Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011973.1 Corchorus olitorius cultivar O-4 contig12006, 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: 45654
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--2701 Score: 4510
Period size: 154 Copynumber: 17.5 Consensus size: 154
* * *
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGACCCATTAGTTCCGTTTTGAATT
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
* * * *
66 GTGTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGACTAACTACAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* *
131 GGTCAGATTAGTCCACTGTGATGT
131 GGTGAGATTAGTCCACTGTGAAGT
* * *
155 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGTCTATCGAGGCCCATTAGTTCCGTTTTGAATT
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
220 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* *
285 GGTGAGATTAGTCGACTGTGATGT
131 GGTGAGATTAGTCCACTGTGAAGT
* * *
309 TTTTAGCTCATTTGGAACACTTGTTATTTCGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATT
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
*
374 GTCTTCGATTTGGCAAACCTCAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* *
439 GGTGAGATTAGTCGATTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
* * * * *
463 TTATAACTCAATTGGAACACTTGTTATTCTGGGTCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
* *
528 GTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
*
593 GGTGAGATTAGTCGACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
* *
617 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTCAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
* * *
682 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGACTAACTACAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* *
747 GGTCAGATTAGTCCACTGTGATGT
131 GGTGAGATTAGTCCACTGTGAAGT
* * *
771 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGACCCATTAGTTCCGTTTTGAATT
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
* * * *
836 GTGTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGACTAACTACAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* * *
901 GGTCAGATTAGACCACTGTGAAGA
131 GGTGAGATTAGTCCACTGTGAAGT
* * * *
925 TTATAGCTGATTTGGAACACTTGTTATTCTGGGCCTAAACGGGGCCCATTAGTTCCGTTTTGAAT
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT-ATCGGGGCCCATTAGTTCCGTTTTGAAT
*
990 CGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
65 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
*
1055 TGGTTGAGATTAGT-GACTGTGAAGT
130 TGG-TGAGATTAGTCCACTGTGAAGT
* * *
1080 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGGTCCGTTTAGAATA
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
* *
1145 TTCTTCGATTTGGCAAAGCTCAATGCTTTTCTTTCCTATTGTTTATGGCCTAACTATAATCATTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC-ATTGTTTATGGCCTAACTATAATCATTT
* *
1210 TGGTGA-ATTAGTCGACTGTAAAGT
130 TGGTGAGATTAGTCCACTGTGAAGT
* * *
1234 TTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCAATAGTTCCGTTTTGAATA
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
* * *
1299 TTCTTCGATTTGGCAAAACTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTA
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
1364 GGTGAGATTAGTCCACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
1388 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1453 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
*
1518 GGTCAGATTAGTCCACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
1542 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1607 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
1672 GGTGAGATTAGTCCACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
1696 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
*
1761 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
*
1826 GGTCAGATTAGTCCACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
*
1850 TTTTAGCTCATTTGGAAAACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1915 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
1980 GGTGAGATTAGTCCACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
2004 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
2069 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
2134 GGTGAGATTAGTCCACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
* * * *
2158 TTTTAGCTCATTTGGAACACTTGTTATTATGGGCCTACCGGGGCCCATTAGTGCCGTTTTGAAAC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
* * * *
2223 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGGTTATGGACTAACTACAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* *
2288 GGTCAGATTAGACCACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
* * * *
2312 TTATAGCTGATTTGGAACACTTGTTATTCTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
* *
2377 GTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
*
2442 GGTGA-ATTAGTCGACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
*
2465 TTTTAGCTCATTTGGAAGACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
*
2530 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTGAT-GCCTAACTATAATCATTTT
66 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
*
2594 GGTGAGATTAGTCGACTGTGAAGT
131 GGTGAGATTAGTCCACTGTGAAGT
* * * *
2618 TTATAGTTCATTTGGTACACTTGTTATTATGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
1 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
*
2683 GTCTTTGATTTGGCAAACC
66 GTCTTCGATTTGGCAAACC
2702 ACACCAACTC
Statistics
Matches: 2409, Mismatches: 132, Indels: 13
0.94 0.05 0.01
Matches are distributed among these distances:
152 24 0.01
153 253 0.11
154 1964 0.82
155 160 0.07
156 8 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
GGTGAGATTAGTCCACTGTGAAGT
Found at i:8813 original size:65 final size:65
Alignment explanation
Indices: 8709--8833 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 65
8699 GCTTGTTATT
* * * ** *
8709 GATTCCAATTTTCTGCACTAGCCCTTGCATGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTACACTAGCCCAGGCATGGGTAGGCCAAGAGTACCCCATGCATGGGTTGGAC
*
8774 GATTCAAACTTTCTACACTAGCCCAGGCGTGGGTAGGCCAAGAGTACCCCATGCATGGGT
1 GATTCAAACTTTCTACACTAGCCCAGGCATGGGTAGGCCAAGAGTACCCCATGCATGGGT
8834 AGAACCAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.22, C:0.26, G:0.27, T:0.24
Consensus pattern (65 bp):
GATTCAAACTTTCTACACTAGCCCAGGCATGGGTAGGCCAAGAGTACCCCATGCATGGGTTGGAC
Found at i:9572 original size:17 final size:17
Alignment explanation
Indices: 9550--9582 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9540 GAAAAAGCGC
9550 TAGATG-GACATCCTGGA
1 TAGATGAGA-ATCCTGGA
9567 TAGATGAGAATCCTGG
1 TAGATGAGAATCCTGG
9583 GAGACGGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (17 bp):
TAGATGAGAATCCTGGA
Found at i:10391 original size:20 final size:20
Alignment explanation
Indices: 10366--10418 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
10356 TTTCATTTTT
*
10366 TTACCCACATGTCATTTAAA
1 TTACCCACATGGCATTTAAA
*
10386 TTACCCACCTGGCATTTAAA
1 TTACCCACATGGCATTTAAA
* *
10406 TTAGCCACCTGGC
1 TTACCCACATGGC
10419 TTTTTTTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (20 bp):
TTACCCACATGGCATTTAAA
Found at i:18916 original size:28 final size:28
Alignment explanation
Indices: 18885--18972 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
18875 CCTCATAACA
18885 AAGTATTAAAGAAATTTCAAATTCAAAT
1 AAGTATTAAAGAAATTTCAAATTCAAAT
* ** *
18913 AAGTTTTGAATA-AAATTTTCTCA-T-AAAA
1 AAGTATT-AA-AGAAA-TTTCAAATTCAAAT
* *
18941 AAGCATTAATGAAATTTCAAATTCAAAT
1 AAGTATTAAAGAAATTTCAAATTCAAAT
18969 AAGT
1 AAGT
18973 TTTGAATAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
26 5 0.12
27 6 0.14
28 20 0.47
29 6 0.14
30 6 0.14
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (28 bp):
AAGTATTAAAGAAATTTCAAATTCAAAT
Found at i:18949 original size:56 final size:56
Alignment explanation
Indices: 18876--18987 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
18866 AATTAAATGC
* *
18876 CTCATAACAAAGTATTAAAGAAATTTCAAATTCAAATAAGTTTTGAATAAAATTTT
1 CTCATAAAAAAGCATTAAAGAAATTTCAAATTCAAATAAGTTTTGAATAAAATTTT
*
18932 CTCATAAAAAAGCATTAATGAAATTTCAAATTCAAATAAGTTTTGAATAAAATTTT
1 CTCATAAAAAAGCATTAAAGAAATTTCAAATTCAAATAAGTTTTGAATAAAATTTT
18988 AATGCAGAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (56 bp):
CTCATAAAAAAGCATTAAAGAAATTTCAAATTCAAATAAGTTTTGAATAAAATTTT
Found at i:20062 original size:2 final size:2
Alignment explanation
Indices: 20055--20095 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
20045 TTCCAAAAGT
* *
20055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20096 TGATAGGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26423 original size:45 final size:42
Alignment explanation
Indices: 26372--26465 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 42
26362 AGCAACAATT
26372 AATATTAGCTTTATTTTGATAAATTA-TCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATAAATTACT-TAGAGAT--A-GAGTAG
*
26417 AATATTAGCTTTATTTTGATGAATTACTTAGAGATAGAGTAG
1 AATATTAGCTTTATTTTGATAAATTACTTAGAGATAGAGTAG
26459 AAT-TTAG
1 AATATTAG
26466 GTAATGCACT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 9 0.19
43 1 0.02
45 32 0.68
46 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.39
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATAAATTACTTAGAGATAGAGTAG
Found at i:30824 original size:54 final size:54
Alignment explanation
Indices: 30567--31090 Score: 536
Period size: 54 Copynumber: 9.7 Consensus size: 54
30557 TGCTAACTAG
* * *
30567 TAATTCTGGGCAATTAAACTAAAAAAGAGTAGAAGAAGAAGTAAAGCAGAAGTTAGTT
1 TAATTCTGGGTAATTAAACT---AAAGAGTAAAAGAAGAAGTAAA-CAGAGGTTAGTT
* *
30625 TAATTCTGGGCAATTAAACTAAAAAAGAGTAAAAGAAGAAGTAAAGCAGAAGTTAGTT
1 TAATTCTGGGTAATTAAACT---AAAGAGTAAAAGAAGAAGTAAA-CAGAGGTTAGTT
* * * *
30683 TAATTCTGGGCAATTGAACTATAAAAGAGTACAAGAAGAAGTAAAGCAGAAGTTAGTT
1 TAATTCTGGGTAATTAAAC--T-AAAGAGTAAAAGAAGAAGTAAA-CAGAGGTTAGTT
* * * * *
30741 TAATTATGGGCAATTGAACTATAAATAGTAAAAGAAGAAGTAAACAGAGGATAGTT
1 TAATTCTGGGTAATTAAAC--TAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTT
* *
30797 TAATTCCGGGTAATTAAACTAAATAGT--AA-AAGAAG---A-AGAGGTTAGTT
1 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTT
* *
30844 TAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGTAAAGAGAGGTTAGTT
1 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTT
* ** * * *
30898 TAGTTCCAGGTAATTAAACTAAATAG--CAA-AAGAAG---A-AGAGTTTAGTT
1 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTT
*
30945 TAATTTTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTT
1 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTT
* * * *
30999 TAATTATGGGTAATTAATCTAAAGAGCAAAAGAAGAAGTAAACAGAGGGTAGTT
1 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTT
* * *
31053 TGATTCCGGGTAATTAAACTAAAGAGTAAAAGAGGAAG
1 TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAG
31091 AGTTTAGAGA
Statistics
Matches: 411, Mismatches: 39, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
47 65 0.16
48 2 0.00
49 4 0.01
50 12 0.03
51 12 0.03
52 4 0.01
53 2 0.00
54 133 0.32
56 25 0.06
57 20 0.05
58 131 0.32
60 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (54 bp):
TAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTT
Found at i:30826 original size:42 final size:44
Alignment explanation
Indices: 30792--30984 Score: 154
Period size: 47 Copynumber: 4.0 Consensus size: 44
30782 AAACAGAGGA
30792 TAGTTTAATTCCGGGTAATTAAACTAAATAGTAAAAGAAGAAGAGG
1 TAGTTTAATTCCGGGTAATTAAACTAAATAGTAAAAGAAG-AGA-G
* * *
30838 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGTAAAGAGAGG
1 -TAGTTTAATTCCGGGTAATTAAACTAAATAG-----TAA-AAG--AAGAGA-G
* * *
30892 TTAGTTTAGTTCCAGGTAATTAAACTAAATAGCAAAAGAAGAAGAG
1 -TAGTTTAATTCCGGGTAATTAAACTAAATAGTAAAAGAAG-AGAG
** *
30938 TTTAGTTTAATTTTGGGTAATTAAACTAAAGAGTAAAAGAAGA-AG
1 --TAGTTTAATTCCGGGTAATTAAACTAAATAGTAAAAGAAGAGAG
30983 TA
1 TA
30985 AACAGAGGTT
Statistics
Matches: 122, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
43 2 0.02
45 2 0.02
46 5 0.04
47 67 0.55
48 3 0.02
49 2 0.02
52 2 0.02
53 3 0.02
54 33 0.27
55 3 0.02
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (44 bp):
TAGTTTAATTCCGGGTAATTAAACTAAATAGTAAAAGAAGAGAG
Found at i:30911 original size:101 final size:101
Alignment explanation
Indices: 30734--31090 Score: 444
Period size: 101 Copynumber: 3.4 Consensus size: 101
30724 TAAAGCAGAA
* * * * *
30734 GTTAGTTTAATTATGGGCAATTGAACTATAAATAGTAAAAGAAGAAGTAAACAGAGGATAGTTTA
1 GTTAGTTTAATTCTGGGTAATTAAAC--TAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTA
*
30799 ATTCCGGGTAATTAAACTAAATAGTAAAAGAAGAAGAG
64 ATTCCGGGTAATTAAACTAAATAGAAAAAGAAGAAGAG
* * *
30837 GTTAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGTAAAGAGAGGTTAGTTTAGT
1 GTTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAAT
* *
30902 TCCAGGTAATTAAACTAAATAGCAAAAGAAGAAGAG
66 TCCGGGTAATTAAACTAAATAGAAAAAGAAGAAGAG
* *
30938 TTTAGTTTAATTTTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAAT
1 GTTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAAT
** * *
31003 TATGGGTAATTAATCTAAAGAGCAAAAGAAGAAGTAAACAGAG
66 TCCGGGTAATTAAACTAAATAG--AAA-AAGAAG---A-AGAG
* * * *
31046 GGTAGTTTGATTCCGGGTAATTAAACTAAAGAGTAAAAGAGGAAG
1 GTTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAG
31091 AGTTTAGAGA
Statistics
Matches: 220, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
101 145 0.66
103 25 0.11
104 6 0.03
107 1 0.00
108 43 0.20
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (101 bp):
GTTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAAT
TCCGGGTAATTAAACTAAATAGAAAAAGAAGAAGAG
Found at i:31003 original size:155 final size:155
Alignment explanation
Indices: 30619--31097 Score: 506
Period size: 155 Copynumber: 3.0 Consensus size: 155
30609 AAAGCAGAAG
* *
30619 TTAGTTTAATTCTGGGCAATTAAACTAAAAAAGAGTAAAAGAAGAAGTAAAGCAGAAGTTAGTTT
1 TTAGTTTAATTCTGGGTAATTAAACT---AAAGAGTAAAAGAAGAAGTAAA-CAGAGGTTAGTTT
* * * * * * **
30684 AATTCTGGGCAATTGAACTATAAAAGAGTACAAGAAGAAGTAAAGCAGAAGTTAGTTTAATTATG
62 AATTCTGGGTAATTAAAC--T-AAAGAGCAAAAGAAGAAGTAAAG-AGAGGTTAGTTTAGTTCCG
* * *
30749 GGCAATTGAACTATAAATAGTAAAAGAAGAAGTAAACAGAGG
123 GGTAATTAAAC--TAAATAG--AAA-AAGAAG---A-AGAGT
* * *
30791 ATAGTTTAATTCCGGGTAATTAAACTAAATAGT--AA-AAGAAG---A-AGAGGTTAGTTTAATT
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATT
*
30849 CTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGTAAAGAGAGGTTAGTTTAGTTCCAGGTAATTA
66 CTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGTAAAGAGAGGTTAGTTTAGTTCCGGGTAATTA
*
30914 AACTAAATAGCAAAAGAAGAAGAGT
131 AACTAAATAGAAAAAGAAGAAGAGT
*
30939 TTAGTTTAATTTTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATT
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATT
* * * *
31004 ATGGGTAATTAATCTAAAGAGCAAAAGAAGAAGTAAACAGAGGGTAGTTT-GATTCCGGGTAATT
66 CTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGTAAAGAGAGGTTAGTTTAG-TTCCGGGTAATT
* * *
31068 AAACTAAAGAGTAAAAGAGGAAGAGT
130 AAACTAAATAGAAAAAGAAGAAGAGT
31094 TTAG
1 TTAG
31098 AGAAAAAGAA
Statistics
Matches: 269, Mismatches: 30, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
148 33 0.12
149 1 0.00
150 2 0.01
151 6 0.02
152 6 0.02
153 2 0.01
154 2 0.01
155 107 0.40
157 23 0.09
158 21 0.08
159 1 0.00
161 27 0.10
163 1 0.00
166 6 0.02
167 2 0.01
169 6 0.02
172 23 0.09
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (155 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATT
CTGGGTAATTAAACTAAAGAGCAAAAGAAGAAGTAAAGAGAGGTTAGTTTAGTTCCGGGTAATTA
AACTAAATAGAAAAAGAAGAAGAGT
Found at i:31111 original size:75 final size:75
Alignment explanation
Indices: 31021--31160 Score: 201
Period size: 75 Copynumber: 1.9 Consensus size: 75
31011 ATTAATCTAA
* * * *
31021 AGAGCAAAAGAAGAAGTAAACAG-AGGGTAGTTTGATTCCGGGTAATTAAACTAAAGAGTAAAAG
1 AGAGAAAAAGAAGAAGTAAACAGTA-AGTAGTTTAATTCCGGGTAATTAAACTAAAAAGTAAAAG
31085 AGGAAGAGTTT
65 AGGAAGAGTTT
* * *
31096 AGAGAAAAAGAAGAAGTAAATAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGA
1 AGAGAAAAAGAAGAAGTAAACAGTAAGTAGTTTAATTCCGGGTAATTAAACTAAAAAGTAAAAGA
31161 AGGAGTAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 56 0.98
76 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (75 bp):
AGAGAAAAAGAAGAAGTAAACAGTAAGTAGTTTAATTCCGGGTAATTAAACTAAAAAGTAAAAGA
GGAAGAGTTT
Found at i:31138 original size:129 final size:129
Alignment explanation
Indices: 30967--31212 Score: 325
Period size: 129 Copynumber: 1.9 Consensus size: 129
30957 ATTAAACTAA
* * * *
30967 AGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTATGGGTAATTAATCTAAAGAGCAAAAGA
1 AGAGAAAAAGAAGAAGTAAACAGAGATTAGTTTAATTATGGGTAATTAAACTAAAAAGCAAAAGA
*** * * *
31032 AGAAGTAAACAGA-GGGTAGTTTGATTCCGGGTAATTAAACTAAAGAGTAAAAGAGGAAGAGTTT
66 AGAAGTAAACA-ATAAATAGTTTAATTCCAGGTAATTAAACTAAAGACTAAAAGAGGAAGAGTTT
* * *
31096 AGAGAAAAAGAAGAAGTAAATAGTA-ATTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAG
1 AGAGAAAAAGAAGAAGTAAACAG-AGATTAGTTTAATTATGGGTAATTAAACTAAAAAGCAAAAG
* *
31160 AAGGAGTAAACAATAAATAGTTTAATTCTAGGTAATTAAACTAAAGACTAAAA
65 AAGAAGTAAACAATAAATAGTTTAATTCCAGGTAATTAAACTAAAGACTAAAA
31213 AAAGGAGTAA
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
128 1 0.01
129 98 0.98
130 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.24
Consensus pattern (129 bp):
AGAGAAAAAGAAGAAGTAAACAGAGATTAGTTTAATTATGGGTAATTAAACTAAAAAGCAAAAGA
AGAAGTAAACAATAAATAGTTTAATTCCAGGTAATTAAACTAAAGACTAAAAGAGGAAGAGTTT
Found at i:31161 original size:54 final size:54
Alignment explanation
Indices: 31096--31287 Score: 251
Period size: 54 Copynumber: 3.6 Consensus size: 54
31086 GGAAGAGTTT
* *
31096 AGAGAAAAAGAAGAAGTAAATAGTAATTAGTTTAATTCTGGGTAATTAAACTAA
1 AGAGTAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAA
* * * * *
31150 AAAGTAAAAGAAGGAGTAAACAATAAATAGTTTAATTCTAGGTAATTAAACTAA
1 AGAGTAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAA
* * * * *
31204 AGACTAAAAAAAGGAGTAAACAGTAATTCGTTTAATTCTGGGTGATTAAACTAA
1 AGAGTAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAA
*
31258 AGAGTAAAAGAA-AGAGTAAGCAGTAATTAG
1 AGAGTAAAAGAAGA-AGTAAACAGTAATTAG
31288 CAATTAAACT
Statistics
Matches: 117, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
54 117 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.26
Consensus pattern (54 bp):
AGAGTAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAA
Found at i:31254 original size:183 final size:183
Alignment explanation
Indices: 30939--31268 Score: 459
Period size: 183 Copynumber: 1.8 Consensus size: 183
30929 GAAGAAGAGT
* * ***
30939 TTAGTTTAATTTTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATT
1 TTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGAAAATAGTTTAATT
* * * * *
31004 ATGGGTAATTAATCTAAAGAGCAAAAGAAGAAGTAAACAGAGGGTAGTTTGATTCCGGGTAATTA
66 ATAGGTAATTAAACTAAAGAGCAAAAAAAGAAGTAAACAGAGAGTAGTTTAATTCCGGGTAATTA
31069 AACTAAAGAGTAAAAGAGGAAGAGTTTAGAGAAAAAGAAGAAGTAAATAGTAA
131 AACTAAAGAGTAAAAGAGGAAGAGTTTAGAGAAAAAGAAGAAGTAAATAGTAA
*
31122 TTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGGAGTAAACA-ATAAATAGTTTAAT
1 TTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGA-AAATAGTTTAAT
* * * * * *
31186 TCTAGGTAATTAAACTAAAGA-CTAAAAAAAGGAGTAAACAGTA-ATTCGTTTAATTCTGGGTGA
65 TATAGGTAATTAAACTAAAGAGC-AAAAAAAGAAGTAAACAG-AGAGTAGTTTAATTCCGGGTAA
31249 TTAAACTAAAGAGTAAAAGA
128 TTAAACTAAAGAGTAAAAGA
31269 AAGAGTAAGC
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
182 2 0.02
183 124 0.98
184 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (183 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGAAAATAGTTTAATT
ATAGGTAATTAAACTAAAGAGCAAAAAAAGAAGTAAACAGAGAGTAGTTTAATTCCGGGTAATTA
AACTAAAGAGTAAAAGAGGAAGAGTTTAGAGAAAAAGAAGAAGTAAATAGTAA
Found at i:37917 original size:9 final size:9
Alignment explanation
Indices: 37903--37955 Score: 63
Period size: 9 Copynumber: 5.7 Consensus size: 9
37893 TCCCAATAAT
37903 AAAAAAATG
1 AAAAAAATG
37912 -AAAAAATG
1 AAAAAAATG
37920 AATGAAAAATTG
1 AA--AAAAA-TG
37932 AAAAAAATG
1 AAAAAAATG
*
37941 AAAAAAAGG
1 AAAAAAATG
37950 AAAAAA
1 AAAAAA
37956 GGAAAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 8 0.21
9 17 0.44
10 5 0.13
11 5 0.13
12 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:38351 original size:16 final size:16
Alignment explanation
Indices: 38321--38364 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
38311 AAGAGATTCC
*
38321 AAAAATATCAAAAAT-
1 AAAAAAATCAAAAATA
38336 AAAAAAATCAATAAATA
1 AAAAAAATCAA-AAATA
38353 AAAAAAATCAAA
1 AAAAAAATCAAA
38365 TCAAAATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 10 0.38
16 5 0.19
17 11 0.42
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAAATCAAAAATA
Found at i:38372 original size:11 final size:11
Alignment explanation
Indices: 38357--38399 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
38347 TAAATAAAAA
38357 AAATC-AAATC
1 AAATCAAAATC
38367 AAAATCAAAATC
1 -AAATCAAAATC
38379 AAATCAAAATC
1 AAATCAAAATC
38390 AAGATCAAAA
1 AA-ATCAAAA
38400 GAGAATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.60
12 12 0.40
ACGTcount: A:0.65, C:0.16, G:0.02, T:0.16
Consensus pattern (11 bp):
AAATCAAAATC
Found at i:38373 original size:6 final size:6
Alignment explanation
Indices: 38356--38399 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
38346 ATAAATAAAA
*
38356 AAAATC -AAATC AAAATC AAAATC -AAATC AAAATC AAGATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
38400 GAGAATTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:38376 original size:17 final size:17
Alignment explanation
Indices: 38356--38398 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
38346 ATAAATAAAA
38356 AAAATCAAATCAAAATC
1 AAAATCAAATCAAAATC
38373 AAAATCAAATCAAAATC
1 AAAATCAAATCAAAATC
*
38390 AAGATCAAA
1 AAAATCAAA
38399 AGAGAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.65, C:0.16, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAATCAAATCAAAATC
Found at i:39079 original size:50 final size:50
Alignment explanation
Indices: 39017--39156 Score: 171
Period size: 50 Copynumber: 2.9 Consensus size: 50
39007 ACAATAAGAT
*
39017 TGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
1 TGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
* * * * * ** *
39067 TGCTTTCCATTTGTAAGTTCAAGATCAAAATTTGCTTTTCAAGGTAGGAT
1 TGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
39117 TGCATTCCA----TGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
39157 GGCATTTAAG
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
46 27 0.36
50 49 0.64
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (50 bp):
TGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
Found at i:39783 original size:91 final size:90
Alignment explanation
Indices: 39605--39773 Score: 266
Period size: 91 Copynumber: 1.9 Consensus size: 90
39595 TCAAGTTATT
* * * *
39605 TTGACCGCACATTGGTCCTTTTTCATCATCGATCAAGAAGTTTTCAGTCACAACATCAGACTCAG
1 TTGACCGCACACTGGTCCTCTTTCATCATCAATCAAGAAGTTTTCAATCACAACATCAGACTCAG
*
39670 AGTTATTTTTCAAGTTGTTTTTCAAG
66 AGTTATTTTCCAAG-TGTTTTTCAAG
* *
39696 TTGACCGCACACTGGTCCTCTTTCATCATCAATCAAGAAGTTTTCAATTACAACATCAGATTCAG
1 TTGACCGCACACTGGTCCTCTTTCATCATCAATCAAGAAGTTTTCAATCACAACATCAGACTCAG
39761 AGTTATTTTCCAA
66 AGTTATTTTCCAA
39774 AGGTATTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 71 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (90 bp):
TTGACCGCACACTGGTCCTCTTTCATCATCAATCAAGAAGTTTTCAATCACAACATCAGACTCAG
AGTTATTTTCCAAGTGTTTTTCAAG
Found at i:40053 original size:69 final size:69
Alignment explanation
Indices: 39971--40266 Score: 393
Period size: 69 Copynumber: 4.3 Consensus size: 69
39961 AATTATCAAT
*
39971 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAG
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
40036 CCAC
66 CCAC
* *
40040 GTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAG
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
40105 CCAC
66 CCAC
*
40109 ATA-GCTTTTCCACAAGCCAGACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
*
40173 CCAT
66 CCAC
* * ** * * * * *
40177 ATAGACTTTTCCATAAATCAAACTCGTTTCCATGCGAGTTAGTGT-AAACATTGGGTCCATCCAT
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGT-TCAAGCCTTGGTTCCATCCA-
40241 A--CAGC
64 AGCCA-C
* *
40246 AAAGGCTTTTCCATAAGCCAA
1 ATAGGCTTTTCCACAAGCCAA
40267 GTTTAATGAG
Statistics
Matches: 201, Mismatches: 22, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
68 67 0.33
69 132 0.66
70 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (69 bp):
ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
CCAC
Found at i:40064 original size:119 final size:119
Alignment explanation
Indices: 39853--40080 Score: 393
Period size: 119 Copynumber: 1.9 Consensus size: 119
39843 TCCGAATGCT
*
39853 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTTAAGCCTTGGTTCCATCCAAAC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAAC
* *
39918 CACGTAGGCTTTTCCAAAAGTCAAACTCGTTTCCATACGAGTCAATTATCAATA
66 CACGTAGGCTTTTCCAAAAGCCAAACTCGTTTCCATACAAGTCAATTATCAATA
* * *
39972 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAAC
*
40037 CACGTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCA
66 CACGTAGGCTTTTCCAAAAGCCAAACTCGTTTCCATACAAGTCA
40081 GTTCAAGCCT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 102 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (119 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAAC
CACGTAGGCTTTTCCAAAAGCCAAACTCGTTTCCATACAAGTCAATTATCAATA
Found at i:40236 original size:137 final size:137
Alignment explanation
Indices: 39975--40239 Score: 388
Period size: 137 Copynumber: 1.9 Consensus size: 137
39965 ATCAATATAG
*
39975 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCCAC
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCAC
* * * * * *
40040 GTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAG
66 ATAGACTTTTCCACAAACCAAACTCGTTTCCATACAAGTCAGTTCAAACATTGGGTCCATCCAAG
40105 CCACATA
131 CCACATA
* *
40112 GCTTTTCCACAAGCCAGACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCAT
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCAC
* * * * *
40177 ATAGACTTTTCCATAAATCAAACTCGTTTCCATGCGAGTTAGTGT-AAACATTGGGTCCATCCA
66 ATAGACTTTTCCACAAACCAAACTCGTTTCCATACAAGTCAGT-TCAAACATTGGGTCCATCCA
40240 TACAGCAAAG
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
137 112 0.99
138 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (137 bp):
GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCAC
ATAGACTTTTCCACAAACCAAACTCGTTTCCATACAAGTCAGTTCAAACATTGGGTCCATCCAAG
CCACATA
Found at i:41218 original size:21 final size:21
Alignment explanation
Indices: 41192--41238 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
41182 ACAATTGAGC
*
41192 CTTAAAACTTTGGTCACTTGT
1 CTTAAAACTTGGGTCACTTGT
*
41213 CTTAAAGCTTGGGTCACTTGT
1 CTTAAAACTTGGGTCACTTGT
*
41234 TTTAA
1 CTTAA
41239 TAAATTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (21 bp):
CTTAAAACTTGGGTCACTTGT
Found at i:41248 original size:21 final size:20
Alignment explanation
Indices: 41201--41248 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
41191 CCTTAAAACT
**
41201 TTGGTCACTTGTCTTAAAGC
1 TTGGTCACTTGTCTTAAAAA
*
41221 TTGGGTCACTTGTTTTAATAAA
1 TT-GGTCACTTGTCTTAA-AAA
41243 TTGGTC
1 TTGGTC
41249 TTAGCACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 18 0.78
22 3 0.13
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (20 bp):
TTGGTCACTTGTCTTAAAAA
Done.