Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008482.1 Corchorus capsularis cultivar CVL-1 contig08503, 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: 35019
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:6370 original size:21 final size:21
Alignment explanation
Indices: 6344--6386 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6334 TTACAAATAA
6344 ACTCACATTCCGTGAGAGTTG
1 ACTCACATTCCGTGAGAGTTG
6365 ACTCACATTCCGTGAGAGTTG
1 ACTCACATTCCGTGAGAGTTG
6386 A
1 A
6387 ACCTAAGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
ACTCACATTCCGTGAGAGTTG
Found at i:7332 original size:32 final size:33
Alignment explanation
Indices: 7291--7355 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
7281 GAATGAAACA
7291 GCCTCGCCATATGGC-GGGTGCATTACCCATGC
1 GCCTCGCCATATGGCGGGGTGCATTACCCATGC
7323 GCCTCGCCATATGGCGGGGTGCATTACCCATGC
1 GCCTCGCCATATGGCGGGGTGCATTACCCATGC
7356 CCATTCCGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.15, C:0.34, G:0.29, T:0.22
Consensus pattern (33 bp):
GCCTCGCCATATGGCGGGGTGCATTACCCATGC
Found at i:9190 original size:3 final size:3
Alignment explanation
Indices: 9182--9251 Score: 83
Period size: 3 Copynumber: 23.0 Consensus size: 3
9172 CTTTTACCAA
9182 AAT AAT AATT AAT AAT AAT AAT ATAT AAT ATAT AAT -AT AAT AAT -AT
1 AAT AAT AA-T AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT
9228 ATAT AAT -AT AAT AAT AAT AAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT
9252 CATCCCATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.10
3 42 0.70
4 12 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:9218 original size:17 final size:15
Alignment explanation
Indices: 9182--9251 Score: 83
Period size: 16 Copynumber: 4.6 Consensus size: 15
9172 CTTTTACCAA
9182 AATAATAATTAATAAT
1 AATAATAA-TAATAAT
9198 AATAATATATAATATAT
1 AATAATA-ATAATA-AT
9215 AAT-ATAATAAT-AT
1 AATAATAATAATAAT
9228 ATATAAT-ATAATAAT
1 A-ATAATAATAATAAT
9243 AATAATAAT
1 AATAATAAT
9252 CATCCCATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.06
14 12 0.25
15 12 0.25
16 15 0.31
17 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATAATAATAATAAT
Found at i:12228 original size:127 final size:126
Alignment explanation
Indices: 12060--12314 Score: 377
Period size: 125 Copynumber: 2.0 Consensus size: 126
12050 AATTTCTCCG
*
12060 TAACTTTGCAATTGCTGGGTTTTTTGGCCTGAAGAAATTAAGGTCCCGGCTTCAGAGATTTTATT
1 TAACTTTGCAATTGCTGGGTTTTTTGGCCTGAAGAAATTAAGGTCCCGGCTTCAGAGATTTTATC
* * *
12125 GGGTTCTATTTTTTTTTCTTTATTTAAAAAAATTACAAGATTTATGATTTTTCTCGATTAAAT
66 GAGTTC--TCTTTTTTCCTTTATTTAAAAAAATTACAAGATTTATGATTTTTCTCGATTAAAT
* * *
12188 TAACTTTTCAATTGCT-GGTTTTTTTGCCTGAAGAAATTAAGGTCCCGGCTTGAGAGATTTTATC
1 TAACTTTGCAATTGCTGGGTTTTTTGGCCTGAAGAAATTAAGGTCCCGGCTTCAGAGATTTTATC
** * * *
12252 GAGTTCTCTTTTTTCCTTTATTTTCAACAATTAGAAGGTTTATGATTTTTCTCGATTAAAT
66 GAGTTCTCTTTTTTCCTTTATTTAAAAAAATTACAAGATTTATGATTTTTCTCGATTAAAT
12313 TA
1 TA
12315 TTATTATCTA
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
125 50 0.43
127 50 0.43
128 15 0.13
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (126 bp):
TAACTTTGCAATTGCTGGGTTTTTTGGCCTGAAGAAATTAAGGTCCCGGCTTCAGAGATTTTATC
GAGTTCTCTTTTTTCCTTTATTTAAAAAAATTACAAGATTTATGATTTTTCTCGATTAAAT
Found at i:27530 original size:13 final size:14
Alignment explanation
Indices: 27514--27549 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
27504 GTTTTAACGA
27514 TTTTTTTTTCTT-C
1 TTTTTTTTTCTTCC
*
27527 TTTTTTCTTCTTCC
1 TTTTTTTTTCTTCC
27541 TTTTTTTTT
1 TTTTTTTTT
27550 TTTTCTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTCTTCC
Found at i:27788 original size:6 final size:6
Alignment explanation
Indices: 27779--27811 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
27769 ATCACATGAG
27779 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAA
27812 TTAATAGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (6 bp):
GAAAAT
Found at i:30125 original size:323 final size:321
Alignment explanation
Indices: 28712--33656 Score: 5948
Period size: 321 Copynumber: 15.4 Consensus size: 321
28702 AAGCAGGGTA
* * * *
28712 TTTTCACGCATTTAATATCATTTTTTAT-AA-TTTTCCCCAATTAAATTT-TAATTAAAATCGAA
1 TTTTCACGCGTCTAATATC-TTTTTT-TCAATTTTTCTCGAATT-AATTTCTAATT-AAATCGAA
* * *
28774 ACAAGATTCAGATGCTCTTA-AAAGGAAATCCTTAAATCTAATGTGTCTGAGATTTGGTTAGATT
62 ACAAGATTCAGATGCTCCTAGAAA-CAAATCCTTAAATC-AATGTGACTGAGATTTGGTTAGATT
* * ** * * *
28838 AATATAGACATTCCAAGGAGTCTTGGCGCCAAAAATCAT-GCAAAGCTGTGCCGGG-CCCCGGAA
125 AATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCG-AAAAATGAGCCGGGACCCTGAAA
* * *
28901 CGCGTTTTTAGCCAGAAAAATCGTGATGGTTAAGTTAAGTACACGATTTCGGCAAAAAACTGACT
189 CGCATTTTTAG-C-TAAAAACCGTGAT-G----GTT-AGTACACGATTTCGGCAAAAAACTGACT
*
28966 CGAAATATTTTTCCTCAATTTTTAGCCATAATACTTATAAAAAATATACAATTCAACGCCAAAAA
246 CGAAATATTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAA
*
29031 GATTAAAGGGC
311 GATTGAAGGGC
29042 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
* * * *
29107 GATTCATATGTTCCTAGAAA-AAAACCTTAAATCAATTGTGACTGAGATTTAGTTAGATTAATAT
66 GATTCAGATGCTCCTAGAAACAAATCCTTAAATCAA-TGTGACTGAGATTTGGTTAGATTAATAT
* * *
29171 AGATATTTAAAGGAGTCTTGGCGCCAAAAATCATCAAAAAATGAGCCGGGATCCTGAAACGCATT
130 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATT
* * *
29236 TTTAGCTAAAAACCGTGATGGTTAGTACATGATTTCGACAAAAAACTGGCTCGAAATATTTTTCC
195 TTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTCC
*
29301 TCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAAGGCCAAAAAGATTGAAGGGC
260 TCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
*
29363 GTTTCACGCGTCTAATATCTTTTTTTCAA-TTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
* * * * * *
29427 GATTCACATGATCTTGGAAACAAATCCTTAAATCCAATGTGACCGAGAATTGGTTAGATTAATAT
66 GATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGTTAGATTAATAT
* * * *
29492 GGATATTTCAAGGAGTCTTGCCGCAAAAAATCATCGTAAAATGAGCCGGGACCCTGAAACGCATT
130 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATT
* * * * * * *
29557 TTTAGCT-AAAACCGTGATTGTTAGTATACGATTTTGGCAAAAGTTTTGTAAAAATTAACCCAAA
195 TTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGC---A-------AAAAACTGACTCGAA
* * * * *
29621 ATATTTTTCCTCAATTTTTAGCCACAATACTTATAAAAAATATATAATTCAATG-TAAAAA-A--
250 ATATTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATT
* *
29682 GATGGAC
315 GAAGGGC
* * * * * * * * *
29689 TTTTCACGCATCTAATATCATCTTATAAATTTTTCCCCAATTAAATTT-TAATTAAAAT-AAAAA
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATT-AATTTCTAATT-AAATCGAAAC
* *
29752 AAGATTCAGATGCTCCTA-AAAGGAAATCCTTAAATCAATTGTGTCTGAGATTTGGTTAGATTAA
64 AAGATTCAGATGCTCCTAGAAA-CAAATCCTTAAATCAA-TGTGACTGAGATTTGGTTAGATTAA
* * * * * *
29816 TAAAGATATTCCAAGGAGTCTTGGCGCCAAAAATTAT-GCAAAACTGAGCCGGGTCCCTGGAACG
127 TATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCG-AAAAATGAGCCGGGACCCTGAAACG
* * * * * *
29880 CATTTTTTGCCAGAAAAATCGTGACGGTTAGTACATGATTTCGGCAAAAAACTGACTCGAAGTAT
191 CATTTTTAG-C-TAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATAT
*
29945 TTTTTCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAG
254 TTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAG
* *
30010 AGT
319 GGC
30013 TTTTCACGCGTCTAATATC-TTTTTTCAATTTTTCTCGAATTAATATT-TAATTAAATCGAAACA
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAAT-TTCTAATTAAATCGAAACA
*
30076 AGATTCAGACGCTCCTAGAAACAAATCCTTAAATGCAATGTGACTGAGATTTGGTTAGATTAATA
65 AGATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGTTAGATTAATA
* *
30141 TAGATATTTCAAGGAGTCTTGGCGTCAAAAATCATCGAAAAATGAGCCGGGACCCTTAAACGCAT
129 TAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCAT
*
30206 TTTTAGCTAAAAACCGTGATGGTTAGTACACAATTTCGGCAAAAAACTGACTCGAAATATTTTTC
194 TTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTC
* *
30271 CTCAATTTTTATCCATAATACTCATAAATAATATACAATTCAACGCCAAAAAGATTGAAGGGC
259 CTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
30334 TTTTCACGCGTCTAATATCTTCTTTTTTTTCAATTTTATCTCGAATTAATTTCTAATTAAATCGA
1 TTTTCACGCGTCTAATA---TC-TTTTTTTCAATTTT-TCTCGAATTAATTTCTAATTAAATCGA
*
30399 AACAAGATTCAGATGCTCTTAGAAACAAATCCTTAAATGCAATGTGACTGAGATTTGGTTAGATT
61 AACAAGATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGTTAGATT
* * * *
30464 AATGTAGACATTTCAAGGAGTCTTGGCGTCTAAAATCATCGAAAAATGAGCCGGGACCCTGAAAC
125 AATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAAC
30529 GCATTTTTAGCTAAAAA-C------------ACACGATTTCGGCAAAAAACTGACTCGAAATATT
190 GCATTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATATT
* * * *
30581 TTCCCTCAATTTTTAGCCATAATAC-CAATAAAAAA-ATACAATTCAATGACAAAAAAATTGAAG
255 TTTCCTCAATTTTTAGCCATAATACTC-ATAAAAAATATACAATTCAACGCCAAAAAGATTGAAG
30644 GGC
319 GGC
* *
30647 TTTTCACCCGTCTAATATCTTTTTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCAAA
1 TTTTCACGCGTCTAATATC----TTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAA
* *
30712 ACAAGATTCAGATGCTCCTAGATACAAATCCTTAAATCCAATGTGACCGAGATTTGGTTAGATTA
62 ACAAGATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGTTAGATTA
* * * * *
30777 ATATAGATATTTTAAGGAGTCTTGTCGCCAAAAATCATCGAAATATGAGCAGGGACCTTGAAACG
126 ATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACG
* * *
30842 CATTTTTAGCT-AAAACCGTGATGGTTAGTATACGATTTC-G-AAAAAAGTTTTGTAAAAATTAA
191 CATTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAA---CTG-----ACT--
* * * * * ** *
30904 CCTAAAATATTTTTCCTCAATTTTCAGCCACAATACTTATAATAAATATTTAATTCAACG-TAAA
246 -C-GAAATATTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAA
*
30968 AA-A--GATGGGC
309 AAGATTGAAGGGC
* * * * * * *
30978 TTTTCACGCATCTAATATCATTTTATAAATTTTTCGCCAATTAAATTT-TAATTAAAATCAAAAC
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATT-AATTTCTAATT-AAATCGAAAC
* * * *
31042 AAGATTCAGATCCTCCTA-AAAGGAAATCCTTAAATCAATTGTGTCTGAGATTTAGTTAGATTAA
64 AAGATTCAGATGCTCCTAGAAA-CAAATCCTTAAATCAA-TGTGACTGAGATTTGGTTAGATTAA
* * * * * **
31106 TATAGATATTCCAAGGAGTCTTGGCGCCAAAAATTA-AGCAAAACTGAGCCGGGGCCCCAAAACG
127 TATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCG-AAAAATGAGCCGGGACCCTGAAACG
* * * * * *
31170 C-GTTTTAGCAAGAAAAATCGTGATAGTTAGTACACAATTTCGGCAAAAAACTGAATCGAAATAT
191 CATTTTTAGC--TAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATAT
** *
31234 TTTTCCTCAATTTTTAGTAATAATACTTATAAAAAATATACAATTCAACGCCAAAAAGATTGAAG
254 TTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAG
*
31299 GGA
319 GGC
*
31302 TTTTCACGCGTCTAATATCTTTTTTTTCAATTTTTCTCGAATTAAATTCTAATTAAATCGAAACA
1 TTTTCACGCGTCTAATATC-TTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACA
*
31367 AGATTCAGATGCTCCTAG------------AAA-CAA--TGACTGAGATTTGGTTAGATTAATGT
65 AGATTCAGATGCTCCTAGAAACAAATCCTTAAATCAATGTGACTGAGATTTGGTTAGATTAATAT
* * *
31417 AGATATTTCAAGGAGTCTTGGCG-TATTAAATCATCGAAAAATGAGCCGGGACCCTGAAACACAT
130 AGATATTTCAAGGAGTCTTGGCGCCA-AAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCAT
*
31481 TTTTAG--------C-T-A----T-GTACACGATTTCGACAAAAAACTGACTCGAAATATTTTTC
194 TTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTC
* * *
31531 CTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTGAAGGCCAAAAAGATTGAAGGGT
259 CTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
* * *
31594 TTTTCACGCGTCTAATATATTTTTTTTTCAATTTTTCTCGAATTAATTTATAATTAAATCGAAAT
1 TTTTCACGCGTCT-A-ATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAAC
* * *
31659 AAGATTCAGATTCTCCTACAAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATTAAT
64 AAGATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGTTAGATTAAT
*
31724 ATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCAAAAAATGAGCCGGGACCCTGAAACGCA
128 ATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCA
*
31789 TTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATATTTCT
193 TTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTT
31854 CCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
258 CCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
31918 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
** *
31983 GATTCAGATGCTCCTTCAAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATTAATAT
66 GATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGTTAGATTAATAT
32048 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCTCGGGACCCTGAAACGCAT
130 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGC-CGGGACCCTGAAACGCAT
** * * *
32113 TTTTAGCTAAAAACCGTGATAATTAGTACACAATTTCGACAAAAAAACTGACTCGAAATATTTTC
194 TTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGC-AAAAAACTGACTCGAAATATTTTT
* *
32178 CCTCAATTTTTAGCCATAATACTCATAAAAAATATAGAATTCAACGCCAAAAAGATTGAATGGC
258 CCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
* * * * *
32242 CTTTCACGCGTCTAATATATTTTTTTCAATTTTTATCGAATTAATTTCTATTTAAAACGAAACAA
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
* *
32307 GATTCAAATGCTCCGAGAAACAAATCCTTAAATTCAATGTGACTGAGATTTGGTTAGATTAATAT
66 GATTCAGATGCTCCTAGAAACAAATCCTTAAA-TCAATGTGACTGAGATTTGGTTAGATTAATAT
* * *
32372 AGATATTTCAAGGAGTCTTGCCGCAAAAAATCATCGAAGAATGAGCCAGGG-CCCTGAAACGCAT
130 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCC-GGGACCCTGAAACGCAT
* * * * * * *
32436 TTTTAGCT-AAAATCGTGATGGTTAGTATATGATTTCGGCAAAAGTTTTGTAAAAATTAACCCAA
194 TTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGC---A-------AAAAACTGACTCGA
* * *
32500 AATATTTTTCCTC-ATTTTTCAGCCACAATACAT-ATAAAAAATATATAATTCAACG-TAAAAA-
249 AATATTTTTCCTCAATTTTT-AGCCATAATAC-TCATAAAAAATATACAATTCAACGCCAAAAAG
** *
32561 A-AAAAGGGG
312 ATTGAAGGGC
* * * * * * * *
32570 TTTTCACACATCTAATATCATTTTATAAATTTTTCGCCAATTAAATTT-TAATTAAAATCAAAAC
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATT-AATTTCTAATT-AAATCGAAAC
* * * * *
32634 AAGATTCAGATGCTCCTA-AAAGGAAATCTTTAAATCAATTGTGTCTGAGATTTAGTTAGATTAG
64 AAGATTCAGATGCTCCTAGAAA-CAAATCCTTAAATCAA-TGTGACTGAGATTTGGTTAGATTAA
* * * * * * * *
32698 TATAGATATTTCAAGAAGTCTTGGCGCCAAAAATTA-AGTAGAATTGAGCCGGGACCCCGGAATG
127 TATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCG-AAAAATGAGCCGGGACCCTGAAACG
* * * * * *
32762 CGTTTTTAGCCAGAAAAATCGTGATAGTTAGTACACGATTTCGGCAGAAAACTGACTTGAAATAT
191 CATTTTTAG-C-TAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATAT
* *
32827 TTTTCCTCAATTTTTAGCCATAATACTTATAAAAAATATACAATTCAAGGCCAAAAAGATTGAAG
254 TTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAG
*
32892 GAC
319 GGC
* *
32895 TTTTCACGCGTCTAATAT-ATTTTTTCAAATTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
* *
32959 GATTCAGATGCTCATAGAAACAAATCCTTAAGTGCAATGTGACTGAGATTTGGTTAGATTAATAT
66 GATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGTTAGATTAATAT
* **
33024 AGATATTTCAAGGTGTCTTGGCGTAAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATT
130 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATT
* * * *
33089 ATTATCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTAACTTGAAATATTTTTCC
195 TTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTCC
* * * *
33154 TCAATTTTTAGCCATAATACTTATAAAAAATATACAATTCATCACCCAAAAGATTGAAGGGC
260 TCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
* * *
33216 TTTTCACGCGTCTAATATCTTTTTTTTCAATTTTTGTCGAATTAATTTTTATTTAAATCGAAACA
1 TTTTCACGCGTCTAATATC-TTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACA
* * ** ** *
33281 AGATTCAGATGCTCCTAGAAACAAATACTTAAATCCAATGTGAATCCGATTTTATTAGATTAATG
65 AGATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGTTAGATTAATA
* * * *
33346 TAAATATTTCAAGTAGTCTTGGCGTCAAAAATCATCGAAAATTGAGCCGGGACCCTGAAACGCAT
129 TAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCAT
* * *
33411 TTTTAGCTAAAAACTGTGATGGTTAGTAAAGGATTTCGGCAAAAAAACTGACTCAGAAATATTTT
194 TTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGC-AAAAAACTGACTC-GAAATATTTT
* * * * * *
33476 TCTTCAATTTTTAGACATAATACTCGTAAAAAATATACAATTCAATGTCAAAAAGATTGAAGGAC
257 TCCTCAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
*
33541 TTTTCACGCGTCTGATATC---TTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
1 TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
* *
33603 GATTCAGATGCTCCTACAAACAAATCCTTAAATGCAATATGACTGAGATTTGGT
66 GATTCAGATGCTCCTAGAAACAAATCCTTAAAT-CAATGTGACTGAGATTTGGT
33657 CAGAAACATT
Statistics
Matches: 3985, Mismatches: 464, Indels: 341
0.83 0.10 0.07
Matches are distributed among these distances:
292 107 0.03
293 60 0.02
294 4 0.00
297 1 0.00
298 1 0.00
299 1 0.00
305 3 0.00
307 3 0.00
308 71 0.02
309 96 0.02
310 3 0.00
311 7 0.00
312 159 0.04
313 60 0.02
314 63 0.02
317 1 0.00
318 1 0.00
319 1 0.00
320 185 0.05
321 580 0.15
322 254 0.06
323 543 0.14
324 497 0.12
325 129 0.03
326 52 0.01
327 341 0.09
328 261 0.07
329 178 0.04
330 158 0.04
331 77 0.02
332 35 0.01
333 2 0.00
334 41 0.01
335 10 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (321 bp):
TTTTCACGCGTCTAATATCTTTTTTTCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCCTAGAAACAAATCCTTAAATCAATGTGACTGAGATTTGGTTAGATTAATATA
GATATTTCAAGGAGTCTTGGCGCCAAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATTT
TTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTCCT
CAATTTTTAGCCATAATACTCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGC
Found at i:32160 original size:324 final size:322
Alignment explanation
Indices: 31491--33656 Score: 2913
Period size: 324 Copynumber: 6.7 Consensus size: 322
31481 TTTTAGCTAT
*
31491 GTACACGATTTCGACAAAAAACTGACTCGAAATATTTTTCCTCAATTTTTAGCCATAATACTCAT
1 GTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTCCTCAATTTTTAGCCATAATACTCAT
* * * *
31556 AAAAAATATACAATTGAAGGCCAAAAAGATTGAAGGGTTTTTCACGCGTCTAATATATTTTTTTT
66 AAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCT-A-ATATCTTTTTT
* * *
31621 TCAATTTTTCTCGAATTAATTTATAATTAAATCGAAATAAGATTCAGATTCTCCTACAAACAAAT
129 TCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTACAAACAAAT
*
31686 CCTTAAATCCATTGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGGCGCC
194 CCTTAAATCCAATGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGGCGCC
*
31751 AAAAATCATCAAAAAATGAGCCGGGACCCTGAAACGCATTTTTAGCTAAAAACCGTGATGGTTA
259 AAAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATTTTTAGCTAAAAACCGTGATGGTTA
*
31815 GTACACGATTTCGGCAAAAAACTGACTCGAAATATTTCTCCTCAATTTTTAGCCATAATACTCAT
1 GTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTCCTCAATTTTTAGCCATAATACTCAT
31880 AAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCTAATATCTTTTTTTC
66 AAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCTAATATCTTTTTTTC
*
31945 AATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTTCAAACAAATCC
131 AATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTACAAACAAATCC
*
32010 TTAAATCCATTGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGGCGCCAA
196 TTAAATCCAATGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGGCGCCAA
**
32075 AAATCATCGAAAAATGAGCTCGGGACCCTGAAACGCATTTTTAGCTAAAAACCGTGATAATTA
261 AAATCATCGAAAAATGAGC-CGGGACCCTGAAACGCATTTTTAGCTAAAAACCGTGATGGTTA
* * *
32138 GTACACAATTTCGACAAAAAAACTGACTCGAAATATTTTCCCTCAATTTTTAGCCATAATACTCA
1 GTACACGATTTCGGC-AAAAAACTGACTCGAAATATTTTTCCTCAATTTTTAGCCATAATACTCA
* * * *
32203 TAAAAAATATAGAATTCAACGCCAAAAAGATTGAATGGCCTTTCACGCGTCTAATATATTTTTTT
65 TAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCTAATATCTTTTTTT
* * * * * *
32268 CAATTTTTATCGAATTAATTTCTATTTAAAACGAAACAAGATTCAAATGCTCCGAGAAACAAATC
130 CAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTACAAACAAATC
* * *
32333 CTTAAATTCAATGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGCCGCAA
195 CTTAAATCCAATGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGGCGCCA
* *
32398 AAAATCATCGAAGAATGAGCCAGGG-CCCTGAAACGCATTTTTAGCT-AAAATCGTGATGGTTA
260 AAAATCATCGAAAAATGAGCC-GGGACCCTGAAACGCATTTTTAGCTAAAAACCGTGATGGTTA
* * * * * *
32460 GTATATGATTTCGGCAAAAGTTTTGTAAAAATTAACCCAAAATATTTTTCCTC-ATTTTTCAGCC
1 GTACACGATTTCGGC---A-------AAAAACTGACTCGAAATATTTTTCCTCAATTTTT-AGCC
* * * ** * * *
32524 ACAATACAT-ATAAAAAATATATAATTCAACG-TAAAAA-A-AAAAGGGGTTTTCACACATCTAA
55 ATAATAC-TCATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCTAA
* * * * * *
32585 TATCATTTTATAAATTTTTCGCCAATTAAATTT-TAATTAAAATCAAAACAAGATTCAGATGCTC
119 TATCTTTTTTTCAATTTTTCTCGAATT-AATTTCTAATT-AAATCGAAACAAGATTCAGATGCTC
* * * * *
32649 CTA-AAAGGAAATCTTTAAAT-CAATTGTGTCTGAGATTTAGTTAGATTAGTATAGATATTTCAA
182 CTACAAA-CAAATCCTTAAATCCAA-TGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAA
* * * * * * * * * *
32712 GAAGTCTTGGCGCCAAAAATTA-AGTAGAATTGAGCCGGGACCCCGGAATGCGTTTTTAGCCAGA
245 GGAGTCTTGGCGCCAAAAATCATCG-AAAAATGAGCCGGGACCCTGAAACGCATTTTTAG-C-TA
* *
32776 AAAATCGTGATAGTTA
307 AAAACCGTGATGGTTA
* * *
32792 GTACACGATTTCGGCAGAAAACTGACTTGAAATATTTTTCCTCAATTTTTAGCCATAATACTTAT
1 GTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTCCTCAATTTTTAGCCATAATACTCAT
* * *
32857 AAAAAATATACAATTCAAGGCCAAAAAGATTGAAGGACTTTTCACGCGTCTAATAT-ATTTTTTC
66 AAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCTAATATCTTTTTTTC
* * *
32921 AAATTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAGAAACAAATCC
131 AATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTACAAACAAATCC
* * * **
32986 TTAAGTGCAATGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGTGTCTTGGCGTAAA
196 TTAAATCCAATGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGGCGCCAA
* *
33051 AAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATTATTATCTAAAAACCGTGATGGTTA
261 AAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATTTTTAGCTAAAAACCGTGATGGTTA
* * *
33113 GTACACGATTTCGGCAAAAAACTAACTTGAAATATTTTTCCTCAATTTTTAGCCATAATACTTAT
1 GTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTCCTCAATTTTTAGCCATAATACTCAT
* * *
33178 AAAAAATATACAATTCATCACCCAAAAGATTGAAGGGCTTTTCACGCGTCTAATATCTTTTTTTT
66 AAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCTAATATC-TTTTTTT
* * * * *
33243 CAATTTTTGTCGAATTAATTTTTATTTAAATCGAAACAAGATTCAGATGCTCCTAGAAACAAATA
130 CAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTACAAACAAATC
* ** ** * * * *
33308 CTTAAATCCAATGTGAATCCGATTTTATTAGATTAATGTAAATATTTCAAGTAGTCTTGGCGTCA
195 CTTAAATCCAATGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGGCGCCA
* *
33373 AAAATCATCGAAAATTGAGCCGGGACCCTGAAACGCATTTTTAGCTAAAAACTGTGATGGTTA
260 AAAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATTTTTAGCTAAAAACCGTGATGGTTA
* * * *
33436 GTAAAGGATTTCGGCAAAAAAACTGACTCAGAAATATTTTTCTTCAATTTTTAGACATAATACTC
1 GTACACGATTTCGGC-AAAAAACTGACTC-GAAATATTTTTCCTCAATTTTTAGCCATAATACTC
* * * * *
33501 GTAAAAAATATACAATTCAATGTCAAAAAGATTGAAGGACTTTTCACGCGTCTGATATC---TTT
64 ATAAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCTAATATCTTTTTT
33563 TCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTACAAACAAAT
129 TCAATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTACAAACAAAT
* *
33628 CCTTAAATGCAATATGACTGAGATTTGGT
194 CCTTAAATCCAATGTGACTGAGATTTGGT
33657 CAGAAACATT
Statistics
Matches: 1615, Mismatches: 191, Indels: 75
0.86 0.10 0.04
Matches are distributed among these distances:
321 215 0.13
322 232 0.14
323 398 0.25
324 404 0.25
325 103 0.06
328 50 0.03
329 119 0.07
330 12 0.01
331 53 0.03
332 29 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (322 bp):
GTACACGATTTCGGCAAAAAACTGACTCGAAATATTTTTCCTCAATTTTTAGCCATAATACTCAT
AAAAAATATACAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCGTCTAATATCTTTTTTTC
AATTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCCTACAAACAAATCC
TTAAATCCAATGTGACTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTGGCGCCAA
AAATCATCGAAAAATGAGCCGGGACCCTGAAACGCATTTTTAGCTAAAAACCGTGATGGTTA
Found at i:34519 original size:50 final size:50
Alignment explanation
Indices: 34460--34670 Score: 302
Period size: 50 Copynumber: 4.2 Consensus size: 50
34450 AAGAGAGAAC
34460 ACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAG
1 ACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAG
* *
34510 ACACGAAGGTACCCGAGAAGAC--AGGCCTCCGCAGTGAGGCGAGGCCGG
1 ACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAG
* *
34558 ACATGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAG
1 ACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAG
* *
34608 ACACGAAGGTACACAAGAAAACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAG
1 ACACGAAGGTACAC--G-AGA-AGA-CAGAGGCCTCCGCAGTGAGGCGAGGCCAG
34663 ACAC-AAGG
1 ACACGAAGG
34671 CCAGACACGA
Statistics
Matches: 144, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
48 44 0.31
50 58 0.40
52 1 0.01
53 2 0.01
54 7 0.05
55 32 0.22
ACGTcount: A:0.33, C:0.26, G:0.35, T:0.06
Consensus pattern (50 bp):
ACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAG
Found at i:34646 original size:55 final size:55
Alignment explanation
Indices: 34532--34921 Score: 389
Period size: 55 Copynumber: 7.0 Consensus size: 55
34522 CCGAGAAGAC
* * *
34532 AGGCCTCCGCAGTGAGGCGAGGCCGGACATGAAGCTACACGAGAAGAC-----AG
1 AGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAG
* *
34582 AGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACAAGAAAACAGAGGAG
1 AGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAG
* ** *
34637 AGGCCTCCGCAGTGAGGCGAGGCCAGACAC-AAGGCCAGACACGAAGGTGCACGAGAAGACAG
1 AGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGG---TACACG-AGAAG-AC-AG-AG-GAG
*** * * * * *
34699 AGGAGAGGCCTCCG-CAGTGAGGCGAGGCCAGATACGAAGGTACACGAGAAGACAGAGGAG
1 A-G-GCCTCCGCAGTGAG-G-CG--AGGCCAGACACGAAGGTACACGAGAAGACAGAGGAG
* * *
34759 AGACCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACTAGAAGACAGAGAAG
1 AGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAG
* *
34814 AGGCCTCCGCAGTGGGGCGAGGCCAGACACGAAGGTGCACGAGAAGACAGAGGAG
1 AGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAG
* *
34869 AGGCCTCTGCAGTGAGGCGAGGCCAGATACGAAGGTACACGAGAAGACAGAGG
1 AGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGG
34922 CCTCTGCAGT
Statistics
Matches: 276, Mismatches: 43, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
50 43 0.16
54 4 0.01
55 164 0.59
57 5 0.02
58 7 0.03
59 5 0.02
60 5 0.02
61 4 0.01
62 5 0.02
63 5 0.02
64 9 0.03
65 6 0.02
67 10 0.04
68 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.37, T:0.07
Consensus pattern (55 bp):
AGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAG
Found at i:34709 original size:67 final size:67
Alignment explanation
Indices: 34601--34730 Score: 233
Period size: 67 Copynumber: 1.9 Consensus size: 67
34591 CAGTGAGGCG
34601 AGGCCAGACACGAAGGTACACAAGAAAACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
1 AGGCCAGACACGAAGGTACACAAGAAAACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
34666 CA
66 CA
* * *
34668 AGGCCAGACACGAAGGTGCACGAGAAGACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGA
1 AGGCCAGACACGAAGGTACACAAGAAAACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGA
34731 TACGAAGGTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.35, C:0.25, G:0.36, T:0.05
Consensus pattern (67 bp):
AGGCCAGACACGAAGGTACACAAGAAAACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
CA
Found at i:34766 original size:122 final size:118
Alignment explanation
Indices: 34580--34895 Score: 450
Period size: 110 Copynumber: 2.7 Consensus size: 118
34570 ACGAGAAGAC
* *
34580 AGAGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACAAGAAAACAGAGGAGAGGCCTCC
1 AGAGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAGAGGCCTCC
* *
34645 GCAGTGAGGCGAGGCCAGACACAAGGCCAGACACGAAGGTGCACGAGAAGACAGAGG
66 GCAGTGAGGCGAGGCCAG----AAGGCCAGACACGAAGGTACACGAGAAGACAGAGA
* *
34702 AGAGGCCTCCGCAGTGAGGCGAGGCCAGATACGAAGGTACACGAGAAGACAGAGGAGAGACCTCC
1 AGAGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAGAGGCCTCC
*
34767 GCAGT-----GAGG-C-G-AGGCCAGACACGAAGGTACACTAGAAGACAGAGA
66 GCAGTGAGGCGAGGCCAGAAGGCCAGACACGAAGGTACACGAGAAGACAGAGA
* * *
34812 AGAGGCCTCCGCAGTGGGGCGAGGCCAGACACGAAGGTGCACGAGAAGACAGAGGAGAGGCCTCT
1 AGAGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAGAGGCCTCC
34877 GCAGTGAGGCGAGGCCAGA
66 GCAGTGAGGCGAGGCCAGA
34896 TACGAAGGTA
Statistics
Matches: 174, Mismatches: 12, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
110 96 0.55
115 5 0.03
116 2 0.01
117 5 0.03
122 66 0.38
ACGTcount: A:0.33, C:0.24, G:0.37, T:0.06
Consensus pattern (118 bp):
AGAGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGAGAGGCCTCC
GCAGTGAGGCGAGGCCAGAAGGCCAGACACGAAGGTACACGAGAAGACAGAGA
Found at i:34846 original size:165 final size:162
Alignment explanation
Indices: 34460--34921 Score: 583
Period size: 165 Copynumber: 2.8 Consensus size: 162
34450 AAGAGAGAAC
* * *
34460 ACACGAAGGTACAC-G-AGA-AGA-CAGAGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTA
1 ACACGAAGGTACACAGAAGACAGAGAAGAGGCCTCCGCAGTGGGGCGAGGCCAGACACGAAGGTG
* * * * *
34521 CCCGAGAAGAC-------AGGCCTCCGCAGTGAGGCGAGGCCGGACATGAAGCTACACGAGAAGA
66 CACGAGAAGACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGATACGAAGGTACACGAGAAGA
34579 C--A-GAGGCCTCCGCAGTGAGGCGAGGCCAG
131 CAGAGGAGGCCTCCGCAGTGAGGCGAGGCCAG
* *
34608 ACACGAAGGTACACAAGAAAACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGACACAAGGCC
1 ACACGAAGGTACAC-AGAAGACAGAGAAGAGGCCTCCGCAGT---G-G-GG-C-G-----AGGCC
34673 AGACACGAAGGTGCACGAGAAGACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGATACGAAG
53 AGACACGAAGGTGCACGAGAAGACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGATACGAAG
34738 GTACACGAGAAGACAGAGGAGAGACCTCCGCAGTGAGGCGAGGCCAG
118 GTACACGAGAAGACAGAGGAG-G-CCTCCGCAGTGAGGCGAGGCCAG
34785 ACACGAAGGTACACTAGAAGACAGAGAAGAGGCCTCCGCAGTGGGGCGAGGCCAGACACGAAGGT
1 ACACGAAGGTACAC-AGAAGACAGAGAAGAGGCCTCCGCAGTGGGGCGAGGCCAGACACGAAGGT
*
34850 GCACGAGAAGACAGAGGAGAGGCCTCTGCAGTGAGGCGAGGCCAGATACGAAGGTACACGAGAAG
65 GCACGAGAAGACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGATACGAAGGTACACGAGAAG
34915 ACAGAGG
130 ACAGAGG
34922 CCTCTGCAGT
Statistics
Matches: 272, Mismatches: 13, Indels: 41
0.83 0.04 0.13
Matches are distributed among these distances:
148 14 0.05
150 1 0.00
151 2 0.01
152 3 0.01
153 15 0.06
156 1 0.00
158 2 0.01
159 1 0.00
160 1 0.00
165 115 0.42
170 1 0.00
171 1 0.00
172 46 0.17
173 1 0.00
174 2 0.01
175 3 0.01
176 1 0.00
177 62 0.23
ACGTcount: A:0.33, C:0.24, G:0.36, T:0.06
Consensus pattern (162 bp):
ACACGAAGGTACACAGAAGACAGAGAAGAGGCCTCCGCAGTGGGGCGAGGCCAGACACGAAGGTG
CACGAGAAGACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGATACGAAGGTACACGAGAAGA
CAGAGGAGGCCTCCGCAGTGAGGCGAGGCCAG
Found at i:34971 original size:110 final size:109
Alignment explanation
Indices: 34668--34972 Score: 312
Period size: 110 Copynumber: 2.8 Consensus size: 109
34658 GCCAGACACA
* * ** * * *
34668 AGGCCAGACACGAAGGTGCACGAGAAGACAGAGGAGAGGCCTCCGCAGTGAGGCGAGGCCAGATA
1 AGGCCAGACACGAAGGTACAC-AGAAGACAGAGAAGAGGCCTCCGCAGTGACACGAAGACAGACA
* *
34733 CGAAGGTACACGAGAAGACAGAGGAGAGACCTCCGCAGTGAGGCG
65 CAAAGGTACACAAGAAGACAGAGGAGAGACCTCCGCAGTGAGGCG
*** * *
34778 AGGCCAGACACGAAGGTACACTAGAAGACAGAGAAGAGGCCTCCGCAGTGGGGCGAGGCCAGACA
1 AGGCCAGACACGAAGGTACAC-AGAAGACAGAGAAGAGGCCTCCGCAGTGACACGAAGACAGACA
* * * * *
34843 CGAAGGTGCACGAGAAGACAGAGGAGAGGCCTCTGCAGTGAGGCG
65 CAAAGGTACACAAGAAGACAGAGGAGAGACCTCCGCAGTGAGGCG
* * *
34888 AGGCCAGATACGAAGGTACAC-G-AGA-AGA-CAGAGGCCTCTGCAGTCGAAACACGAAGACAGA
1 AGGCCAGACACGAAGGTACACAGAAGACAGAGAAGAGGCCTCCGCAGT-G--ACACGAAGACAGA
*
34949 CACAAAGGTTCACACAATAAGACA
63 CACAAAGG-T-ACACAAGAAGACA
34973 CGGTGGTGCT
Statistics
Matches: 170, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
105 14 0.08
106 4 0.02
107 3 0.02
108 16 0.09
109 1 0.01
110 132 0.78
ACGTcount: A:0.35, C:0.23, G:0.34, T:0.08
Consensus pattern (109 bp):
AGGCCAGACACGAAGGTACACAGAAGACAGAGAAGAGGCCTCCGCAGTGACACGAAGACAGACAC
AAAGGTACACAAGAAGACAGAGGAGAGACCTCCGCAGTGAGGCG
Done.