Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008269.1 Corchorus capsularis cultivar CVL-1 contig08290, 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: 3180
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Found at i:1005 original size:41 final size:41
Alignment explanation
Indices: 950--3179 Score: 1227
Period size: 41 Copynumber: 54.4 Consensus size: 41
940 GGCAAACTGG
* * * *
950 TAAACAACATCTTCCGACGGGAAAGGGCACACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* *
991 TAAACAACACCTTCCGACTGGGAAGGG-AAAGTTGGGAATTGGCAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAA-CTGGGAA-----AAC
* * ** * *
1037 TAGACAACACCTCCCGGTGGGGAAGGGCAAACTAGGAGAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * ** * *
1078 TAGACAACACCTTTCGGTGGGGAAAGGAAAACT-GG-----
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* *
1113 TAAACAACACCTTCCGAC-GGGAAGGGCACACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * ** * *
1153 AAAACAACAACTTCCGACTAGGAAGAGCAAGCTGGGAATTGGCAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAA-----AAC
* * *
1199 -AAGACAACACCTT-C--C--GG-TGGG-AAA--GGGCACAC
1 TAA-ACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * ** *
1231 TAGACAACAACTTTCGTTGGGGAAGGGCAAACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* **
1272 TAAACAACACCTTCTGGTGGGGAAGGGCAAACT-GG-----
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * *
1307 TAAAAAACACGTTCCGATGGGGAAGGGCAAAATGGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * *
1348 TAAACAACACCTTCCGATGAGGAAGGACAGACT-GGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * *
1388 TAATCAACACCTTCCGATGGGGAAGGGCAAACTCGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* *
1429 TAAACAACACCTTCCGACCGGGAAGGGCAAAATGGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * * * *
1470 TAAACAACACATTCCTATGGGGAAGGGCGAACTAGG--AAT
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* *
1509 TAAAACAACACCTTCCGATGGGGAAGGGCAAAATGGGAAAAC
1 T-AAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
** * *
1551 TAAACAACACCTTCCGACAAGGAAGGGCAGACT-AGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * *
1591 TAATCAACACCTTCCAACGGGGAAGGGCAAACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * * *
1632 TAAACAACATCTTCCGATC-GCGAATGGCAAGCTGGGAATTGGCAAT
1 TAAACAACACCTTCCGA-CGGGGAAGGGCAAACTGGGAA-----AAC
* * * * *
1678 TAGACAACACCTTCC-AGTGGGGAAGGGCAAACTAGGAGAGC
1 TAAACAACACCTTCCGA-CGGGGAAGGGCAAACTGGGAAAAC
* * ** ***
1719 TAAACGACACCTTCCGGCAAGGAAGGGCAAACTGGGACTTC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
** *
1760 -AAACAACACCTTCCGATTGGGAAGGGCAAAATGGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * *
1800 TAATCAACACCTTCCAACGGGGAAGGGCAAACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * *
1841 TAAACAACACCTTCCGACTGCGAAGGGCAAGCTGGGAATTGGCATC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAA-----AAC
* * ** * *
1887 TAGACAACACCTCCCGGTGGGGAAGGGCAAACTAGGAGAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * *
1928 TAGACAACACCATCC-AGTGGGGAAGGGCAAACT-GG-----
1 TAAACAACACCTTCCGA-CGGGGAAGGGCAAACTGGGAAAAC
* *
1963 TAAACAACACCTTCCGACGGGGAAGAGCAAGCTGGGAATTGGCAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAA-----AAC
* ** * *
2009 TAGACAACACCTTCCGATTGAGAAGGGCAAAATGGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
** * * *
2050 TAATTAACACCTTTCGATGAGGAAGGG-AAGACT-GGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAA-ACTGGGAAAAC
* *
2090 -AAATCAACACCTTCCGATGGGGAAGGGCAAACTGGGATAAC
1 TAAA-CAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * *
2131 TAAAAAACACCTTCCGACTGGGAAGGGCAAAATGGGAAAAT
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * *
2172 TAAACAACACTTTCCGACGGGGAAGGGCAGACT-AGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* *
2212 TAATCAACACCTTCCGACGGGGAAGGGCAAACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * * *
2253 TAAACAACACATTCCGACTGCGAAGGGCAAGCTGGGAATTGGCAAT
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAA-----AAC
* * **
2299 TATACAACACCTTCC-A-GTAGGGAAGGCCAAACT-GG-AATT
1 TAAACAACACCTTCCGACG--GGGAAGGGCAAACTGGGAAAAC
* *
2338 TAAACAACACCTTCCGATGGGGAAGGGCAAAATGGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* *** *
2379 TAAACAACACCTTCTGATAAGGAAGGGCAGACT-GGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* *
2419 TAATCAACACCTTCCGACGGGGAAGGGCAAACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * * *
2460 TAAACAACACCTTCCGACTGCGAAGGGTAAGCTGGGAATTGGCAAT
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAA-----AAC
* * * * *
2506 TAGACAACACCTTCC-A-GTGGGTAAGGGCAGACTAGGAGAGC
1 TAAACAACACCTTCCGACG-GGG-AAGGGCAAACTGGGAAAAC
* * * * ***
2547 TAAACGACACCTTTCGGCAGGGAAGGGCAAACTGGGACTTC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
** * *
2588 -AAACAACACCTTCCGATTGGGTAGGGCAAAATGGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * *
2628 TAAACAACACCTTCCGACGGGGAAGGGCAAACTAGCAAAGC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * ** ***
2669 TAAACAACACCTTCCGACAGTGGAAAGGCAAGTTGGGAGTTGTC
1 TAAACAACACCTTCCGAC-GGGGAAGGGCAAACTGGGA--AAAC
* * * ** * * * * *
2713 AAATAGAATTTACC-TCCTGGTGAGGAAGGGCAAATTAGGAGAGC
1 TAA-ACAA--CACCTTCC-GACGGGGAAGGGCAAACTGGGAAAAC
* * *
2757 TAAACAACA-CTTTCTAGTGGGGAAGGGCAAAC------AAC
1 TAAACAACACCTTCCGA-CGGGGAAGGGCAAACTGGGAAAAC
* *
2792 TAAACAACACCTTCCGACGGAGAAGGGCAAACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
*** * ** * *
2833 TAAACAACACCTTCCGAAATTGGAAAGGCAAGTTGGGAGTTAGC
1 TAAACAACACCTTCCG-ACGGGGAAGGGCAAACTGGGA--AAAC
* * * ** * * *
2877 AAATAGAATTTACC-TCCTGGTGGGGAAGGGCAAACTAGGAGAGC
1 TAA-ACAA--CACCTTCC-GACGGGGAAGGGCAAACTGGGAAAAC
* * * * *
2921 TAAACAACA-CTTTCTAGTGGGGAAGGGCAAACTAGGAGAAC
1 TAAACAACACCTTCCGA-CGGGGAAGGGCAAACTGGGAAAAC
* *
2962 TAGACAACACCTTCC-A-GTGGGAAAGGCAAACT-GG-----
1 TAAACAACACCTTCCGACG-GGGAAGGGCAAACTGGGAAAAC
* * * *
2996 TAAACAACACCTTCCGACAGGAAAGGGCACACTAGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
* * * * * *
3037 AAAACAACAACTTCCGACTGGGAAGAGCAAGCTGGGAATTGGGTAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAA-----AAC
* ** * *
3083 TAGACAACACCTTCCGATTGAGAAGGGCAAAATGGGAAAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
** * * * *
3124 TAATTAACACCTTCCGATGAGGAAGGG-AGGACT-AG-AAAC
1 TAAACAACACCTTCCGACGGGGAAGGGCA-AACTGGGAAAAC
*
3163 TAATCAACACCTTCCGA
1 TAAACAACACCTTCCGA
3180 T
Statistics
Matches: 1677, Mismatches: 375, Indels: 276
0.72 0.16 0.12
Matches are distributed among these distances:
32 11 0.01
33 2 0.00
34 25 0.01
35 106 0.06
36 12 0.01
37 6 0.00
38 3 0.00
39 61 0.04
40 308 0.18
41 802 0.48
42 40 0.02
43 7 0.00
44 16 0.01
45 16 0.01
46 251 0.15
47 11 0.01
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.15
Consensus pattern (41 bp):
TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGGAAAAC
Found at i:1209 original size:162 final size:163
Alignment explanation
Indices: 903--1233 Score: 504
Period size: 162 Copynumber: 2.0 Consensus size: 163
893 AGAGGAGGTT
* * *
903 AACTAGGAGAACTAAAAAACACCTTCTGGTGGGGAAGGGCAAACTGGTAAACAACATCTTCCGAC
1 AACTAGGAGAACTAAAAAACACCTTCTGGTGGGGAAAGGAAAACTGGTAAACAACACCTTCCGAC
* * * * *
968 GGGAAAGGGCACACTAGGAAAACTAAACAACACCTTCCGACTGGGAAGGGAAAGTTGGGAATTGG
66 GGGAAAGGGCACACTAGGAAAACAAAACAACAACTTCCGACTAGGAAGAGAAAGCTGGGAATTGG
* *
1033 CAACTAGACAACACCTCCCGGTGGGGAAGGGCA
131 CAACAAGACAACACCTCCCGGTGGGAAAGGGCA
* *
1066 AACTAGGAGAACTAGACAACACCTT-TCGGTGGGGAAAGGAAAACTGGTAAACAACACCTTCCGA
1 AACTAGGAGAACTAAAAAACACCTTCT-GGTGGGGAAAGGAAAACTGGTAAACAACACCTTCCGA
*
1130 CGGG-AAGGGCACACTAGGAAAACAAAACAACAACTTCCGACTAGGAAGAGCAAGCTGGGAATTG
65 CGGGAAAGGGCACACTAGGAAAACAAAACAACAACTTCCGACTAGGAAGAGAAAGCTGGGAATTG
*
1194 GCAACAAGACAACACCTTCCGGTGGGAAAGGGCA
130 GCAACAAGACAACACCTCCCGGTGGGAAAGGGCA
*
1228 CACTAG
1 AACTAG
1234 ACAACAACTT
Statistics
Matches: 152, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
162 91 0.60
163 61 0.40
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.13
Consensus pattern (163 bp):
AACTAGGAGAACTAAAAAACACCTTCTGGTGGGGAAAGGAAAACTGGTAAACAACACCTTCCGAC
GGGAAAGGGCACACTAGGAAAACAAAACAACAACTTCCGACTAGGAAGAGAAAGCTGGGAATTGG
CAACAAGACAACACCTCCCGGTGGGAAAGGGCA
Found at i:1237 original size:32 final size:32
Alignment explanation
Indices: 1200--1265 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
1190 ATTGGCAACA
* *
1200 AGACAACACCTTCCGGTGGGAAAGGGCACACT
1 AGACAACAACTTCCGGTGGGAAAGGGCAAACT
* * *
1232 AGACAACAACTTTCGTTGGGGAAGGGCAAACT
1 AGACAACAACTTCCGGTGGGAAAGGGCAAACT
1264 AG
1 AG
1266 GAAAACTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.23, G:0.29, T:0.15
Consensus pattern (32 bp):
AGACAACAACTTCCGGTGGGAAAGGGCAAACT
Found at i:1428 original size:81 final size:83
Alignment explanation
Indices: 1307--3179 Score: 1163
Period size: 81 Copynumber: 22.7 Consensus size: 83
1297 GGCAAACTGG
* * * *
1307 TAAAAAACACGTTCCGATGGGGAAGGGCAAAATGGGAAAACTAAACAACACCTTCCGA-TGAGGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
* *
1371 AGGACAGACT-GGAAAAC
66 AGGGCAAACTGGGAAAAC
* * *
1388 TAATCAACACCTTCCGATGGGGAAGGGCAAACTCGGAAAACTAAACAACACCTTCCGAC-CGGGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
*
1452 AGGGCAAAATGGGAAAAC
66 AGGGCAAACTGGGAAAAC
* * * * *
1470 TAAACAACACATTCCTATGGGGAAGGGCGAACTAGG--AATTAAAACAACACCTTCCGA-TGGGG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACT-AAACAACACCTTCCGACTGGGG
*
1532 AAGGGCAAAATGGGAAAAC
65 AAGGGCAAACTGGGAAAAC
*** * * * *
1551 TAAACAACACCTTCCGACAAGGAAGGGCAGACT-AGAAAACTAATCAACACCTTCCAAC-GGGGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
*
1614 AGGGCAAACTAGGAAAAC
66 AGGGCAAACTGGGAAAAC
* * * * * * * *
1632 TAAACAACATCTTCCGATCGCGAATGGCAAGCTGGGAATTGGCAATTAGACAACACCTTCC-AGT
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGACT
* * *
1696 GGGGAAGGGCAAACTAGGAGAGC
61 GGGGAAGGGCAAACTGGGAAAAC
* **** *** *
1719 TAAACGACACCTTCCGGCAAGGAAGGGCAAACTGGGACTTC-AAACAACACCTTCCGA-TTGGGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
*
1782 AGGGCAAAATGGGAAAAC
66 AGGGCAAACTGGGAAAAC
* * * * *
1800 TAATCAACACCTTCCAACGGGGAAGGGCAAACTAGGAAAACTAAACAACACCTTCCGACT-GCGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
* *
1864 AGGGCAAGCTGGGAATTGGCATC
66 AGGGCAAACTGGGAA-----AAC
* * * * * * * *
1887 TAGACAACACCTCCCGGTGGGGAAGGGCAAACTAGGAGAACTAGACAACACCATCC-AGTGGGGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
1951 AGGGCAAACT-GG-----
66 AGGGCAAACTGGGAAAAC
* * * *
1963 TAAACAACACCTTCCGACGGGGAAGAGCAAGCTGGGAATTGGCAACTAGACAACACCTTCCGA-T
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGACT
* * *
2027 TGAGAAGGGCAAAATGGGAAAAC
61 GGGGAAGGGCAAACTGGGAAAAC
** * *
2050 TAATTAACACCTTTCGATGAGGAAGGG-AAGACT-GGAAAAC-AAATCAACACCTTCCGA-TGGG
1 TAAACAACACCTTCCGATGGGGAAGGGCAA-ACTGGGAAAACTAAA-CAACACCTTCCGACTGGG
*
2111 GAAGGGCAAACTGGGATAAC
64 GAAGGGCAAACTGGGAAAAC
* * * *
2131 TAAAAAACACCTTCCGACT-GGGAAGGGCAAAATGGGAAAATTAAACAACACTTTCCGAC-GGGG
1 TAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGG
* *
2194 AAGGGCAGACT-AGAAAAC
65 AAGGGCAAACTGGGAAAAC
* * * * *
2212 TAATCAACACCTTCCGACGGGGAAGGGCAAACTAGGAAAACTAAACAACACATTCCGACT-GCGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
* *
2276 AGGGCAAGCTGGGAATTGGCAAT
66 AGGGCAAACTGGGAA-----AAC
* * * **
2299 TATACAACACCTTCC-AGTAGGGAAGGCCAAACT-GG-AATTTAAACAACACCTTCCGA-TGGGG
1 TAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGG
*
2360 AAGGGCAAAATGGGAAAAC
65 AAGGGCAAACTGGGAAAAC
* ** * *
2379 TAAACAACACCTTCTGATAAGGAAGGGCAGACT-GGAAAACTAATCAACACCTTCCGAC-GGGGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
*
2442 AGGGCAAACTAGGAAAAC
66 AGGGCAAACTGGGAAAAC
* * * * * *
2460 TAAACAACACCTTCCGACT-GCGAAGGGTAAGCTGGGAATTGGCAATTAGACAACACCTTCC-AG
1 TAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGAC
* * * * *
2523 TGGGTAAGGGCAGACTAGGAGAGC
60 TGGGGAAGGGCAAACTGGGAAAAC
* * *** *** * *
2547 TAAACGACACCTTTCGGCAGGGAAGGGCAAACTGGGACTTC-AAACAACACCTTCCGA-TTGGGT
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
*
2610 AGGGCAAAATGGGAAAAC
66 AGGGCAAACTGGGAAAAC
* * * * * *
2628 TAAACAACACCTTCCGACGGGGAAGGGCAAACTAGCAAAGCTAAACAACACCTTCCGACAGTGGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
* ** ***
2693 AAGGCAAGTTGGGAGTTGTC
66 AGGGCAAACTGGGA--AAAC
* * * * * * * * * * * *
2713 AAATAGAATTTACC-TCCTGGTGAGGAAGGGCAAATTAGGAGAGCTAAACAACA-CTTTCTAGTG
1 TAA-ACAA--CACCTTCC-GATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTG
2776 GGGAAGGGCAAAC------AAC
62 GGGAAGGGCAAACTGGGAAAAC
* * * * *
2792 TAAACAACACCTTCCGACGGAGAAGGGCAAACTAGGAAAACTAAACAACACCTTCCGAAAT-TGG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCG-ACTGGGG
* ** * *
2856 AAAGGCAAGTTGGGAGTTAGC
65 AAGGGCAAACTGGGA--AAAC
* * * * * * * * * *
2877 AAATAGAATTTACC-TCCTGGTGGGGAAGGGCAAACTAGGAGAGCTAAACAACA-CTTTCTAGTG
1 TAA-ACAA--CACCTTCC-GATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTG
* *
2940 GGGAAGGGCAAACTAGGAGAAC
62 GGGAAGGGCAAACTGGGAAAAC
* * * *
2962 TAGACAACACCTTCC-A-GTGGGAAAGGCAAACT-GG-----TAAACAACACCTTCCGAC-AGGA
1 TAAACAACACCTTCCGATG-GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGG
* *
3018 AAGGGCACACTAGGAAAAC
65 AAGGGCAAACTGGGAAAAC
* * * * * *
3037 AAAACAACAACTTCCGACT-GGGAAGAGCAAGCTGGGAATTGGGTACTAGACAACACCTTCCGA-
1 TAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGAC
* * *
3100 TTGAGAAGGGCAAAATGGGAAAAC
60 TGGGGAAGGGCAAACTGGGAAAAC
** * * * *
3124 TAATTAACACCTTCCGATGAGGAAGGG-AGGACT-AG-AAACTAATCAACACCTTCCGA
1 TAAACAACACCTTCCGATGGGGAAGGGCA-AACTGGGAAAACTAAACAACACCTTCCGA
3180 T
Statistics
Matches: 1379, Mismatches: 304, Indels: 219
0.73 0.16 0.12
Matches are distributed among these distances:
75 40 0.03
76 78 0.06
77 18 0.01
78 5 0.00
79 3 0.00
80 56 0.04
81 545 0.40
82 143 0.10
83 20 0.01
84 4 0.00
85 45 0.03
86 26 0.02
87 331 0.24
88 65 0.05
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.15
Consensus pattern (83 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGACTGGGGA
AGGGCAAACTGGGAAAAC
Found at i:1472 original size:122 final size:122
Alignment explanation
Indices: 1307--3179 Score: 1201
Period size: 122 Copynumber: 15.1 Consensus size: 122
1297 GGCAAACTGG
* * * * *
1307 TAAAAAACACGTTCCGATGGGGAAGGGCAAAATGGGAAAACTAAACAACACCTTCCGATGAGGAA
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCGATGGGGAA
* * * *
1372 GGACAGACT-GGAAAACTAATCAACACCTTCCGATGGGGAAGGGCAAACTCGGAAAAC
65 GGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
* * * *
1429 TAAACAACACCTTCCGACCGGGAAGGGCAAAATGGGAAAACTAAACAACACATTCCTATGGGGAA
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCGATGGGGAA
* * * *
1494 GGGCGAACTAGG--AATTAAAACAACACCTTCCGATGGGGAAGGGCAAAATGGGAAAAC
65 GGGCAAACTGGGAAAACT-AAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
** * * * * *
1551 TAAACAACACCTTCCGACAAGGAAGGGCAGACTAGAAAACTAATCAACACCTTCCAACGGGGAAG
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGAAG
* * * * * * *
1616 GGCAAACTAGGAAAACTAAACAACATCTTCCGATCGCGAATGGCAAGCTGGGAATTGGCAAT
66 GGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA-----AAC
* * * * * ****
1678 TAGACAACACCTTCC-AGTGGGGAAGGGCAAACTAGGAGAGCTAAACGACACCTTCCGGCAAGGA
1 TAAACAACACCTTCCGA-CGGGGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCGATGGGGA
*** * *
1742 AGGGCAAACTGGGACTTC-AAACAACACCTTCCGATTGGGAAGGGCAAAATGGGAAAAC
64 AGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
* * *
1800 TAATCAACACCTTCCAACGGGGAAGGGCAAACTAGGAAAACTAAACAACACCTTCCGACT-GCGA
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCGA-TGGGGA
* * * * * * *
1864 AGGGCAAGCTGGGAATTGGCATCTAGACAACACCTCCCGGTGGGGAAGGGCAAACTAGGAGAAC
64 AGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
* * * *
1928 TAGACAACACCATCC-AGTGGGGAAGGGCAAACTGG-----TAAACAACACCTTCCGACGGGGAA
1 TAAACAACACCTTCCGA-CGGGGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGAA
* * * * * *
1987 GAGCAAGCTGGGAATTGGCAACTAGACAACACCTTCCGATTGAGAAGGGCAAAATGGGAAAAC
65 GGGCAAACTGGGAA-----AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
** * * *
2050 TAATTAACACCTTTCGATGAGGAAGGG-AAGACTGGAAAAC-AAATCAACACCTTCCGATGGGGA
1 TAAACAACACCTTCCGACGGGGAAGGGCAA-ACTGGAAAACTAAA-CAACACCTTCCGATGGGGA
* * * *
2113 AGGGCAAACTGGGATAACTAAAAAACACCTTCCGACT-GGGAAGGGCAAAATGGGAAAAT
64 AGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAAAC
* * * * *
2172 TAAACAACACTTTCCGACGGGGAAGGGCAGACTAGAAAACTAATCAACACCTTCCGACGGGGAAG
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGAAG
* * * * *
2237 GGCAAACTAGGAAAACTAAACAACACATTCCGACT-GCGAAGGGCAAGCTGGGAATTGGCAAT
66 GGCAAACTGGGAAAACTAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAA-----AAC
* * **
2299 TATACAACACCTTCC-A-GTAGGGAAGGCCAAACTGG-AATTTAAACAACACCTTCCGATGGGGA
1 TAAACAACACCTTCCGACG--GGGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGA
* * ** *
2361 AGGGCAAAATGGGAAAACTAAACAACACCTTCTGATAAGGAAGGGCAGACT-GGAAAAC
64 AGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
* *
2419 TAATCAACACCTTCCGACGGGGAAGGGCAAACTAGGAAAACTAAACAACACCTTCCGACT-GCGA
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCGA-TGGGGA
* * * * * * * * *
2483 AGGGTAAGCTGGGAATTGGCAATTAGACAACACCTTCC-AGTGGGTAAGGGCAGACTAGGAGAGC
64 AGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAAAC
* * * * * * *
2547 TAAACGACACCTTTCGGCAGGGAAGGGCAAACTGG--GACTTCAAACAACACCTTCCGATTGGGT
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGAAAAC-T-AAACAACACCTTCCGATGGGGA
* * * * *
2610 AGGGCAAAATGGGAAAACTAAACAACACCTTCCGACGGGGAAGGGCAAACTAGCAAAGC
64 AGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
* * ** *** * * * *
2669 TAAACAACACCTTCCGACAGTGGAAAGGCAAGTTGGGAGTTGTCAAATAGAATTTACC-TCCTGG
1 TAAACAACACCTTCCGAC-GGGGAAGGGCAAACT-GGA--AAACTAA-ACAA--CACCTTCC-GA
* * * * * * *
2733 TGAGGAAGGGCAAATTAGGAGAGCTAAACAACA-CTTTCTAGTGGGGAAGGGCAAAC------AA
58 TGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAAA
2791 C
122 C
* *
2792 TAAACAACACCTTCCGACGGAGAAGGGCAAACTAGGAAAACTAAACAACACCTTCCGAAAT-TGG
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCG--ATGGGG
* ** * * * * * * * * *
2856 AAAGGCAAGTTGGGAGTTAGCAAATAGAATTTACC-TCCTGGTGGGGAAGGGCAAACTAGGAGAG
63 AAGGGCAAACTGGGA--AAACTAA-ACAA--CACCTTCC-GATGGGGAAGGGCAAACTGGGAAAA
2920 C
122 C
* * * * *
2921 TAAACAACA-CTTTCTAGTGGGGAAGGGCAAACTAGGAGAACTAGACAACACCTTCC-A-GTGGG
1 TAAACAACACCTTCCGA-CGGGGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCGATG-GGG
* ** * * *
2983 AAAGGCAAACT-GG-----TAAACAACACCTTCCGACAGGAAAGGGCACACTAGGAAAAC
63 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
* * * * * * * *
3037 AAAACAACAACTTCCGACTGGGAAGAGCAAGCTGGGAATTGGGTACTAGACAACACCTTCCGATT
1 TAAACAACACCTTCCGACGGGGAAGGGCAAACT-GGAA-----AACTAAACAACACCTTCCGATG
* * ** * * *
3102 GAGAAGGGCAAAATGGGAAAACTAATTAACACCTTCCGATGAGGAAGGG-AGGACT-AG-AAAC
60 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCA-AACTGGGAAAAC
*
3163 TAATCAACACCTTCCGA
1 TAAACAACACCTTCCGA
3180 T
Statistics
Matches: 1380, Mismatches: 269, Indels: 200
0.75 0.15 0.11
Matches are distributed among these distances:
116 45 0.03
117 12 0.01
118 20 0.01
119 6 0.00
120 36 0.03
121 65 0.05
122 571 0.41
123 63 0.05
124 3 0.00
125 8 0.01
126 95 0.07
127 199 0.14
128 167 0.12
129 90 0.07
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.15
Consensus pattern (122 bp):
TAAACAACACCTTCCGACGGGGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGAAG
GGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
Found at i:2758 original size:88 final size:87
Alignment explanation
Indices: 2648--2930 Score: 254
Period size: 88 Copynumber: 3.4 Consensus size: 87
2638 CTTCCGACGG
* *
2648 GGAAGGGCAAACTAGCAAAGCTAAACAACACCTTCCGACAGTGGAAAGGCAAGTTGGGAGTTGTC
1 GGAAGGGCAAACTAGGAAAGCTAAACAACACCTTCCGAAAGTGGAAAGGCAAGTTGGGAGTTG-C
2713 AAATAGAATTTACCTCCTGGTGA
65 AAATAGAATTTACCTCCTGGTGA
* * * * * **
2736 GGAAGGGCAAATTAGGAGAGCTAAACAACA-CTTTC--TAGTGG---GG-AAG--GGCA--AACA
1 GGAAGGGCAAACTAGGAAAGCTAAACAACACCTTCCGAAAGTGGAAAGGCAAGTTGGGAGTTGCA
* ***
2790 ACTA-AACAACACCTTCC-GACG-GA
66 AATAGAA-TTTACC-TCCTG--GTGA
* *
2813 -GAAGGGCAAACTAGGAAAACTAAACAACACCTTCCGAAATTGGAAAGGCAAGTTGGGAGTTAGC
1 GGAAGGGCAAACTAGGAAAGCTAAACAACACCTTCCGAAAGTGGAAAGGCAAGTTGGGAGTT-GC
*
2877 AAATAGAATTTACCTCCTGGTGG
65 AAATAGAATTTACCTCCTGGTGA
*
2900 GGAAGGGCAAACTAGGAGAGCTAAACAACAC
1 GGAAGGGCAAACTAGGAAAGCTAAACAACAC
2931 TTTCTAGTGG
Statistics
Matches: 147, Mismatches: 28, Indels: 40
0.68 0.13 0.19
Matches are distributed among these distances:
75 2 0.01
76 35 0.24
77 9 0.06
78 1 0.01
79 7 0.05
81 3 0.02
82 4 0.03
83 3 0.02
85 8 0.05
86 1 0.01
87 8 0.05
88 64 0.44
89 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (87 bp):
GGAAGGGCAAACTAGGAAAGCTAAACAACACCTTCCGAAAGTGGAAAGGCAAGTTGGGAGTTGCA
AATAGAATTTACCTCCTGGTGA
Done.