Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014232.1 Corchorus olitorius cultivar O-4 contig14265, 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: 169288
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:908 original size:15 final size:15
Alignment explanation
Indices: 888--932 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
878 TACATTAGGT
*
888 GGATTTGTATATGAC
1 GGATTTGCATATGAC
*
903 GGATTTGCATATCAC
1 GGATTTGCATATGAC
*
918 GGATTTGGATATGAC
1 GGATTTGCATATGAC
933 CCCTGCAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (15 bp):
GGATTTGCATATGAC
Found at i:3756 original size:960 final size:956
Alignment explanation
Indices: 1891--3965 Score: 2924
Period size: 960 Copynumber: 2.1 Consensus size: 956
1881 ACTCCTAACA
* * * * * * * *
1891 TTAAATCCATTCTGACTGAGATTTGATTC-ATGAATATAGATATTTTAAAGAGGCTTTTTACACA
1 TTAAATCCATTGTG-CTGAGATTTGGTTCGATAAATATAGATATTTCAAGGAGACTTTCTGC-CA
* * * * * *
1955 AAAATCATGCAAAACTAAGCCGGGTCTCGGAAACTCGTTTTTAGCCCAAAAAACGTGATGGTAAG
64 AAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTA-CCCAAAAACCGTGATGGTTAG
*
2020 TACACGATTTTCAGCTAAAAAGTTACCCAAAATATTTTTTCTGAAATTCTTGCCACAATACTCAG
128 TACACGA-TTTCAGCTAAAAAGTGACCCAAAATATTTTTTCTGAAATTCTTGCCACAATACTCAG
* * *
2085 AAAAAACATATAATTCAACGCAAAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATTGTTTTT
192 AAAAAACATATAATTCAAAGCAAAAAAAAAATTGAAGGGTTTTTCACGCTTCCAAAATCGTTTTT
* *
2150 CCATTTTTTCCCGAATTTATTTGTAATTAAATCGAAAAAAATTCAGATGCTCGTAAAAACAAATC
257 CCATTTTTTCCCGAATTTATTTCTAATTAAACCGAAAAAAATTCAGATGCTCGTAAAAACAAATC
* * * *
2215 CTTGAATCGAATGTGGCTGAAATTTGGTTCGATGAATACAGATATTTCATGGAGACTTTCTTGCC
322 CTTAAATCGAATCTGCCTGAAATTTGGTTCGATGAATACAGATATTTCAAGGAGACTTTCTTGCC
* * *
2280 AAAAATCATGCAAAACTGAGCCGGGTCCCCGAAACTCGTTTTTAGCCCCAAAACAGTGATGGTTA
387 AAAAATCATGCAAAACTGAGCCGGATCCCCGAAACGCGTTTTTAGCCCAAAAACAGTGATGGTTA
2345 GTACACGATTTCGGCTAAAAAGTGACCCAAAAATATTTTCTGAATTTTTTGCCACAATACTGAGA
452 GTACACGATTTCGGCTAAAAAGTGACCCAAAAATATTTTCTGAATTTTTTGCCACAATACTGAGA
*
2410 AAAAATATATAATTCAACGCAAAAAAAATTGAAAGGTATTTCACGCTTCCAATATCGTTTTCCAT
517 AAAAATATATAATTCAACGCAAAAAAAATTGAAAGGTATTTCACGCTTCCAATACCGTTTTCCAT
* *
2475 TTTTTTCCGAATTTATTTCTAATTAAACCGAAACAAATTCAGATACTCGTAAGAACAAATCCTTA
582 TTTTTTCCGAATTTATTTCTAATTAAACCGAAAAAAATTCAGATACTCGTAAAAACAAATCCTTA
* * * *
2540 AATCCATTCTTCCTGAAATTTGGTTCAATGAATATAGATATTTCAAAGAGGCTTTCTGCCCAAAA
647 AATCCAATCTGCCTGAAATTTGGTTCAATGAATACAGATATTTCAAAGAGGCTTTCTGCCAAAAA
*
2605 TCATGCAAAACTGAGCCGGGTTCCCGAAACCAAATCTCAGACCCAAAAAACAGTGATACACGATT
712 TCATGCAAAACTGAGCCGGGTCCCCGAAACCAAATCTCAGA-CCAAAAAACAGTGATACACGATT
2670 TTGACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAAAATATAG
776 TTGACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAAAATATAG
2735 AATTTAACGCAAAAAAAATTGAAGGTTTTTCACGCTTCTAATACCGTTTTTTTTCATTTTTT-C-
841 AATTTAACGCAAAAAAAATTGAAGGTTTTTCACGCTTCTAATACCG------TTCATTTTTTCCA
* *
2798 G-GAATTTATTTCTAATTAAATTGAAATAAAATTCAGATACTCGTAAGAACAAATCC
900 GTGAATTTATTTCTAATTAAATTGAAACAAAATTCAGATACTCGTAAAAACAAATCC
*
2854 TTAAATCCATTGTAGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGGAGACTTTCTGCTAA
1 TTAAATCCATTGT-GCTGAGATTTGGTTCGATAAATATAGATATTTCAAGGAGACTTTCTGCCAA
*
2919 AAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTACCCAAAAACCATGATGGTTAGTA
65 AAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTACCCAAAAACCGTGATGGTTAGTA
* * *
2984 CACGATTTCAGCTAAAAGGTGACCCGAAAAT-TTTTTTCTGAAATT-TTGCGACAATACTCGGAA
130 CACGATTTCAGCTAAAAAGTGACCC-AAAATATTTTTTCTGAAATTCTTGCCACAATACTCAGAA
**
3047 AAAACATATAATTCAAAGCAAAAAAAATCTTGAAGGGTTTTTCACGCTTCCAAAATCG-TTTTCC
194 AAAACATATAATTCAAAGCAAAAAAAAAATTGAAGGGTTTTTCACGCTTCCAAAATCGTTTTTCC
*
3111 ATTTTTTTCCCGAATTTATTTCTAATTAAACCGAAACAAATTCAGATGCTCGTAAAAACAAATCC
259 A-TTTTTTCCCGAATTTATTTCTAATTAAACCGAAAAAAATTCAGATGCTCGTAAAAACAAATCC
* * * * *
3176 TTAAATTC-ATTCTGCCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGCCTTTTTTTGC
323 TTAAA-TCGAATCTGCCTGAAATTTGGTTCGATGAATACAGATATTTCAAGGAGAC-TTTCTTGC
*
3240 CAAAAATCATGCAAAACTGAGCCGGATCCCCGAAACGCGTTTTTTGCCCAAAAACAGTGATGGTT
386 CAAAAATCATGCAAAACTGAGCCGGATCCCCGAAACGCGTTTTTAGCCCAAAAACAGTGATGGTT
* *
3305 AGTACACGATTTTCGGCTAAAAAGTGTCCCGAAAATATTTTCTGAATTTTTTTGCCACAATACTG
451 AGTACACGA-TTTCGGCTAAAAAGTGACCCAAAAATATTTTCTGAA-TTTTTTGCCACAATACTG
* * * * *
3370 AGAAAAAATATATAATTTAACGCAATAAAAAAATTG-AAGGTTTTTCATGCTTCCATTACCCTTT
514 AGAAAAAATATATAATTCAACGC-A-AAAAAAATTGAAAGGTATTTCACGCTTCCAATA-CC-GT
* * *
3434 TTTCCTCTTTTTTTTCCGAATTTATTTGTAATTAAATCGAAAAAAATTCAGATGA-TCGTAAAAA
575 TTT-C-CATTTTTTTCCGAATTTATTTCTAATTAAACCGAAAAAAATTCAGAT-ACTCGTAAAAA
* ** * ** ****
3498 CAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTTGATGAATACAGATATTTTGTGGAGGCTTT
637 CAAATCCTTAAATCCAATCTGCCTGAAATTTGGTTCAATGAATACAGATATTTCAAAGAGGCTTT
* ** * * *
3563 CTGCGAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAACTC-GTTTTTAG-CCAAAAATCAGTG
702 CTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAAC-CAAATCTCAGACCAAAAAACAGTG
3626 ATACACG-TTTTCGACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAG
766 ATACACGATTTT-GACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAG
*
3690 AAAAAATATATAATTTAACGCAAAAAATAAATTGAAGGTTTTTCACGCTTCTAATACCG-T-ATT
830 AAAAAATATAGAATTTAACGC-AAAAA-AAATTGAAGGTTTTTCACGCTTCTAATACCGTTCATT
3753 TTTTCCATGTTTTTTCCGAATTTATTTCTAATTAAATTGAAACAAAATTCAGATACTCGTAAAAA
893 TTTTCCA-G-----T--GAATTTATTTCTAATTAAATTGAAACAAAATTCAGATACTCGTAAAAA
3818 CAAATCC
950 CAAATCC
* *
3825 TTAAATCCATTGTGGTTGAGATTTGGTTCGATAAGTACT-GATATTTC-AGGAAGACTTTCTGCC
1 TTAAATCCATTGT-GCTGAGATTTGGTTCGATAAATA-TAGATATTTCAAGG-AGACTTTCTGCC
**
3888 AAAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTACCCAAAAACCGTGATAATTAG
63 AAAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTACCCAAAAACCGTGATGGTTAG
*
3953 TACACAATTTCAG
128 TACACGATTTCAG
3966 TTAATGGAAG
Statistics
Matches: 994, Mismatches: 86, Indels: 56
0.88 0.08 0.05
Matches are distributed among these distances:
959 7 0.01
960 180 0.18
961 113 0.11
962 64 0.06
963 106 0.11
964 47 0.05
965 15 0.02
966 95 0.10
967 6 0.01
968 175 0.18
969 2 0.00
970 3 0.00
971 180 0.18
972 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (956 bp):
TTAAATCCATTGTGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGGAGACTTTCTGCCAAA
AATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTACCCAAAAACCGTGATGGTTAGTAC
ACGATTTCAGCTAAAAAGTGACCCAAAATATTTTTTCTGAAATTCTTGCCACAATACTCAGAAAA
AACATATAATTCAAAGCAAAAAAAAAATTGAAGGGTTTTTCACGCTTCCAAAATCGTTTTTCCAT
TTTTTCCCGAATTTATTTCTAATTAAACCGAAAAAAATTCAGATGCTCGTAAAAACAAATCCTTA
AATCGAATCTGCCTGAAATTTGGTTCGATGAATACAGATATTTCAAGGAGACTTTCTTGCCAAAA
ATCATGCAAAACTGAGCCGGATCCCCGAAACGCGTTTTTAGCCCAAAAACAGTGATGGTTAGTAC
ACGATTTCGGCTAAAAAGTGACCCAAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAAA
ATATATAATTCAACGCAAAAAAAATTGAAAGGTATTTCACGCTTCCAATACCGTTTTCCATTTTT
TTCCGAATTTATTTCTAATTAAACCGAAAAAAATTCAGATACTCGTAAAAACAAATCCTTAAATC
CAATCTGCCTGAAATTTGGTTCAATGAATACAGATATTTCAAAGAGGCTTTCTGCCAAAAATCAT
GCAAAACTGAGCCGGGTCCCCGAAACCAAATCTCAGACCAAAAAACAGTGATACACGATTTTGAC
TAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAAAATATAGAATTT
AACGCAAAAAAAATTGAAGGTTTTTCACGCTTCTAATACCGTTCATTTTTTCCAGTGAATTTATT
TCTAATTAAATTGAAACAAAATTCAGATACTCGTAAAAACAAATCC
Found at i:3852 original size:320 final size:320
Alignment explanation
Indices: 1891--3939 Score: 2476
Period size: 320 Copynumber: 6.4 Consensus size: 320
1881 ACTCCTAACA
* * * * * * * *
1891 TTAAATCCATTCTGACTGAGATTTGATTC-ATGAATATAGATATTTTAAAGAGGCTTTTTACACA
1 TTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGACTTTCTGC-CA
* * * * * *
1955 AAAATCATGCAAAACTAAGCCGGGTCTCGGAAACTCGTTTTTAGCCCAAAAAACGTGATGGTAAG
65 AAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCC-AAAAA--TCAT-GTGAG
* * * *
2020 TACACGATTTTC-AGCTAAAAAGTTACCC-AAAATATTTTTTCTGAAATTCTTGCCACAATACTC
126 TACACGATTTTCGA-CTAAAAAGTGACCCGAAAATA--TTTTCTGAATTTTTTGCCACAATACTG
* **
2083 AGAAAAAACATATAATTCAACGCAAAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATTG-TT
188 AGAAAAAATATATAATTCAACGC-AAAAAAAAATTGAA-GGTTTTTCACGCTTCCAATACCGTTT
* * *
2147 TTTCCATTTTTTCCCGAATTTATTTGTAATTAAATCGAAA-AAAATTCAGATGCTCGTAAAAACA
251 TTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACA
2211 AATCC
316 AATCC
* * * * * *
2216 TTGAATCGAATGTGGCTGAAATTTGGTTCGATGAATACAGATATTTCATGGAGACTTTCTTGCCA
1 TTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGACTTTC-TGCCA
* * *
2281 AAAATCATGCAAAACTGAGCCGGGTCCCCGAAACTCGTTTTTAGCCCCAAAACAGTGATGGTTAG
65 AAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAG-CCCAAAA-A-TCAT-GTGAG
* *
2346 TACACGA-TTTCGGCTAAAAAGTGACCCAAAAATATTTTCTGAATTTTTTGCCACAATACTGAGA
126 TACACGATTTTCGACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGA
* *
2410 AAAAATATATAATTCAACGC-AAAAAAAATTGAAAGGTATTTCACGCTTCCAATATCG--TTTTC
191 AAAAATATATAATTCAACGCAAAAAAAAATTG-AAGGTTTTTCACGCTTCCAATACCGTTTTTTC
* *
2472 CATTTTTTTCCGAATTTATTTCTAATTAAACCGAAAC-AAATTCAGATACTCGTAAGAACAAATC
255 CATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATC
2536 C
320 C
* ** * * * * *
2537 TTAAATCCATTCTTCCTGAAATTTGGTTCAATGAATATAGATATTTCAAAGAGGCTTTCTGCCCA
1 TTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGACTTTCTGCCAA
* ** * * *
2602 AAATCATGCAAAACTGAGCCGGGTTCCCGAAAC-CAAATCTCAGACCCAAAAAACA-GTGA-TAC
66 AAATCATGCAAAACTGAGCCGGGTCCCCGAAACGC-GTTTTTAG-CCCAAAAATCATGTGAGTAC
2664 ACGATTTT-GACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAA
129 ACGATTTTCGACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAA
* * * *
2728 AATATAGAATTTAACGC-AAAAAAAATTGAAGGTTTTTCACGCTTCTAATACCGTTTTTTTTCA-
194 AATATATAATTCAACGCAAAAAAAAATTGAAGGTTTTTCACGCTTCCAATACCG-TTTTTTCCAT
* * * *
2791 TTTTTTCGGAATTTATTTCTAATTAAATTGAAATAAAATTCAGATACTCGTAAGAACAAATCC
258 TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCC
* * *
2854 TTAAATCCATTGTAGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGGAGACTTTCTGCTAA
1 TTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGACTTTCTGCCAA
*
2919 AAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTA-CCCAAAAACCATGATGGTTAGT
66 AAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCCAAAAATCATG-T-G--AGT
* * * *
2983 ACACGA-TTTC-AGCTAAAAGGTGACCCGAAAATTTTTTTCTGAA-ATTTTGCGACAATACTCG-
127 ACACGATTTTCGA-CTAAAAAGTGACCCGAAAA-TATTTTCTGAATTTTTTGCCACAATACT-GA
* * * * *
3044 GAAAAAACATATAATTCAAAGCAAAAAAAATCTTGAAGGGTTTTTCACGCTTCCAAAATCG--TT
189 GAAAAAATATATAATTCAACGCAAAAAAAA-ATTGAA-GGTTTTTCACGCTTCCAATACCGTTTT
* *
3107 TTCCATTTTTTTCCCGAATTTATTTCTAATTAAACCGAAAC-AAATTCAGATGCTCGTAAAAACA
252 TTCCATTTTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACA
3171 AATCC
316 AATCC
* * * * *
3176 TTAAATTCATTCTGCCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGCCTTTTTTTGCC
1 TTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGAC--TTTCTGCC
* *
3241 AAAAATCATGCAAAACTGAGCCGGATCCCCGAAACGCGTTTTTTGCCCAAAAA-CAGTGATGGTT
64 AAAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCCAAAAATCA-TG-T-G--
* *
3305 AGTACACGATTTTCGGCTAAAAAGTGTCCCGAAAATATTTTCTGAATTTTTTTGCCACAATACTG
124 AGTACACGATTTTCGACTAAAAAGTGACCCGAAAATATTTTCTGAA-TTTTTTGCCACAATACTG
* * * *
3370 AGAAAAAATATATAATTTAACGCAATAAAAAAATTGAAGGTTTTTCATGCTTCCATTACCCTTTT
188 AGAAAAAATATATAATTCAACGCAA-AAAAAAATTGAAGGTTTTTCACGCTTCCAATACCGTTTT
* *
3435 TTCCTCTTTTTTTTCCGAATTTATTTGTAATTAAATCGAAA-AAAATTCAGATGA-TCGTAAAAA
252 TT-C-CATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGAT-ACTCGTAAAAA
3498 CAAATCC
314 CAAATCC
* * * * *** * *
3505 TTAAATCCAATGTGGTTGAGATTTGGTTTGATGAATACAGATATTTTGTGGAGGCTTTCTGCGAA
1 TTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGACTTTCTGCCAA
*
3570 AAATCATGCAAAACTGAGCCGGGTCCCCGAAACTCGTTTTTAG-CCAAAAATCA-GTGA-TACAC
66 AAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCCAAAAATCATGTGAGTACAC
3632 G-TTTTCGACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAAAA
131 GATTTTCGACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAAAA
* *
3696 TATATAATTTAACGCAAAAAATAAATTGAAGGTTTTTCACGCTTCTAATACCGTATTTTTTCCAT
196 TATATAATTCAACGCAAAAAA-AAATTGAAGGTTTTTCACGCTTCCAATACCG--TTTTTTCCAT
*
3761 GTTTTTTCCGAATTTATTTCTAATTAAATTGAAACAAAATTCAGATACTCGTAAAAACAAATCC
258 -TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCC
*
3825 TTAAATCCATTGTGGTTGAGATTTGGTTCGAT-AAGTACT-GATATTTC-AGGAAGACTTTCTGC
1 TTAAATCCATTGTGGCTGAGATTTGGTTCGATGAA-TA-TAGATATTTCAAGG-AGACTTTCTGC
3887 CAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTA-CCCAAAAA
63 CAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCCAAAAA
3940 CCGTGATAAT
Statistics
Matches: 1506, Mismatches: 161, Indels: 119
0.84 0.09 0.07
Matches are distributed among these distances:
314 22 0.01
315 97 0.06
316 37 0.02
317 129 0.09
318 75 0.05
319 74 0.05
320 191 0.13
321 176 0.12
322 131 0.09
323 32 0.02
324 117 0.08
325 75 0.05
326 140 0.09
327 96 0.06
328 10 0.01
329 96 0.06
330 8 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (320 bp):
TTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGACTTTCTGCCAA
AAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCGTTTTTAGCCCAAAAATCATGTGAGTACAC
GATTTTCGACTAAAAAGTGACCCGAAAATATTTTCTGAATTTTTTGCCACAATACTGAGAAAAAA
TATATAATTCAACGCAAAAAAAAATTGAAGGTTTTTCACGCTTCCAATACCGTTTTTTCCATTTT
TTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCC
Found at i:4866 original size:16 final size:16
Alignment explanation
Indices: 4845--4879 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4835 TCATAACTCG
*
4845 TCTACTGCTTTTTTCC
1 TCTACTGCTTGTTTCC
*
4861 TCTACTTCTTGTTTCC
1 TCTACTGCTTGTTTCC
4877 TCT
1 TCT
4880 TGTTGATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.31, G:0.06, T:0.57
Consensus pattern (16 bp):
TCTACTGCTTGTTTCC
Found at i:18797 original size:52 final size:51
Alignment explanation
Indices: 18715--18812 Score: 187
Period size: 52 Copynumber: 1.9 Consensus size: 51
18705 TTGAGTTTCG
18715 ATTAATTCGGCGTTAAAGACACAAAAATCTCACTACCTATTTTCTCACTCA
1 ATTAATTCGGCGTTAAAGACACAAAAATCTCACTACCTATTTTCTCACTCA
18766 ATTAATTCGGCGTTAAAAGACACAAAAATCTCACTACCTATTTTCTC
1 ATTAATTCGGCGTT-AAAGACACAAAAATCTCACTACCTATTTTCTC
18813 CATCAGCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 14 0.30
52 32 0.70
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (51 bp):
ATTAATTCGGCGTTAAAGACACAAAAATCTCACTACCTATTTTCTCACTCA
Found at i:27662 original size:11 final size:11
Alignment explanation
Indices: 27646--27707 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
27636 ACTCGGATTC
27646 AGAGGAGGAGG
1 AGAGGAGGAGG
27657 AGAGGAGGAGG
1 AGAGGAGGAGG
* *
27668 AGGAAGAGGAAG
1 A-GAGGAGGAGG
*
27680 AGAAG-GGAGAG
1 AGAGGAGGAG-G
27691 AGAGGA-GAGGG
1 AGAGGAGGA-GG
27702 AGAGGA
1 AGAGGA
27708 AGTTGAGGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 3 0.07
11 30 0.70
12 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (11 bp):
AGAGGAGGAGG
Found at i:27761 original size:23 final size:21
Alignment explanation
Indices: 27713--27813 Score: 75
Period size: 23 Copynumber: 4.6 Consensus size: 21
27703 GAGGAAGTTG
27713 AGGAAGA-AAG-AGAAGGAAA
1 AGGAAGAGAAGAAGAAGGAAA
*
27732 A-GAAGAGGAGAAGGAAGGAAA
1 AGGAAGAGAAGAA-GAAGGAAA
27753 AGGAGAGAGAAGAAGAGAGGAAA
1 AGGA-AGAGAAGAAGA-AGGAAA
* *
27776 AGAAAGAAGAGAAAAGAGAAAG-AA
1 AG---GAAGAGAAGA-AGAAGGAAA
27800 AGGAAAGAGAAGAA
1 AGG-AAGAGAAGAA
27814 AAAGAAGGAG
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
18 5 0.08
19 3 0.05
20 1 0.02
21 11 0.17
22 12 0.18
23 16 0.24
24 4 0.06
25 9 0.14
26 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (21 bp):
AGGAAGAGAAGAAGAAGGAAA
Found at i:27782 original size:17 final size:16
Alignment explanation
Indices: 27756--27810 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
27746 AAGGAAAAGG
27756 AGAGAGAAGAAGAGAGGAA
1 AGAGA-AAGAAGAGA--AA
27775 A-AGAAAGAAGAGAAA
1 AGAGAAAGAAGAGAAA
*
27790 AGAGAAAGAA-AGGAA
1 AGAGAAAGAAGAGAAA
27805 AGAGAA
1 AGAGAA
27811 GAAAAAGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 13 0.38
16 8 0.24
17 9 0.26
18 3 0.09
19 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAGAGAAA
Found at i:27797 original size:20 final size:20
Alignment explanation
Indices: 27773--27819 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
27763 AGAAGAGAGG
27773 AAAAGAAA-GAAGAGAAAAGA
1 AAAAGAAAGGAA-AGAAAAGA
* *
27793 GAAAGAAAGGAAAGAGAAGA
1 AAAAGAAAGGAAAGAAAAGA
27813 AAAAGAA
1 AAAAGAA
27820 GGAGAAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGGAAAGAAAAGA
Found at i:27800 original size:25 final size:24
Alignment explanation
Indices: 27719--27819 Score: 79
Period size: 25 Copynumber: 4.3 Consensus size: 24
27709 GTTGAGGAAG
*
27719 AAAGAGAAGGAAAAG-AAGAG-GA
1 AAAGAGAAAGAAAAGAAAGAGAGA
* * *
27741 GAAG-GAAGGAAAAG-GAGAGAGA
1 AAAGAGAAAGAAAAGAAAGAGAGA
*
27763 AGAAGAG-AGGAAAAGAAAGAAGAGA
1 A-AAGAGAAAGAAAAGAAAG-AGAGA
*
27788 AAAGAGAAAGAAAGGAAAGAGAAGA
1 AAAGAGAAAGAAAAGAAAGAG-AGA
27813 AAA-AGAA
1 AAAGAGAA
27820 GGAGAAGTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
21 14 0.21
22 5 0.08
23 11 0.17
24 14 0.21
25 22 0.33
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (24 bp):
AAAGAGAAAGAAAAGAAAGAGAGA
Found at i:39779 original size:249 final size:248
Alignment explanation
Indices: 39334--39818 Score: 749
Period size: 249 Copynumber: 1.9 Consensus size: 248
39324 AACAGATAAG
* * *
39334 AATTTAGAGGTTTTGACACTGTCTGGAGATAGTATTCTTGTTGATATTCCTAATGACATGTCAGT
1 AATTTACAGGTTTTGAAACTGTCTGGAAATAGTATTCTTGTTGATATTCCTAATGACATGTCAGT
* * *
39399 TTGTTTTCCAAGTCTCAAGATTTTGCATCTCGTGAAATCTGTTATGTATGCCAATGATGAATCCT
66 TTGGTTCCCAAGTCTCAAGATTTTGCATCTCG-GAAATCTGTTAAGTATGCCAATGATGAATCCT
* * ** * *
39464 TATCGAGGCTTCTTCACGGTTGCGCTGTTTTGGAAGAGTTGTTGGTTACGACCGGATCCGACTGC
130 TATCGAGGCTTCTTCACGGTTGCGCTGTTTTGGAAGAATTGCTAATTACGACCAGATACGACTGC
39529 AACGTGAGAAATCTCCTTATTTTCGTGCCTACATTGAAGACATTGAGTCTAGCT
195 AACGTGAGAAATCTCCTTATTTTCGTGCCTACATTGAAGACATTGAGTCTAGCT
39583 AATTTACAGGTTTTGAAACTGTCTGGAAATAGTATTCTTGTTGATATTCCTAATGACATGATGTC
1 AATTTACAGGTTTTGAAACTGTCTGGAAATAGTATTCTTGTTGATATTCCTAATGAC---ATGTC
*
39648 AGTTTGGTTCCCAAGTCTCAAGATTTTGCATCTC-G-ATTCTGTTAAGTATGCCAATGATGAATC
63 AGTTTGGTTCCCAAGTCTCAAGATTTTGCATCTCGGAAATCTGTTAAGTATGCCAATGATGAATC
* ** *
39711 CTTGTTTAGGCTTCTTGACGGTTGCGCTGTTTTGGAAGAATTGCTAATTACGACCAGATACGACT
128 CTTATCGAGGCTTCTTCACGGTTGCGCTGTTTTGGAAGAATTGCTAATTACGACCAGATACGACT
* *
39776 GCAACGTGAGAGATCTCGTTATTTTCGTGCCTACATTGAAGAC
193 GCAACGTGAGAAATCTCCTTATTTTCGTGCCTACATTGAAGAC
39819 TCTGGGCCTA
Statistics
Matches: 214, Mismatches: 19, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
249 176 0.82
250 1 0.00
252 37 0.17
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (248 bp):
AATTTACAGGTTTTGAAACTGTCTGGAAATAGTATTCTTGTTGATATTCCTAATGACATGTCAGT
TTGGTTCCCAAGTCTCAAGATTTTGCATCTCGGAAATCTGTTAAGTATGCCAATGATGAATCCTT
ATCGAGGCTTCTTCACGGTTGCGCTGTTTTGGAAGAATTGCTAATTACGACCAGATACGACTGCA
ACGTGAGAAATCTCCTTATTTTCGTGCCTACATTGAAGACATTGAGTCTAGCT
Found at i:41534 original size:32 final size:27
Alignment explanation
Indices: 41454--41543 Score: 180
Period size: 27 Copynumber: 3.3 Consensus size: 27
41444 TTCTTCCCTG
41454 TTATTATATTCTTCTCTAGCTAAGCTA
1 TTATTATATTCTTCTCTAGCTAAGCTA
41481 TTATTATATTCTTCTCTAGCTAAGCTA
1 TTATTATATTCTTCTCTAGCTAAGCTA
41508 TTATTATATTCTTCTCTAGCTAAGCTA
1 TTATTATATTCTTCTCTAGCTAAGCTA
41535 TTATTATAT
1 TTATTATAT
41544 GTTGCAAGGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (27 bp):
TTATTATATTCTTCTCTAGCTAAGCTA
Found at i:41976 original size:24 final size:24
Alignment explanation
Indices: 41915--41965 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
41905 ACCAAAGCAA
41915 TATACAAAATACAATTATAAAGGT
1 TATACAAAATACAATTATAAAGGT
41939 TATACAAAATACAATTATAAAGGT
1 TATACAAAATACAATTATAAAGGT
41963 TAT
1 TAT
41966 TATGACTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (24 bp):
TATACAAAATACAATTATAAAGGT
Found at i:49498 original size:333 final size:333
Alignment explanation
Indices: 48160--53393 Score: 7427
Period size: 333 Copynumber: 15.8 Consensus size: 333
48150 TTTCTTTTCA
* * *
48160 GCGTTGAATTATATGATTTTT-TGAGTATTGTGGCTAATAATTGGGGAAAAATTTTTCGGGTCAA
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
*
48224 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCTGAAAACGCGTTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
* *
48289 TGGGGACCATGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
131 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
* * *
48354 TAATCAAATCTTAGCCACAATGGATTTACGGATTTGTTTTTACGAGTATCTGAATCTTGTTACGA
196 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
* *
48419 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCATAAAA
261 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAAA
48484 TATTTTTG
326 TATTTTTG
* *
48492 GCATTGAATTATATGATTTTTCTGAGTATTGTGGC-AAAATATTGGGGAAAAACTTTTCGGGTCA
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAA-ATTGGGGAAAAACTTTTCGGGTCA
* * * * * * * * *
48556 GTTTTTTGCAAAATTTTAACTGAAATCGTGTACTAATCATCACGATTATTGGCTAAAAATGCCTT
65 GTTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTT
* * * *
48621 TCGGGG-CC-CTGACTCAGTTTTGCAT-ATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTC
130 TCGGGGACCAC-G-CTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTC
* *
48683 ATCTAATCAAATCTCTCAGCCACAATGGATCTACGGATTTATTTTTACGAGTATCTGAATATTGT
193 ATTTAATCAAATCT-T-AGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGT
* *
48748 TTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGAGTGAAAACCCC
256 TTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCC
48813 TAAAATATTTTTG
321 TAAAATATTTTTG
*
48826 GCGTTGAATTACATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* *
48891 TTTTTATATAAAATTTTAGCCGAAACCGTG---T-ACCATCACGGTTTTTGGCTGAAAACGCGTT
66 TTTTT-TACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTT
48952 TCGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCAT
130 TCGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCAT
* * * *
49017 TTAATCAAATATTAGCCACAATGGATTTACGAATTTGTTTTTACGAGTATCTGAATCTTGTTTCG
195 TTAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCG
* *
49082 GTTTAATTAGAAATAAATTTAGAAAAAAATGGAAATAA-GATATTAGAAGCGTGAAAAACCCTAA
260 ATTTAATTAGAAATAAATTCAGAAAAAAATGGAAA-AATGATATTAGAAGCGTGAAAAACCCTAA
*
49146 AATATTTTCG
324 AATATTTTTG
* * * *
49156 GCGTTGAATTATATGATTTTTCTAAGTATTGTGGCAAAAAAATTGGGGAAAAACTTTTCGGGACA
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGC-TAAAAATTGGGGAAAAACTTTTCGGGTCA
* * *
49221 GTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATAACGGTTTTTTGCTGAAAACGCGTT
65 GTTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTT
49286 TCGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCAT
130 TCGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCAT
* * * * * * **
49351 TTAATTAAATCTTAGCCACAATGGATTTATGTATTTGTTTTTACGACTATCTGTATCCTGTTTCG
195 TTAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCG
* *
49416 ATTTAAATAGAAATAAATTCAG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAA
260 ATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAA
49480 ATATTTTTG
325 ATATTTTTG
* * * *
49489 GCTTTGAATTATATGATTTTTCTGAGTATTGTGGCCAAATATTGGGGAAAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* * * * * * *
49554 TTTTTTGCAAAATTTTAACTGAAATCGTGTACTAACCATCACGGTTTTTGGATAAAAATGCCTTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
* * * *
49619 CGGGG-CC-CTGACTCAGTTTTGCAT-ATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCA
131 CGGGGACCAC-G-CTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCA
* * *
49681 -CTAATCAAATCTCTTAGCCACAATAGATCTACGGATTTATTTTTACGAGTATCTGAATATTGTT
194 TTTAATCAAA--TCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTT
* * * *
49745 TCGATTTAATTAGAAATAAGTTTAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAAGCCT
257 TCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCT
49810 AAAATATTTTTG
322 AAAATATTTTTG
* * * * * *
49822 GCTTTGAGTTATTTGATTTTTCTGAGTATTGT-TCCAAAATATTGGGGAAAAACTTTTCGGGTCA
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAA-ATTGGGGAAAAACTTTTCGGGTCA
* * * * * *
49886 GTTTTTTGCAAAATTTTAACTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCCTT
65 GTTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTT
* * * * *
49951 TCGTGG-CC-CTGACTCAGTTCTGCAT-A-TTTATGGCAGAAAGACTTCTCGAAATATCTATATT
130 TCGGGGACCAC-G-CTCAGTTTTGCATGATTTTA-GGCAGAAAGACTGCTTGAAATATCAATATT
* * *
50012 CA-CTAATCAAATCTCTCAGCCACAATAGATCTACGGATTTATTTTTACGAGTATCTGAATATTG
192 CATTTAATCAAATCT-T-AGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTG
* ** *
50076 TTTCGATTTAATTAGAAATAAATTTAGAAAAAAATGTTAAAATGATATTAGAAGCGTGAAAACCC
255 TTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACC
*
50141 CTAAAATACTTTTG
320 CTAAAATATTTTTG
* * *
50155 GCGTTGAATTATTTGATTTTTGTGAGTGTTGTGGCTAGAAATTGGGGAAAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* * * * * *
50220 TTTGTTACAAAATTTTA-TCGAAACCGTGTACTATCCATCACAGTTTTTGGCTGAAAACACGTTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
* * * * *
50284 CGGGGACCACACTAAGTTTTGCATGATTTT-GGCAGAAAGACTTCTCGAAATATCTATATTCATT
131 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
50348 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCT-ATATATTGTTTCG
196 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGA-ATATTGTTTCG
* *
50412 ATTTAATTAGAAATAAATTTAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAA
260 ATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAA
50477 ATATTTTTG
325 ATATTTTTG
* * *
50486 GCTTTGAATTATATGA-TTTTCTGAGTATTGTGGC-AAAATATTAGGGAAAAAC-TTTCGGGTCA
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAA-ATTGGGGAAAAACTTTTCGGGTCA
* * * *
50548 G----TT------TTTT-G-CAAAAT--T-T--TAACCATCACGGTTTTTGGCTAAAAATGCCTT
65 GTTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTT
* * * * * *
50596 TCGGGG-CC-CTGACTCAGTTCTGCAT-ATTTTTGGCAAAAAGACTTCTCGAAATATCTATATTC
130 TCGGGGACCAC-G-CTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTC
** * * * *
50658 A-CAAATCAAATCTCTCAGCCCCAATAGATCTAGGGATTTATTTTTACGAGTATCTGAATATTGT
193 ATTTAATCAAATCT-T-AGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGT
* *
50722 TTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGATGCGTGAAAACCCC
256 TTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCC
50787 TAAAATATTTTTG
321 TAAAATATTTTTG
* * * **
50800 GCATTGAATTATATGATTTTTGTGAATTTTGTGGCTAAAAATTGGTAAAAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* * * *
50865 TTTTTTATAAAATTTTAGCCGAAACCGTGTACTAACCACCACGGTTTTTGGCTGAAAACACGTTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
50930 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
131 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
*
50995 TAATCAAATCTTAGCCACAATGTATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
196 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
*
51060 TTTAATTAGAAATAAATTCAGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAACCCCTAAA
261 TTTAATTAGAAATAAATTCA-GAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAA
51125 ATATTTTTG
325 ATATTTTTG
*
51134 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTACAAATTGGGGAAAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* * * *
51199 TTTGTTATAAAATTTTAGCCGAAACCGTGTACTAACCATCACGGTTTTTGGCTGAAAACACGTTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
51264 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
131 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
51329 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
196 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
* *
51394 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGATGCGTGAAAACCCCTAAAA
261 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAAA
51459 TATTTTTG
326 TATTTTTG
*
51467 GCGTTGAATTAAATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGG-AAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* * * * *
51531 TTTGTTATAAAATTTTAGCCGAAA-CTGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCCTT
66 TTTTTTACAAAATTTTAGCCGAAATC-GTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTT
* * * * * * *
51595 TTGGGG-CC-CTGACTCTGTTTTCCAT-ATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTC
130 TCGGGGACCAC-G-CTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTC
* * * * * *
51657 ATCTAATGAAATCTCTCAGCCTCAATGGATTTACAGATTTATTTTTACGAGTATCTAAAGATTGT
193 ATTTAATCAAATCT-T-AGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGT
* *
51722 TTCGATTTAATTAGAAATAAATTCAGAAAAATATGGAAAAATGATATTCGAAGCGTG-AAAACCC
256 TTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCC
51786 GTAAAATATTTTTG
321 -TAAAATATTTTTG
51800 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGG-AAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* * * *
51864 TTTGTTACAAAATTTTAGCCGAAACCGTGTACTAACTATCACGGTTTTTGGCTGAAAACACGTTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
51929 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
131 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
* *
51994 TAATCAAATCTTAGTCACAATGGATTTACGAATTTATTTTTACGAGTATCTGAATATTGTTTCGA
196 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
*
52059 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAACCCCTAAAA
261 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAAA
52124 TATTTTTG
326 TATTTTTG
* **
52132 GCGTTGAATTATATGATTTTTCTGAGTATTGTGGCTAAAAATTATGGAAAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* *
52197 TTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCTCGGTTTTTGGCTGAAAACGCGTTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
* *
52262 CGGGGACCTCACTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
131 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
* * *
52327 GAATCAAATCTTAGCCACAATGGTTTTACGGATATATTTTTACGAGTATCTGAATATTGTTTCGA
196 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
* * *
52392 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCATAAAA
261 TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAAA
52457 TATTTTTG
326 TATTTTTG
* * * *
52465 GCATTGAATTATATGATTTTTCTGAGTATTGTAGC-AAAATATTGGGGAAAAATTTTTCGGGTCA
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAA-ATTGGGGAAAAACTTTTCGGGTCA
* * * * * * * * *
52529 GTTTTTTGCAAAATTTTAACTGAAATCGTGTACTAACCAT-AAGGTTATAGGCTAAAAATGTCTT
65 GTTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACG-CGT
* * * * *
52593 TTCGGGG-CC-CTGACTCAGTTTTGCAT-ATTTTTGCCAGAGAGACTGCTCGAAATATCTATATT
129 TTCGGGGACCAC-G-CTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATT
* *
52655 CATCTAATCAAATCTCTCGACCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTG
192 CATTTAATCAAATCT-TAG-CCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTG
* *
52720 TTTTGATTTAATTAGAAATAAATTCAGAAAAAAATGGAACAATGATATTAGAAGCGTG-AAAACC
255 TTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACC
52784 CTAAAATATTTTTG
320 CTAAAATATTTTTG
*
52798 GCGTTGAAATATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* * * * *
52863 TATTTTACAAAATTATAGCCGAAACCGTGTACGTTA-CATCACGGTTTTTGGCTGAAAACGTGTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTGGCTGAAAACGCGTT
* *
52927 TCAGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACAGCTTGAAATATCAATATTCAT
130 TCGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCAT
* * * * * *
52992 TTAAGCAAATCTTAGCCACAATGGATTTACGGATTTGTTTTTACTAGTATATGTATCTTGTTTCG
195 TTAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCG
* *
53057 ATTTAATTAGAAATAAATTCAGAATAAAATGGAAAAATGATATTAGAAGCGTGAAAACCCCTAAA
260 ATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAA
53122 ATATTTTT-
325 ATATTTTTG
53130 --G--GAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
1 GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
* * * * *
53191 TTTGTTATAAAATTTTAGCCGAAACCGTGTACTAACCATCA-GGTTTTTGGCTGAAAACACTTTT
66 TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
* *
53255 CGGGGACCACGCTCAATTTTGCATTATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
131 CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
* *
53320 TAATCAAATCTTAGCCACAAAGGATTTACGGATATATTTTTACGAGTATCTGAATATTGTTTCGA
196 TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
53385 TTTAATTAG
261 TTTAATTAG
53394 CCGAAATCAT
Statistics
Matches: 4432, Mismatches: 377, Indels: 191
0.89 0.08 0.04
Matches are distributed among these distances:
311 1 0.00
312 17 0.00
313 75 0.02
314 131 0.03
315 27 0.01
316 16 0.00
318 4 0.00
319 4 0.00
320 2 0.00
325 2 0.00
326 4 0.00
327 150 0.03
328 96 0.02
329 14 0.00
330 207 0.05
331 301 0.07
332 797 0.18
333 1617 0.36
334 931 0.21
335 36 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (333 bp):
GCGTTGAATTATATGATTTTTGTGAGTATTGTGGCTAAAAATTGGGGAAAAACTTTTCGGGTCAG
TTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGAAAACGCGTTT
CGGGGACCACGCTCAGTTTTGCATGATTTTAGGCAGAAAGACTGCTTGAAATATCAATATTCATT
TAATCAAATCTTAGCCACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATATTGTTTCGA
TTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCTAAAA
TATTTTTG
Found at i:53556 original size:12 final size:12
Alignment explanation
Indices: 53539--53566 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53529 AAATCCCTGA
53539 TTTAGAACAATT
1 TTTAGAACAATT
53551 TTTAGAACAATT
1 TTTAGAACAATT
53563 TTTA
1 TTTA
53567 ATTGACCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (12 bp):
TTTAGAACAATT
Found at i:53841 original size:33 final size:33
Alignment explanation
Indices: 53804--53874 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
53794 GTAAAAACTC
53804 TGAATCATGGCCCTATTTTAGACATGTAATCTT
1 TGAATCATGGCCCTATTTTAGACATGTAATCTT
*
53837 TGAATCATGGCCCTGTTTTAGACATGTAATCTT
1 TGAATCATGGCCCTATTTTAGACATGTAATCTT
53870 T-AATC
1 TGAATC
53875 TTCAGCGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (33 bp):
TGAATCATGGCCCTATTTTAGACATGTAATCTT
Found at i:54211 original size:10 final size:10
Alignment explanation
Indices: 54196--54220 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54186 TTATAGAAAT
54196 TTAAATGAAC
1 TTAAATGAAC
54206 TTAAATGAAC
1 TTAAATGAAC
54216 TTAAA
1 TTAAA
54221 AATAGTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (10 bp):
TTAAATGAAC
Found at i:54849 original size:70 final size:70
Alignment explanation
Indices: 54735--54867 Score: 239
Period size: 70 Copynumber: 1.9 Consensus size: 70
54725 GGATTTTTTG
* *
54735 CATACGATTTCAAAGGGAGAAACTGGCACACCATTGATGGCATGCTTGAATCTGAGCCATTTCTT
1 CATACGATTTCAAAGGGAGAAACTGGCACACCATTGATGACATGCTTCAATCTGAGCCATTTCTT
54800 TTCTA
66 TTCTA
*
54805 CATACGATTTCAAGGGGAGAAACTGGCACACCATTGATGACATGCTTCAATCTGAGCCATTTC
1 CATACGATTTCAAAGGGAGAAACTGGCACACCATTGATGACATGCTTCAATCTGAGCCATTTC
54868 ACGAAACTCT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (70 bp):
CATACGATTTCAAAGGGAGAAACTGGCACACCATTGATGACATGCTTCAATCTGAGCCATTTCTT
TTCTA
Found at i:55058 original size:87 final size:87
Alignment explanation
Indices: 54912--55076 Score: 303
Period size: 87 Copynumber: 1.9 Consensus size: 87
54902 CCGAGGAATT
* *
54912 TAATTCTTTAGGTAAGGAGGTTGATGGTTGCACAGAACCCGGTGGCAAGGGACTCGGTCATGCAG
1 TAATTCTTTAGGTAAAGAGGTTGATGGTTGCACAAAACCCGGTGGCAAGGGACTCGGTCATGCAG
54977 CAGTATTTTGTGTAGATAGTTC
66 CAGTATTTTGTGTAGATAGTTC
*
54999 TAATTCTTTAGGTAAAGAGGTTGATGGTTGCACAAAACCCGGTTGCAAGGGACTCGGTCATGCAG
1 TAATTCTTTAGGTAAAGAGGTTGATGGTTGCACAAAACCCGGTGGCAAGGGACTCGGTCATGCAG
55064 CAGTATTTTGTGT
66 CAGTATTTTGTGT
55077 GGAAGTCGAC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (87 bp):
TAATTCTTTAGGTAAAGAGGTTGATGGTTGCACAAAACCCGGTGGCAAGGGACTCGGTCATGCAG
CAGTATTTTGTGTAGATAGTTC
Found at i:55800 original size:17 final size:18
Alignment explanation
Indices: 55766--55809 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
55756 CCATTTATTC
*
55766 TTTAAAATAATTAAAAAT
1 TTTAAAATAATAAAAAAT
55784 TTTAAAA-AATAAAAAA-
1 TTTAAAATAATAAAAAAT
55800 -TTAAAATAAT
1 TTTAAAATAAT
55810 TATCTCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
17 8 0.33
18 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTTAAAATAATAAAAAAT
Found at i:61540 original size:16 final size:16
Alignment explanation
Indices: 61519--61550 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
61509 GGATGGATGT
61519 TACTCTGAGATTGAGC
1 TACTCTGAGATTGAGC
61535 TACTCTGAGATTGAGC
1 TACTCTGAGATTGAGC
61551 AATAGGCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (16 bp):
TACTCTGAGATTGAGC
Found at i:71815 original size:59 final size:59
Alignment explanation
Indices: 71748--71865 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
71738 TTTGTCTCCC
71748 ATGGTAATAATTTGTCTGTTCTTGAGTTCAAATGAATGAAAATGTTCTGAAACCATGAT
1 ATGGTAATAATTTGTCTGTTCTTGAGTTCAAATGAATGAAAATGTTCTGAAACCATGAT
* * *
71807 ATGGTAATAATTTTTTTGTTCTTGAGTTCAAATGAATGAAATTGTTCTGAAACCATGAT
1 ATGGTAATAATTTGTCTGTTCTTGAGTTCAAATGAATGAAAATGTTCTGAAACCATGAT
71866 TAATGTACTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (59 bp):
ATGGTAATAATTTGTCTGTTCTTGAGTTCAAATGAATGAAAATGTTCTGAAACCATGAT
Found at i:72912 original size:18 final size:17
Alignment explanation
Indices: 72883--72948 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
72873 ATCAGGAGGA
*
72883 AGTGGCACTGGATATGG
1 AGTGGAACTGGATATGG
72900 AGTAGGAACTGGA-AGTGGG
1 AGT-GGAACTGGATA-T-GG
*
72919 AGTGGAACCGGATATGG
1 AGTGGAACTGGATATGG
*
72936 AGTTGGAATTGGA
1 AG-TGGAACTGGA
72949 ACTGGATCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 8 0.20
18 26 0.65
19 6 0.15
ACGTcount: A:0.29, C:0.08, G:0.42, T:0.21
Consensus pattern (17 bp):
AGTGGAACTGGATATGG
Found at i:72974 original size:42 final size:41
Alignment explanation
Indices: 72928--73055 Score: 113
Period size: 42 Copynumber: 3.2 Consensus size: 41
72918 GAGTGGAACC
72928 GGATATGGAGTTGGAATTGGAACTGGATCGGGTGGATCAAAT
1 GGATATGGAGTTGGAATTGGAACTGG-TCGGGTGGATCAAAT
** * * * *
72970 GGATATGGAGCAGGAAGTGGAAGTGG--GAGTGG---AACT
1 GGATATGGAGTTGGAATTGGAACTGGTCGGGTGGATCAAAT
* * **
73006 GGATATGGAATTGGAATTGGAACCGGGTCGGGTGGATCAGGT
1 GGATATGGAGTTGGAATTGGAA-CTGGTCGGGTGGATCAAAT
73048 GGATATGG
1 GGATATGG
73056 GATTGGGCAA
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
36 21 0.32
37 2 0.03
39 10 0.15
42 32 0.49
ACGTcount: A:0.27, C:0.07, G:0.43, T:0.23
Consensus pattern (41 bp):
GGATATGGAGTTGGAATTGGAACTGGTCGGGTGGATCAAAT
Found at i:72991 original size:78 final size:78
Alignment explanation
Indices: 72891--73055 Score: 258
Period size: 78 Copynumber: 2.1 Consensus size: 78
72881 GAAGTGGCAC
* * *
72891 TGGATATGGAGTAGGAACTGGAAGTGGGAGTGGAACCGGATATGGAGTTGGAATTGGAACTGGAT
1 TGGATATGGAGCAGGAACTGGAAGTGGGAGTGGAACCGGATATGGAATTGGAATTGGAACCGGAT
72956 CGGGTGGATCAAA
66 CGGGTGGATCAAA
* * *
72969 TGGATATGGAGCAGGAAGTGGAAGTGGGAGTGGAACTGGATATGGAATTGGAATTGGAACCGGGT
1 TGGATATGGAGCAGGAACTGGAAGTGGGAGTGGAACCGGATATGGAATTGGAATTGGAACCGGAT
**
73034 CGGGTGGATCAGG
66 CGGGTGGATCAAA
73047 TGGATATGG
1 TGGATATGG
73056 GATTGGGCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.28, C:0.07, G:0.43, T:0.22
Consensus pattern (78 bp):
TGGATATGGAGCAGGAACTGGAAGTGGGAGTGGAACCGGATATGGAATTGGAATTGGAACCGGAT
CGGGTGGATCAAA
Found at i:73027 original size:36 final size:36
Alignment explanation
Indices: 72883--73027 Score: 137
Period size: 36 Copynumber: 3.9 Consensus size: 36
72873 ATCAGGAGGA
* *
72883 AGTGGCACTGGATATGGAGTAGGAACTGGAAGTGGG
1 AGTGGAACTGGATATGGAGTAGGAATTGGAAGTGGG
* * *
72919 AGTGGAACCGGATATGGAGTTGGAATTGGAACTGGATCG
1 AGTGGAACTGGATATGGAGTAGGAATTGGAAGTGG---G
* * * *
72958 GGTGGATCAAATGGATATGGAGCAGGAAGTGGAAGTGGG
1 AGTGG---AACTGGATATGGAGTAGGAATTGGAAGTGGG
* *
72997 AGTGGAACTGGATATGGAATTGGAATTGGAA
1 AGTGGAACTGGATATGGAGTAGGAATTGGAA
73028 CCGGGTCGGG
Statistics
Matches: 85, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
36 51 0.60
39 10 0.12
42 24 0.28
ACGTcount: A:0.30, C:0.07, G:0.41, T:0.21
Consensus pattern (36 bp):
AGTGGAACTGGATATGGAGTAGGAATTGGAAGTGGG
Found at i:73266 original size:18 final size:18
Alignment explanation
Indices: 73198--73257 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
73188 CAGTTTACCT
*
73198 ATTCCAAAAATCCCACCC
1 ATTCCAAAAATCCCACCA
* *
73216 TTTCCCAAAATCCCACCA
1 ATTCCAAAAATCCCACCA
*
73234 ATTCCAAAAATCCCACCG
1 ATTCCAAAAATCCCACCA
73252 ATTCCA
1 ATTCCA
73258 GATATCCCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.37, C:0.42, G:0.02, T:0.20
Consensus pattern (18 bp):
ATTCCAAAAATCCCACCA
Found at i:73377 original size:36 final size:30
Alignment explanation
Indices: 73299--73359 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
73289 GTCAACCTGG
73299 AGGCAATTGCAATTTACCACCACCATGTTC
1 AGGCAATTGCAATTTACCACCACCATGTTC
73329 AGGCAATTGCAATTTACCACCACCATGTTC
1 AGGCAATTGCAATTTACCACCACCATGTTC
73359 A
1 A
73360 CCTGGGAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (30 bp):
AGGCAATTGCAATTTACCACCACCATGTTC
Found at i:78048 original size:1 final size:1
Alignment explanation
Indices: 78042--78077 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
78032 TGACAGAAAT
78042 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
78078 CTTTAACCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:84411 original size:53 final size:53
Alignment explanation
Indices: 84348--84453 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
84338 AATTGATTTT
*
84348 CACCATAAATTTCCCATAGGACAAACCATACTAAAAACCACATGGGTAAATAA
1 CACCATAAATTTCCCATAGGACAAACCATACTAAAAACAACATGGGTAAATAA
*
84401 CACCATAAATTTCCCATAGGACAAACCATACTAAATACAACATGGGTAAATAA
1 CACCATAAATTTCCCATAGGACAAACCATACTAAAAACAACATGGGTAAATAA
84454 TTACAACAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.20
Consensus pattern (53 bp):
CACCATAAATTTCCCATAGGACAAACCATACTAAAAACAACATGGGTAAATAA
Found at i:95922 original size:21 final size:20
Alignment explanation
Indices: 95897--95958 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
95887 CTTTTCCTCA
*
95897 ACATCTTCACCATCCTCATC
1 ACATCTCCACCATCCTCATC
* *
95917 ATCATCTCCACCATCCTCTTGG
1 A-CATCTCCACCATCCTCAT-C
95939 ACATCTCCACCATCCTCATC
1 ACATCTCCACCATCCTCATC
95959 CACACCTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.45, G:0.03, T:0.29
Consensus pattern (20 bp):
ACATCTCCACCATCCTCATC
Found at i:115261 original size:7 final size:7
Alignment explanation
Indices: 115249--115280 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
115239 TTTTCACCGT
*
115249 GTTTCAG
1 GTTTCAA
115256 GTTTCAA
1 GTTTCAA
115263 GTTTCAA
1 GTTTCAA
115270 GTTTCAA
1 GTTTCAA
115277 GTTT
1 GTTT
115281 TAGTTTTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (7 bp):
GTTTCAA
Found at i:122975 original size:12 final size:12
Alignment explanation
Indices: 122958--122989 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
122948 TACCCTATGT
122958 AAACACGACACG
1 AAACACGACACG
122970 AAACACGACACG
1 AAACACGACACG
122982 AAACACGA
1 AAACACGA
122990 ATTGCCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:123301 original size:21 final size:19
Alignment explanation
Indices: 123275--123333 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
123265 CGCTGCTCTA
*
123275 ATAATCCCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
*
123294 ACATAATCTAATCTGTACAGT
1 --ATAATCTCATCTGTACAGT
*
123315 GTAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
123334 TGCCAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:127323 original size:17 final size:17
Alignment explanation
Indices: 127270--127324 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
127260 GATTACCCCC
* *
127270 AGATCACTAGTGATCTA
1 AGATCACCAGTGATCAA
127287 AGATCACCAGTGAT-ACA
1 AGATCACCAGTGATCA-A
*
127304 AGATCACCAGTAATCAA
1 AGATCACCAGTGATCAA
127321 AGAT
1 AGAT
127325 TATATGGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 32 0.97
18 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (17 bp):
AGATCACCAGTGATCAA
Found at i:139622 original size:24 final size:24
Alignment explanation
Indices: 139590--139638 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
139580 TGTTATTGGA
139590 AAGAATTTGGTAAGAAGCTCTAGC
1 AAGAATTTGGTAAGAAGCTCTAGC
139614 AAGAATTTGGTAAGAAGCTCTAGC
1 AAGAATTTGGTAAGAAGCTCTAGC
139638 A
1 A
139639 TTTAAGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (24 bp):
AAGAATTTGGTAAGAAGCTCTAGC
Found at i:157761 original size:6 final size:7
Alignment explanation
Indices: 157747--157771 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
157737 TTTGATTTTG
157747 TTGGTTT
1 TTGGTTT
157754 TTGGTTT
1 TTGGTTT
157761 TTGGTTT
1 TTGGTTT
157768 TTGG
1 TTGG
157772 GGTTTGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (7 bp):
TTGGTTT
Found at i:159348 original size:15 final size:15
Alignment explanation
Indices: 159328--159360 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
159318 TATTGAATTT
159328 AAATTCCTTCATTCA
1 AAATTCCTTCATTCA
*
159343 AAATTCCTTCATTGA
1 AAATTCCTTCATTCA
159358 AAA
1 AAA
159361 GAAAAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (15 bp):
AAATTCCTTCATTCA
Found at i:161759 original size:86 final size:86
Alignment explanation
Indices: 161614--161786 Score: 319
Period size: 86 Copynumber: 2.0 Consensus size: 86
161604 CAACCACTTG
**
161614 TTGGTAAATTCTTTTCAAACTTCGGTAATGGGTGTGTTTAAGATTTTTTTATATTTTGATATGGA
1 TTGGTAAATTCTTTTCAAACTTCGGTAATGAATGTGTTTAAGATTTTTTTATATTTTGATATGGA
161679 GATGGAAATTAAATGTAAAGA
66 GATGGAAATTAAATGTAAAGA
*
161700 TTGGTAAATTCTTTTCAAACTTCGGTAATGAATGTGTTTAAGATTTTTTTATATTTTGATTTGGA
1 TTGGTAAATTCTTTTCAAACTTCGGTAATGAATGTGTTTAAGATTTTTTTATATTTTGATATGGA
161765 GATGGAAATTAAATGTAAAGA
66 GATGGAAATTAAATGTAAAGA
161786 T
1 T
161787 ATACTATATA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (86 bp):
TTGGTAAATTCTTTTCAAACTTCGGTAATGAATGTGTTTAAGATTTTTTTATATTTTGATATGGA
GATGGAAATTAAATGTAAAGA
Found at i:168746 original size:21 final size:20
Alignment explanation
Indices: 168720--168761 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
168710 ACATATCACG
168720 CCATGTGTACCAAAAAAGTGA
1 CCATGTGTACC-AAAAAGTGA
**
168741 CCATGTGTTTCAAAAAGTGA
1 CCATGTGTACCAAAAAGTGA
168761 C
1 C
168762 ACGTGGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
CCATGTGTACCAAAAAGTGA
Done.