAATCCTTATATCTAATGT
* * *
52173 GGTTGACATTTGGTTAGATAAATATAGATATTTCAAGAAGCATTTGTACCAAAAATCAACCAAA
254 GGCTGACATTTGGTTCGATAAATATAGATATTTCAAGAAGCATTTGTACCAAAAATCAAGCAAA
* *
52237 ATTGAGTCGGGGCTCCGGAACGCCTTTTTA
1 ATTGAGCCGGGGCTCCGGAACGCGTTTTTA
52267 CCGGTTAAAA
Statistics
Matches: 854, Mismatches: 114, Indels: 59
0.83 0.11 0.06
Matches are distributed among these distances:
320 99 0.12
321 128 0.15
322 132 0.15
323 301 0.35
324 177 0.21
325 17 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (317 bp):
ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAACCCGTGATGGTTAGTACACGATTTCGGC
TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCAAATACTCCGAAAAAATATATAATTC
AACGCCAAAAAGATTGACGGGTTTTCACGTTAATATTGTTTTTTCATTTTTTTCCGAATTAATTT
CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTAATGTGGCTGAC
ATTTGGTTCGATAAATATAGATATTTCAAGAAGCATTTGTACCAAAAATCAAGCAAA
Found at i:53138 original size:321 final size:318
Alignment explanation
Indices: 52272--53535 Score: 1593
Period size: 319 Copynumber: 4.0 Consensus size: 318
52262 TTTTACCGGT
* *
52272 TAAAATCTGGCCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
1 TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
* * *
52337 CAACGCCAAATAGATTCATGACATTTTCACGCTTATAATATTATTTTTTCA-TTTTTTCCGAATT
66 CAACGCCAAATAGATTCACGACCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCGAATT
* * *
52401 AATTTCTAATTATATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATTATTTAATGTG
131 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA-TATCTAATGTG
* * * *
52466 GCTGACATTTGGTTCGATAAATATAGATATTTCAAGGAGTATTTTTACAAAAAATCAAGCAAAAT
195 GCTGACATTTGGTTCGATAAATATAGATATTTCAAGAAGCATTTGTACCAAAAATCAAGCAAAAT
* * * *
52531 TGAGCCGGGGCTACGAAACGCGTTTTTAGCCATAAACC------GTGCACAATTTCAGC
260 TGAGCCGGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTGCACGATTTCGGC
**** * * ** * *
52584 TAAAAACTGAAAAAATATATAACGCGTTTTTCTAAATTTTTCACCACTATAAT-CTGAAAAAATA
1 TAAAAACTG--ACCCGA-A-AA-G-TTTTTTCTCAATTTTTTGCCACAATACTCCT-AAAAAATA
* * * ** * *
52648 TATAATTCAATGCCAAATAGAATGACGGGCATTTCACGCTTAT-ATATTG-TTTTTCTTTTTTTT
59 TATAATTCAACGCCAAATAGATTCACGACCTTTTCACGCTTATAATATTGTTTTTTC-ATTTTTT
* * * * *
52711 TCCCCGAATTTATTTCTAATGAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCTTTCTA
123 T--CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATA
* * * *
52776 TCTAATGTGGTTGACATTTGGTTCGATAAATATAGATATTTCCAGAAACATTCGTACCAAAAATC
186 TCTAATGTGGCTGACATTTGGTTCGATAAATATAGATATTTCAAGAAGCATTTGTACCAAAAATC
* *
52841 AAGTAAAATTGAGTCGGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
251 AAGCAAAATTGAGCCGGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG-T-G--CACGA
52906 TTTCGGC
312 TTTCGGC
52913 TAAAAACTGACCCGAAAAG-TTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
1 TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
* * *
52977 CAACGCCAAATACATTCATGACCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCTGAATT
66 CAACGCCAAATAGATTCACGACCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCGAATT
* * *
53042 AATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCTAATGTTG
131 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTAATGTGG
* * * *
53107 TTGACATTTGGTTCGA-AGAATATATATATTTCAAGAACCATTTGTACCAAAAATCAAGCGAAAT
196 CTGACATTTGGTTCGATA-AATATAGATATTTCAAGAAGCATTTGTACCAAAAATCAAGCAAAAT
* * *
53171 TGAGCCGGGGCTCCGGAATGCGTTTTTAGTCAAAAACCGTGATGCGTGCACGATTTCGGC
260 TGAGCCGGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATG-GTGCACGATTTCGGC
** *
53231 TAAAATTTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCA-ATTTACTCCTAAAAAATATATAAT
1 TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACA-ATACTCCTAAAAAATATATAAT
* * * *
53295 TCAATGCCAAAAAGATTGACGGCCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCGAAT
65 TCAACGCCAAATAGATTCACGACCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCGAAT
* * * **
53360 TAATTACTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAACAGATCCTTATAT-TCAACAT
130 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCT-AATGT
* * * *
53424 GGCTGACATTTGGTTCAATAAATATAGTTATTTCAAGAAGCATTTGTACCAAAAATCTAGCACAA
194 GGCTGACATTTGGTTCGATAAATATAGATATTTCAAGAAGCATTTGTACCAAAAATCAAGCAAAA
*
53489 TTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGT
259 TTGAGCCGGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGT
53536 TAGTATACGA
Statistics
Matches: 815, Mismatches: 107, Indels: 54
0.84 0.11 0.06
Matches are distributed among these distances:
312 8 0.01
314 1 0.00
315 1 0.00
316 8 0.01
317 8 0.01
318 104 0.13
319 352 0.43
320 56 0.07
321 162 0.20
322 66 0.08
323 15 0.02
324 7 0.01
325 3 0.00
326 2 0.00
327 3 0.00
329 19 0.02
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (318 bp):
TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
CAACGCCAAATAGATTCACGACCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCCGAATT
AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTAATGTGG
CTGACATTTGGTTCGATAAATATAGATATTTCAAGAAGCATTTGTACCAAAAATCAAGCAAAATT
GAGCCGGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTGCACGATTTCGGC
Found at i:53503 original size:640 final size:639
Alignment explanation
Indices: 52272--53546 Score: 1746
Period size: 640 Copynumber: 2.0 Consensus size: 639
52262 TTTTACCGGT
* *
52272 TAAAATCTGGCCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
1 TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
*
52337 CAACGCCAAATAGATTCATGACATTTTCACGCTTATAATATTATTTTTTCATTTTTTCCGAATTA
66 CAACGCCAAATACATTCATGACATTTTCACGCTTATAATATTATTTTTTCATTTTTTCCGAATTA
* *
52402 ATTTCTAATTATATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATTATTTAATGTGG
131 ATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATTATCTAATGTGG
* ** *
52467 CTGACATTTGGTTCGATAAATATAGATATTTCAAGGAGTATTTTTACAAAAAATCAAGCAAAATT
196 CTGACATTTGGTTCGATAAATATAGATATTTCAAGAACCATTTGTACAAAAAATCAAGCAAAATT
*
52532 GAGCCGGGGCTACGAAACGCGTTTTTAGCCATAAACCGTGCACAATTTCAGCTAAAAACTGAAAA
261 GAGCCGGGGCTACGAAACGCGTTTTTAGCCAAAAACCGTGCACAATTTCAGCTAAAAACTG-AAA
* *
52597 AATATATAACGCGTTTTTCTAAATTTTTCACCACTATAATCTGAAAAAATATATAATTCAATGCC
325 AAGATATAACGCGTTTTTCTAAATTTTTCACCAATATAATCTGAAAAAATATATAATTCAATGCC
* * * * *
52662 AAATAGAATGACGGGCATTTCACGCTTATATATTGTTTTTCTTTTTTTTTCCCCGAATTTATTTC
390 AAAAAGAATGACGGCCATTTCACGCTTATATATTGTTTTTCTATTTTTTT-CCCGAATTAATTAC
* * * * ** *
52727 TAATGAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCTTTCTATCTAATGTGGTTGACA
454 TAATGAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCTTATATCTAACATGGCTGACA
* * * *
52792 TTTGGTTCGATAAATATAGATATTTCCAGAAACATTCGTACCAAAAATCAAGTAAAATTGAGTCG
519 TTTGGTTCAATAAATATAGATATTTCAAGAAACATTCGTACCAAAAATCAAGCAAAATTGAGCCG
52857 GGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
584 GGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
52913 TAAAAACTGACCCGAAAAG-TTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
1 TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
* * *
52977 CAACGCCAAATACATTCATGACCTTTTCACGCTTATAATATTGTTTTTTCATTTTTTTCTGAATT
66 CAACGCCAAATACATTCATGACATTTTCACGCTTATAATATTATTTTTTCA-TTTTTTCCGAATT
* *
53042 AATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTA-TATCTAATGTT
130 AATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATTATCTAATGTG
* * * *
53106 GTTGACATTTGGTTCGA-AGAATATATATATTTCAAGAACCATTTGTACCAAAAATCAAGCGAAA
195 GCTGACATTTGGTTCGATA-AATATAGATATTTCAAGAACCATTTGTACAAAAAATCAAGCAAAA
* * * * * *
53170 TTGAGCCGGGGCTCCGGAATGCGTTTTTAGTCAAAAACCGTGATGCGTGCACGATTTCGGCTAAA
259 TTGAGCCGGGGCTACGAAACGCGTTTTTAGCCAAAAA-C------CGTGCACAATTTCAGCTAAA
** *** * * ** * *
53235 ATTTG-ACCCGA-A-AA-G-TTTTTTCTCAATTTTTTGCCAATTTACTCCT-AAAAAATATATAA
317 AACTGAAAAAGATATAACGCGTTTTTCTAAATTTTTCACCAATATAAT-CTGAAAAAATATATAA
* *
53294 TTCAATGCCAAAAAGATTGACGGCCTTTTCACGCTTATAATATTGTTTTT-TCATTTTTTT-CCG
381 TTCAATGCCAAAAAGAATGACGGCCATTTCACGCTTAT-ATATTGTTTTTCT-ATTTTTTTCCCG
* *
53357 AATTAATTACTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAACAGATCCTTATAT-TCAA
444 AATTAATTACTAATGAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCTTATATCT-AA
* * * *
53421 CATGGCTGACATTTGGTTCAATAAATATAGTTATTTCAAGAAGCATTTGTACCAAAAATCTAGCA
508 CATGGCTGACATTTGGTTCAATAAATATAGATATTTCAAGAAACATTCGTACCAAAAATCAAGCA
* * *
53486 CAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTATACGAT
573 AAATTGAGCCGGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAT
Statistics
Matches: 556, Mismatches: 65, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
639 2 0.00
640 357 0.64
641 150 0.27
642 21 0.04
643 2 0.00
644 1 0.00
645 2 0.00
647 21 0.04
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (639 bp):
TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCCTAAAAAATATATAATT
CAACGCCAAATACATTCATGACATTTTCACGCTTATAATATTATTTTTTCATTTTTTCCGAATTA
ATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATTATCTAATGTGG
CTGACATTTGGTTCGATAAATATAGATATTTCAAGAACCATTTGTACAAAAAATCAAGCAAAATT
GAGCCGGGGCTACGAAACGCGTTTTTAGCCAAAAACCGTGCACAATTTCAGCTAAAAACTGAAAA
AGATATAACGCGTTTTTCTAAATTTTTCACCAATATAATCTGAAAAAATATATAATTCAATGCCA
AAAAGAATGACGGCCATTTCACGCTTATATATTGTTTTTCTATTTTTTTCCCGAATTAATTACTA
ATGAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCTTATATCTAACATGGCTGACATT
TGGTTCAATAAATATAGATATTTCAAGAAACATTCGTACCAAAAATCAAGCAAAATTGAGCCGGG
GCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
Done.