Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005178.1 Hibiscus syriacus cultivar Beakdansim tig00011684_pilon, 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: 97806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2986 original size:21 final size:21
Alignment explanation
Indices: 2960--3003 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2950 AAGGATTGAT
2960 CCTTTCACCAAAGGATCAATC
1 CCTTTCACCAAAGGATCAATC
*
2981 CCTTTCACCAAAGGGTCAATC
1 CCTTTCACCAAAGGATCAATC
3002 CC
1 CC
3004 ACTACTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.36, G:0.11, T:0.23
Consensus pattern (21 bp):
CCTTTCACCAAAGGATCAATC
Found at i:3150 original size:13 final size:13
Alignment explanation
Indices: 3132--3209 Score: 93
Period size: 13 Copynumber: 6.0 Consensus size: 13
3122 ATCATAAATC
3132 TATGACGCGCATT
1 TATGACGCGCATT
*
3145 TATGACGTGCATT
1 TATGACGCGCATT
*
3158 TATGACACGCATT
1 TATGACGCGCATT
* **
3171 TATGACACATATT
1 TATGACGCGCATT
*
3184 TATGACGCTCATT
1 TATGACGCGCATT
*
3197 TATGACGCACATT
1 TATGACGCGCATT
3210 GAGAGTTATT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 56 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:3373 original size:2 final size:2
Alignment explanation
Indices: 3366--3399 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3356 TTTCATAAAT
3366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3400 CTGTAGATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14847 original size:19 final size:21
Alignment explanation
Indices: 14823--14872 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
14813 TCTAATTTTG
*
14823 GTATCGATAT-TGGTAGGG-A
1 GTATCGATATATAGTAGGGTA
14842 GTATCGATATCATAGTAGGGTA
1 GTATCGATAT-ATAGTAGGGTA
14864 GTATCGATA
1 GTATCGATA
14873 CCATGGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.37
21 7 0.26
22 10 0.37
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.32
Consensus pattern (21 bp):
GTATCGATATATAGTAGGGTA
Found at i:14941 original size:95 final size:96
Alignment explanation
Indices: 14764--14971 Score: 211
Period size: 95 Copynumber: 2.2 Consensus size: 96
14754 ATACTGATGA
* * ** *
14764 GGTAGTATTGATACCATGATAAGGGGTATCAATACCAAACAACTTCGAATCTAATTTTGGTATCG
1 GGTAGTATCGATACCATGATAAGAGGTATCAATACCAAACAAAATCGAACCTAATTTTGGTATCG
***** *
14829 ATATTGGTAGGGAGTATCGATATCATAGTAG
66 ATACCCAAAGGGAGTATCGATACCATAGTAG
* ** * *
14860 GGTAGTATCGATACCATGGTAA-AGGTATTGATACCAGACAAAATCGAACCTATTTTTGGTATCG
1 GGTAGTATCGATACCATGATAAGAGGTATCAATACCAAACAAAATCGAACCTAATTTTGGTATCG
* * *
14924 ATACCCAAAGGGGGTATCGGTACCATAGTAT
66 ATACCCAAAGGGAGTATCGATACCATAGTAG
* * *
14955 AGAAGTATCGGTACCAT
1 GGTAGTATCGATACCAT
14972 AGCATTGAAA
Statistics
Matches: 90, Mismatches: 22, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
95 70 0.78
96 20 0.22
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (96 bp):
GGTAGTATCGATACCATGATAAGAGGTATCAATACCAAACAAAATCGAACCTAATTTTGGTATCG
ATACCCAAAGGGAGTATCGATACCATAGTAG
Found at i:14962 original size:22 final size:22
Alignment explanation
Indices: 14937--14992 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
14927 CCCAAAGGGG
*
14937 GTATCGGTACCATAGTATAGAA
1 GTATCGGTACCATAGCATAGAA
*
14959 GTATCGGTACCATAGCATTGAA
1 GTATCGGTACCATAGCATAGAA
*
14981 ATATCGGTACCA
1 GTATCGGTACCA
14993 CGGTAGTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (22 bp):
GTATCGGTACCATAGCATAGAA
Found at i:16840 original size:30 final size:30
Alignment explanation
Indices: 16805--16895 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
16795 GAATCTAAAA
16805 TTAGTCTTCTAACTCATAGCTATAAAAATT
1 TTAGTCTTCTAACTCATAGCTATAAAAATT
16835 TTAGTCTTCTAACTCATAGCTATAAAAATT
1 TTAGTCTTCTAACTCATAGCTATAAAAATT
* *
16865 TTAGTCTTCTAACTAATAGCTATGAAAATT
1 TTAGTCTTCTAACTCATAGCTATAAAAATT
16895 T
1 T
16896 CAGGATGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (30 bp):
TTAGTCTTCTAACTCATAGCTATAAAAATT
Found at i:17666 original size:21 final size:21
Alignment explanation
Indices: 17642--17681 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17632 AAGACTTTAT
17642 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
17663 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
17682 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:21528 original size:23 final size:22
Alignment explanation
Indices: 21495--21575 Score: 67
Period size: 23 Copynumber: 3.7 Consensus size: 22
21485 TTCTGCGTGC
* *
21495 TTGGTATCGATACCCCCTTTGCA
1 TTGGTACCGATACCCCC-TTGAA
*
21518 TTGGTACCGATACCATCCTTGAA
1 TTGGTACCGATACC-CCCTTGAA
* * *
21541 TGGGTACTGATACCCCCATG-A
1 TTGGTACCGATACCCCCTTGAA
*
21562 -GGGTACCGATACCC
1 TTGGTACCGATACCC
21576 TCTACGGGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 13 0.27
21 1 0.02
22 4 0.08
23 29 0.59
24 2 0.04
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (22 bp):
TTGGTACCGATACCCCCTTGAA
Found at i:21673 original size:29 final size:29
Alignment explanation
Indices: 21633--21693 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
21623 AACTCTCTAT
* *
21633 TCTTCTCTCTTTCACCGTGCACCTCTCTC
1 TCTTCTCTCTTTCACAGTGCACCTCCCTC
* *
21662 TCTTCTTTCTTTCACAGTGCGCCTCCCTC
1 TCTTCTCTCTTTCACAGTGCACCTCCCTC
21691 TCT
1 TCT
21694 CAAACCCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.07, C:0.43, G:0.08, T:0.43
Consensus pattern (29 bp):
TCTTCTCTCTTTCACAGTGCACCTCCCTC
Found at i:23103 original size:23 final size:23
Alignment explanation
Indices: 23077--23134 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
23067 CCACAGCTCA
*
23077 TATAATTACACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* * *
23100 TATAATTGTACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
*
23123 TAGAATTGCACC
1 TATAATTGCACC
23135 ATAGTGACAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:23140 original size:23 final size:23
Alignment explanation
Indices: 23091--23140 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
23081 ATTACACCGA
* * *
23091 AGTGCCACGTATAATTGTACCGG
1 AGTGCCACGTAGAATTGCACCAG
* *
23114 AGTGCCGCGTAGAATTGCACCAT
1 AGTGCCACGTAGAATTGCACCAG
23137 AGTG
1 AGTG
23141 ACATATAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCAG
Found at i:23332 original size:103 final size:103
Alignment explanation
Indices: 23159--23376 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
23149 TAATGTCCAT
* * *
23159 AAGGACCACATATCATTCCTTAAGAATAATATACATATACTAGGGATCAAGTATGTGTCTCATCA
1 AAGGACCACATATCATTCCTTAAGAATAATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
23224 GACTTCACACATGTTCCAAAGGATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
23262 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATAATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
23327 TACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
23365 AAGGACCACATA
1 AAGGACCACATA
23377 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATAATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:28944 original size:23 final size:23
Alignment explanation
Indices: 28918--28984 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
28908 CCACAGCTCA
*
28918 TATAATTACACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* * *
28941 TATAATTGTACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
*
28964 TAGAATTGCACC-ATAGTGCCA
1 TATAATTGCACCGA-AGTGCCA
28985 TATAATAATG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:29173 original size:103 final size:103
Alignment explanation
Indices: 29000--29217 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
28990 TAATGTCCAT
* * *
29000 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCATCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
29065 GACTTCACACATGTTCCAAAGGATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
29103 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
29168 TACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
29206 AAGGACCACATA
1 AAGGACCACATA
29218 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:33531 original size:110 final size:110
Alignment explanation
Indices: 33197--33577 Score: 450
Period size: 110 Copynumber: 3.5 Consensus size: 110
33187 AGACACCTTG
* ** * *
33197 TGTGCAAATCCAC-GAAATTCATCATGAGTAT-ATGAATCATAGTATAGGTACTTCGTGTGCATA
1 TGTGCATATCCACAG-AATTCATCATGAGT-TGATGAATCACCGTACAGGCACTTCGTGTGCATA
* * *
33260 TCCATAGAATTCATCATGAGTTGATGAATCACCGTACATGCA-TTTCA
64 TCCACAGAATTCATCATGAGTTGATGAATCACTGTACAAGCACTTT-A
* * *
33307 TGTACATATCCACAGAATTCATCGTGAGTTGATGAATCACCATACAGGCACTTCGTGTGCATATC
1 TGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCATATC
* *
33372 CACAGAATTCATCATGAGTTGAAGAATCACTGTACAAGCACTTTG
66 CACAGAATTCATCATGAGTTGATGAATCACTGTACAAGCACTTTA
* * *
33417 TGTGCATATCCACAGAATTCATCATGAGTTGATGACTCACCGTACAGACACTTCGTGTGCATATT
1 TGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCATATC
* * * *
33482 CACGGAATTCATCATGAGTTGATGAATCATTGTACAAGAACTATA
66 CACAGAATTCATCATGAGTTGATGAATCACTGTACAAGCACTTTA
** * * *
33527 TGTGCA-GCCCTC-GAAATTCATCATGGGTTGATGAATTC-CCGTATAGGCACT
1 TGTGCATATCCACAG-AATTCATCATGAGTTGATGAA-TCACCGTACAGGCACT
33578 AATTGTGAAT
Statistics
Matches: 234, Mismatches: 32, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
108 1 0.00
109 34 0.15
110 195 0.83
111 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (110 bp):
TGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCATATC
CACAGAATTCATCATGAGTTGATGAATCACTGTACAAGCACTTTA
Found at i:33532 original size:55 final size:55
Alignment explanation
Indices: 33196--33519 Score: 402
Period size: 55 Copynumber: 5.9 Consensus size: 55
33186 CAGACACCTT
* ** * * *
33196 GTGTGCAAATCCAC-GAAATTCATCATGAGTAT-ATGAATCATAGTATAGGTACTTC
1 GTGTGCATATCCACAG-AATTCATCATGAGT-TGATGAATCACCGTACAAGCACTTC
* * *
33251 GTGTGCATATCCATAGAATTCATCATGAGTTGATGAATCACCGTACATGCATTTC
1 GTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTC
* * * * *
33306 ATGTACATATCCACAGAATTCATCGTGAGTTGATGAATCACCATACAGGCACTTC
1 GTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTC
* * *
33361 GTGTGCATATCCACAGAATTCATCATGAGTTGAAGAATCACTGTACAAGCACTTT
1 GTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTC
*
33416 GTGTGCATATCCACAGAATTCATCATGAGTTGATGACTCACCGTAC-AGACACTTC
1 GTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAAG-CACTTC
* * **
33471 GTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATTGTACAAG
1 GTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAAG
33520 AACTATATGT
Statistics
Matches: 233, Mismatches: 32, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
54 3 0.01
55 227 0.97
56 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (55 bp):
GTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTC
Found at i:36941 original size:22 final size:22
Alignment explanation
Indices: 36910--37049 Score: 152
Period size: 22 Copynumber: 6.7 Consensus size: 22
36900 GGACCATTAC
*
36910 GTCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
*
36932 GTCCCGAAGGACCACT--ACA-
1 GTCCCGAAGGACCACTGGATAT
* *
36951 -TCCCGAAGGACAACT--ACA-
1 GTCCCGAAGGACCACTGGATAT
**
36969 -TCCCGAAGGACCACTATATAT
1 GTCCCGAAGGACCACTGGATAT
* *
36990 GTCCCGAATGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAT
37012 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
37034 GTCCCGAAGGACCACT
1 GTCCCGAAGGACCACT
37050 ATAAACCTTC
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.30
20 4 0.04
22 68 0.66
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.17
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAT
Found at i:36956 original size:18 final size:18
Alignment explanation
Indices: 36933--36984 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
36923 ACTGGATATG
36933 TCCCGAAGGACCACTACA
1 TCCCGAAGGACCACTACA
*
36951 TCCCGAAGGACAACTACA
1 TCCCGAAGGACCACTACA
36969 TCCCGAAGGACCACTA
1 TCCCGAAGGACCACTA
36985 TATATGTCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.35, C:0.37, G:0.17, T:0.12
Consensus pattern (18 bp):
TCCCGAAGGACCACTACA
Found at i:36990 original size:58 final size:58
Alignment explanation
Indices: 36893--37005 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
36883 TGAATATTTG
* * * * *
36893 TCCCAAAGGACCATTACGTCCCTAAGGACCACTGGATATGTCCCGAAGGACCACTACA
1 TCCCAAAGGACAACTACATCCCGAAGGACCACTAGATATGTCCCGAAGGACCACTACA
* * *
36951 TCCCGAAGGACAACTACATCCCGAAGGACCACTATATATGTCCCGAATGACCACT
1 TCCCAAAGGACAACTACATCCCGAAGGACCACTAGATATGTCCCGAAGGACCACT
37006 GGATACGTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.32, C:0.33, G:0.18, T:0.18
Consensus pattern (58 bp):
TCCCAAAGGACAACTACATCCCGAAGGACCACTAGATATGTCCCGAAGGACCACTACA
Found at i:43952 original size:22 final size:22
Alignment explanation
Indices: 43920--44039 Score: 168
Period size: 22 Copynumber: 5.5 Consensus size: 22
43910 TTACGTCTTT
* **
43920 AAGGACTACTGGATATATCCCG
1 AAGGACCACTGGATACGTCCCG
43942 AAGGACCACTGGATACGTCCCG
1 AAGGACCACTGGATACGTCCCG
43964 AAGGACCACTGGATACGTCCCG
1 AAGGACCACTGGATACGTCCCG
* *
43986 AATGACCACTAGATACGTCCCG
1 AAGGACCACTGGATACGTCCCG
* *
44008 AAGGACCACTGGATATGTCCCA
1 AAGGACCACTGGATACGTCCCG
*
44030 AATGACCACT
1 AAGGACCACT
44040 ATAAACCCTT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 88 1.00
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (22 bp):
AAGGACCACTGGATACGTCCCG
Found at i:43969 original size:44 final size:44
Alignment explanation
Indices: 43920--44040 Score: 188
Period size: 44 Copynumber: 2.8 Consensus size: 44
43910 TTACGTCTTT
* * * *
43920 AAGGACTACTGGATATATCCCGAAGGACCACTGGATACGTCCCG
1 AAGGACCACTGGATATGTCCCGAATGACCACTAGATACGTCCCG
*
43964 AAGGACCACTGGATACGTCCCGAATGACCACTAGATACGTCCCG
1 AAGGACCACTGGATATGTCCCGAATGACCACTAGATACGTCCCG
*
44008 AAGGACCACTGGATATGTCCCAAATGACCACTA
1 AAGGACCACTGGATATGTCCCGAATGACCACTA
44041 TAAACCCTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.17
Consensus pattern (44 bp):
AAGGACCACTGGATATGTCCCGAATGACCACTAGATACGTCCCG
Found at i:44657 original size:63 final size:63
Alignment explanation
Indices: 44582--44729 Score: 197
Period size: 63 Copynumber: 2.3 Consensus size: 63
44572 GATGCATCCT
* *
44582 TTAACGGGTGCATCGATGCACTACCTGTGCATCGGTACACAAATCCCATTCGATGTTTGAATA
1 TTAAGGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCCCATTCGATGTTTGAATA
* * ** ** *
44645 TTAAGGGGTGCATCGATGCACTACTTGTGCATCGATACACTAATGGCATTCGATGTTTTTATT
1 TTAAGGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCCCATTCGATGTTTGAATA
*
44708 TTAAAGGAGTGCATCGATGCAC
1 TT-AAGGGGTGCATCGATGCAC
44730 CTTCAATAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
63 56 0.76
64 18 0.24
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (63 bp):
TTAAGGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCCCATTCGATGTTTGAATA
Found at i:48935 original size:20 final size:19
Alignment explanation
Indices: 48906--48960 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
48896 TGATTCAATC
* *
48906 AGTATTGATACCAATGAGG
1 AGTATCGATACCAATAAGG
48925 TAGTATCGATACCATGATAAGG
1 -AGTATCGATACCA--ATAAGG
*
48947 GGTATCGATACCAA
1 AGTATCGATACCAA
48961 GCAACTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.40
21 12 0.40
22 5 0.17
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (19 bp):
AGTATCGATACCAATAAGG
Found at i:49027 original size:22 final size:23
Alignment explanation
Indices: 49002--49065 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 23
48992 CAGTCGGGGA
49002 TATCGATAACATAGT-AGGGTAG
1 TATCGATAACATAGTAAGGGTAG
* *
49024 TATCGATACCATGGTAA-GG--G
1 TATCGATAACATAGTAAGGGTAG
* *
49044 TATCGATACCATGGTAAGGGTA
1 TATCGATAACATAGTAAGGGTA
49066 TCGATACCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 15 0.42
23 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (23 bp):
TATCGATAACATAGTAAGGGTAG
Found at i:49048 original size:20 final size:20
Alignment explanation
Indices: 49023--49074 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
49013 TAGTAGGGTA
49023 GTATCGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
49043 GTATCGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
49063 GTATCGATACCA
1 GTATCGATACCA
49075 GACAACATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (20 bp):
GTATCGATACCATGGTAAGG
Found at i:49541 original size:55 final size:55
Alignment explanation
Indices: 49470--49807 Score: 425
Period size: 55 Copynumber: 6.2 Consensus size: 55
49460 CTATATGTAC
* * * *
49470 TACAGGCACCTT-GTGTGTAAATTCACGGAATTCATCATGAGTTAATGAATCACCA
1 TACAGGCA-CTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
*
49525 TACAGGCACTTCGTGTGCAAATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * *
49580 TACAGGCACTTAGTGTGCATATCCA-GGAATTTATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * **
49634 TACAGGCACTTCGTGTGCATATCCACGGAATTCATCATGAGTTGATAAATCATTG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* **
49689 TACAGGCACTTCGTGTGCATATTAACGGAATTCATCATGAGTTGATGAATCATTG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *** *
49744 TACATGCACTAT-GTGTGCA-GCCCACGGAATTCATCATGGGTTGATGAATTC-CCG
1 TACAGGCACT-TCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAA-TCACCG
*
49798 TATAGGCACT
1 TACAGGCACT
49808 AATTGTGCAT
Statistics
Matches: 254, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
54 88 0.35
55 165 0.65
56 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (55 bp):
TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
Found at i:49692 original size:109 final size:108
Alignment explanation
Indices: 49470--49807 Score: 421
Period size: 109 Copynumber: 3.1 Consensus size: 108
49460 CTATATGTAC
* * * *
49470 TACAGGCACCTTGTGTGTAAATTCACGGAATTCATCATGAGTTAATGAATCACCATACAGGCACT
1 TACAGGCA-CTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACT
* *
49535 TCGTGTGCAAATTCACGGAATTCATCATGAGTTGATGAATCACCG
65 TCGTGTGC-AATCCACGGAATTCATCATGAGTTGATAAATCACCG
* *
49580 TACAGGCACTTAGTGTGCATATCCA-GGAATTTATCATGAGTTGATGAATCACCGTACAGGCACT
1 TACAGGCACTT-GTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACT
**
49644 TCGTGTGCATATCCACGGAATTCATCATGAGTTGATAAATCATTG
65 TCGTGTGCA-ATCCACGGAATTCATCATGAGTTGATAAATCACCG
* ** *
49689 TACAGGCACTTCGTGTGCATATTAACGGAATTCATCATGAGTTGATGAATCATTGTACATGCACT
1 TACAGGCACTT-GTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACT
** * *
49754 AT-GTGTGCAGCCCACGGAATTCATCATGGGTTGATGAATTC-CCG
65 -TCGTGTGCAATCCACGGAATTCATCATGAGTTGAT-AAATCACCG
*
49798 TATAGGCACT
1 TACAGGCACT
49808 AATTGTGCAT
Statistics
Matches: 199, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
108 1 0.01
109 133 0.67
110 64 0.32
111 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (108 bp):
TACAGGCACTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTT
CGTGTGCAATCCACGGAATTCATCATGAGTTGATAAATCACCG
Found at i:49762 original size:164 final size:163
Alignment explanation
Indices: 49470--49807 Score: 448
Period size: 164 Copynumber: 2.1 Consensus size: 163
49460 CTATATGTAC
* * *
49470 TACAGGCACCTTGTGTGTAAATTCACGGAATTCATCATGAGTTAATGAATCACCATACAGGCACT
1 TACAGGCA-CTTGTGTGCAAATCCACGGAATTCATCATGAGTTAATAAATCACCATACAGGCACT
*
49535 TCGTGTGCAAATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTAGTGTGCAT
65 TCGTGTGCAAATTAACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTAGTGTGCA-
* *
49600 ATCCA-GGAATTTATCATGAGTTGATGAA-TCACCG
129 ACCCACGGAATTCATCATGAGTTGATGAATTC-CCG
* * ***
49634 TACAGGCACTTCGTGTGCATATCCACGGAATTCATCATGAGTTGATAAATCATTGTACAGGCACT
1 TACAGGCACTT-GTGTGCAAATCCACGGAATTCATCATGAGTTAATAAATCACCATACAGGCACT
* ** *
49699 TCGTGTGCATATTAACGGAATTCATCATGAGTTGATGAATCATTGTACATGCAC-TATGTGTGCA
65 TCGTGTGCAAATTAACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTA-GTGTGCA
* *
49763 GCCCACGGAATTCATCATGGGTTGATGAATTCCCG
129 ACCCACGGAATTCATCATGAGTTGATGAATTCCCG
*
49798 TATAGGCACT
1 TACAGGCACT
49808 AATTGTGCAT
Statistics
Matches: 152, Mismatches: 18, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
163 8 0.05
164 142 0.93
165 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (163 bp):
TACAGGCACTTGTGTGCAAATCCACGGAATTCATCATGAGTTAATAAATCACCATACAGGCACTT
CGTGTGCAAATTAACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTAGTGTGCAAC
CCACGGAATTCATCATGAGTTGATGAATTCCCG
Found at i:50489 original size:14 final size:14
Alignment explanation
Indices: 50470--50502 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
50460 AATGGTAAAT
50470 GAACACAAACGAAC
1 GAACACAAACGAAC
50484 GAACACAAACGAAC
1 GAACACAAACGAAC
50498 GAACA
1 GAACA
50503 TAAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.27, G:0.15, T:0.00
Consensus pattern (14 bp):
GAACACAAACGAAC
Found at i:54223 original size:2 final size:2
Alignment explanation
Indices: 54216--54323 Score: 79
Period size: 2 Copynumber: 58.0 Consensus size: 2
54206 AAATAATTAT
*
54216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
54257 T- TA -A TA AA TT TA -A TT TA AA T- TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
54294 -A TA TT TA TA TA TT TA -A TT TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54324 CCCGACCCGA
Statistics
Matches: 80, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
1 8 0.10
2 72 0.90
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:54283 original size:40 final size:38
Alignment explanation
Indices: 54237--54323 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 38
54227 ATATATATAT
54237 ATATATATATATACATAATATTAATAAATTTAATTTAA
1 ATATATATATATACATAATATTAATAAATTTAATTTAA
* * *
54275 ATTAATATATATATATATAATATTTATATATTTAATTTAA
1 A-T-ATATATATATACATAATATTAATAAATTTAATTTAA
54315 ATATATATA
1 ATATATATA
54324 CCCGACCCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 8 0.18
39 2 0.05
40 34 0.77
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (38 bp):
ATATATATATATACATAATATTAATAAATTTAATTTAA
Found at i:56675 original size:14 final size:14
Alignment explanation
Indices: 56647--56683 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
56637 GGCGTGAATT
*
56647 GTGATGG-AGGATG
1 GTGATGGAAAGATG
56660 GTGATGGAAAGATG
1 GTGATGGAAAGATG
56674 GTGATGGAAA
1 GTGATGGAAA
56684 TAGTATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (14 bp):
GTGATGGAAAGATG
Found at i:57066 original size:19 final size:20
Alignment explanation
Indices: 57021--57069 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
57011 ATCCCCTTTT
**
57021 AAAATACATGATTTTTGATG
1 AAAATACATGATTTTAAATG
57041 AAAATACATGA-TTTAAATG
1 AAAATACATGATTTTAAATG
*
57060 AAGATACATG
1 AAAATACATG
57070 CTCTTGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
AAAATACATGATTTTAAATG
Found at i:60154 original size:18 final size:20
Alignment explanation
Indices: 60106--60155 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
60096 TTTTGTAACT
60106 TTTTCTTCTCTTCTCTTTTGC
1 TTTTCTT-TCTTCTCTTTTGC
**
60127 TTTTGATTCTTCT-TTTT-C
1 TTTTCTTTCTTCTCTTTTGC
60145 TTTTCTTTCTT
1 TTTTCTTTCTT
60156 TTGCACTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 10 0.40
19 4 0.16
20 6 0.24
21 5 0.20
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.72
Consensus pattern (20 bp):
TTTTCTTTCTTCTCTTTTGC
Found at i:60207 original size:15 final size:15
Alignment explanation
Indices: 60183--60212 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60173 TGTATGAGTC
60183 TTTTTATTTCTTTTT
1 TTTTTATTTCTTTTT
*
60198 TTTTTCTTTCTTTTT
1 TTTTTATTTCTTTTT
60213 CTTCTTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTATTTCTTTTT
Found at i:60459 original size:15 final size:15
Alignment explanation
Indices: 60426--60461 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
60416 AATATGGAAG
*
60426 AAGAAAGGAAATGAT
1 AAGAAAGGAAATGAC
*
60441 AAGAAAGGAAATGGC
1 AAGAAAGGAAATGAC
60456 AAGAAA
1 AAGAAA
60462 TGATATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.28, T:0.08
Consensus pattern (15 bp):
AAGAAAGGAAATGAC
Found at i:60649 original size:14 final size:14
Alignment explanation
Indices: 60618--60657 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
60608 ATGGGCGTGA
*
60618 ATGGTGATGG-AGG
1 ATGGTGATGGAAAG
60631 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
60645 ATGGTGATGGAAA
1 ATGGTGATGGAAA
60658 TAGTATCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.45, T:0.23
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:61040 original size:19 final size:20
Alignment explanation
Indices: 60995--61043 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
60985 AACCCCTTTA
**
60995 AAAATACATGATTTTTTATG
1 AAAATACATGATTTTAAATG
61015 AAAATACATGA-TTTAAATG
1 AAAATACATGATTTTAAATG
*
61034 AAGATACATG
1 AAAATACATG
61044 CTCATGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
AAAATACATGATTTTAAATG
Found at i:62997 original size:15 final size:16
Alignment explanation
Indices: 62969--63119 Score: 52
Period size: 19 Copynumber: 8.5 Consensus size: 16
62959 TTTGCTTAAT
*
62969 TTTTAAAATCATATTA
1 TTTTAAAATAATATTA
*
62985 TTTTAAATAATATTAATTAA
1 TTTT-AA-AATAAT-ATT-A
63005 TTATTTAAAATAATATTA
1 -T-TTTAAAATAATATTA
* *
63023 ATTTAAATTATAATTTTTAA
1 TTTTAAA--ATAA-TATT-A
* *
63043 ATTT-AAATAATATTG
1 TTTTAAAATAATATTA
* * *
63058 TATGAAACTAAATATATAA
1 TTTTAAAAT-AATAT-T-A
*
63077 TTTAAAAATAATATTA
1 TTTTAAAATAATATTA
*
63093 TTTCTAATAAATAATATAA
1 TTT-T-A-AAATAATATTA
63112 TTTTAAAA
1 TTTTAAAA
63120 ATTAAATAAA
Statistics
Matches: 101, Mismatches: 17, Indels: 34
0.66 0.11 0.22
Matches are distributed among these distances:
15 1 0.01
16 23 0.23
17 13 0.13
18 17 0.17
19 30 0.30
20 11 0.11
21 3 0.03
22 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (16 bp):
TTTTAAAATAATATTA
Found at i:63007 original size:23 final size:23
Alignment explanation
Indices: 62981--63025 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
62971 TTAAAATCAT
*
62981 ATTATTTTAAATAATATTAATTA
1 ATTATTTAAAATAATATTAATTA
63004 ATTATTTAAAATAATATTAATT
1 ATTATTTAAAATAATATTAATT
63026 TAAATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTATTTAAAATAATATTAATTA
Found at i:63127 original size:19 final size:19
Alignment explanation
Indices: 63025--63199 Score: 56
Period size: 20 Copynumber: 8.7 Consensus size: 19
63015 TAATATTAAT
* *
63025 TTAAATTATAATTTTTAAAT
1 TTAAA-TATAATTTTAAAAA
* *
63045 TTAAATA-ATATTGTATGAAA
1 TTAAATATA-ATTTTA-AAAA
* *
63065 CTAAATATATAATTTAAAAA
1 TTAAATATA-ATTTTAAAAA
*
63085 -T-AATATTATTTCTAATAAA
1 TTAAATATAATTT-TAA-AAA
63104 -T-AATATAATTTTAAAAA
1 TTAAATATAATTTTAAAAA
* *
63121 TTAAATAAAAATTTTATAATAC
1 TTAAAT-ATAATTTTA-AA-AA
*
63143 TATAAATATACATTTTAGAATGA
1 T-TAAATATA-ATTTTA-AA-AA
* *
63166 TTTAATATAAATTATAAAAA
1 TTAAATAT-AATTTTAAAAA
63186 TATATAA-ATAATTT
1 T-TA-AATATAATTT
63200 AATTATTTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
17 6 0.05
18 13 0.11
19 23 0.19
20 30 0.25
21 13 0.11
22 17 0.14
23 16 0.14
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAAATATAATTTTAAAAA
Found at i:65381 original size:13 final size:13
Alignment explanation
Indices: 65365--65407 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
65355 ATTTCATTTA
65365 AATATTTTTAAAT
1 AATATTTTTAAAT
* *
65378 AATAATTTTGAAAA
1 AAT-ATTTTTAAAT
65392 AATATTTTATAAAT
1 AATATTTT-TAAAT
65406 AA
1 AA
65408 AAAAATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
AATATTTTTAAAT
Found at i:66280 original size:2 final size:2
Alignment explanation
Indices: 66273--66301 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66263 CCATGTTTGC
66273 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66302 AGCAATGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71403 original size:3 final size:3
Alignment explanation
Indices: 71397--71487 Score: 155
Period size: 3 Copynumber: 30.3 Consensus size: 3
71387 TGTTGTCTCT
71397 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
71445 TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA ATA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
71488 AGGCCCAATT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:72783 original size:28 final size:28
Alignment explanation
Indices: 72726--72786 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
72716 GTTCTTTACG
*
72726 TTTTATATTTTACATTTTAATCACTGAT
1 TTTTATATTTTACATTTTAACCACTGAT
* *
72754 TTTTATAATTTT-CATTTTGACCA-TGAA
1 TTTTAT-ATTTTACATTTTAACCACTGAT
72781 TTTTAT
1 TTTTAT
72787 GTATTTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 9 0.31
28 15 0.52
29 5 0.17
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (28 bp):
TTTTATATTTTACATTTTAACCACTGAT
Found at i:77408 original size:8 final size:8
Alignment explanation
Indices: 77395--77442 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
77385 AATAACAAAT
77395 AAAAAAAG
1 AAAAAAAG
77403 AAAAAAAG
1 AAAAAAAG
77411 --AAAAAG
1 AAAAAAAG
77417 AAAAAAAG
1 AAAAAAAG
77425 --AAAAAG
1 AAAAAAAG
77431 AAAGAAAAG
1 AAA-AAAAG
77440 AAA
1 AAA
77443 GAGAAGAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
6 12 0.34
8 15 0.43
9 8 0.23
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:77429 original size:23 final size:22
Alignment explanation
Indices: 77395--77442 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
77385 AATAACAAAT
77395 AAAAAAAGAAAA-AAAGAAAAAG
1 AAAAAAAGAAAAGAAAG-AAAAG
77417 AAAAAAAGAAAAAGAAAGAAAAG
1 AAAAAAAG-AAAAGAAAGAAAAG
77440 AAA
1 AAA
77443 GAGAAGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 12 0.50
24 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAAAGAAAGAAAAG
Found at i:77443 original size:9 final size:9
Alignment explanation
Indices: 77398--77450 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
77388 AACAAATAAA
77398 AAAAGAAA-
1 AAAAGAAAG
77406 AAAAGAAAAAG
1 AAAAG--AAAG
77417 AAAA-AAAG
1 AAAAGAAAG
77425 AAAAAGAAAG
1 -AAAAGAAAG
77435 AAAAGAAAG
1 AAAAGAAAG
*
77444 AGAAGAA
1 AAAAGAA
77451 GTTGCTAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
8 9 0.23
9 19 0.49
10 7 0.18
11 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:77450 original size:14 final size:14
Alignment explanation
Indices: 77397--77447 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
77387 TAACAAATAA
77397 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
77411 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
77425 AAAAAGAAAGAAAAG
1 AAAAAGAAA-AAAAG
*
77440 AAAGAGAA
1 AAAAAGAA
77448 GAAGTTGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:78708 original size:54 final size:54
Alignment explanation
Indices: 78636--78781 Score: 247
Period size: 54 Copynumber: 2.7 Consensus size: 54
78626 ATCTGTAAAG
*
78636 AAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTGCGAACATCTATGCAA
1 AAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTGCGAACATCTATGCAA
* * *
78690 AAGCCACAAGAAATGATGAATGTGTTGTCAAATGTTTTGCGAACATCTGTGCAG
1 AAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTGCGAACATCTATGCAA
*
78744 AAGCCACAGGAAATGATGAATGTGTTGTTAAATGTTTT
1 AAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTT
78782 ATGAACCAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (54 bp):
AAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTGCGAACATCTATGCAA
Found at i:79185 original size:22 final size:22
Alignment explanation
Indices: 79157--79217 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
79147 ATCTACATTA
79157 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATTCTCTC
*
79179 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTC
*
79201 TTCAAAGATGAAAGATT
1 TTCAAAGATGATAGATT
79218 TATTGGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTC
Found at i:80419 original size:177 final size:176
Alignment explanation
Indices: 80113--80512 Score: 604
Period size: 177 Copynumber: 2.3 Consensus size: 176
80103 AGCAAGATGA
* * * * * * *
80113 TAAGACCTCTGGGCCATCCATAAGACCTCCGAGCAGGATGTTTTCAAATGATATTTTAGAAATCA
1 TAAGTCCTATGGGCCATCCATAAGACTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCA
*
80178 AACCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAATAAAGGGG
66 AACCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGG
* * *
80243 TTCCTTGACAACTAAGAAACTAAGCCTTTGAGGGTTTCTTGATTTG
131 TTCCTTGACAACAAAAAAACTAAGCCTTCGAGGGTTTCTTGATTTG
*
80289 TAAGTCCTATGGGCCATCCATAAGACATTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAACC
1 TAAGTCCTATGGGCCATCCATAAGAC-TTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACC
* * *
80354 AAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTACAAAGGG
65 AAACCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGG
80419 GTTCCTTGACAACAAAAAAACTAAGCCTTCGAGGGTTTCTTGATTTG
130 GTTCCTTGACAACAAAAAAACTAAGCCTTCGAGGGTTTCTTGATTTG
* ** *
80466 TAAGTCGTGCGGGCCAT-CATAAGACCTTCAGTGCAGGATGCTTTCAA
1 TAAGTCCTATGGGCCATCCATAAGA-CTTCAGTGCAGGATGTTTTCAA
80513 TTAAATTTTA
Statistics
Matches: 202, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
176 50 0.25
177 152 0.75
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (176 bp):
TAAGTCCTATGGGCCATCCATAAGACTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCA
AACCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGG
TTCCTTGACAACAAAAAAACTAAGCCTTCGAGGGTTTCTTGATTTG
Found at i:80882 original size:13 final size:12
Alignment explanation
Indices: 80821--80893 Score: 58
Period size: 12 Copynumber: 6.0 Consensus size: 12
80811 TTTTGTCTCT
*
80821 TTATTATTATTA
1 TTATTAATATTA
*
80833 TTA-TAATAATA
1 TTATTAATATTA
* * *
80844 ATAATAATAATAA
1 TTATTAAT-ATTA
* *
80857 TAATTATTATTA
1 TTATTAATATTA
80869 TTATTAAATATTA
1 TTATT-AATATTA
80882 TTATTAATATTA
1 TTATTAATATTA
80894 CAAACCCAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
11 8 0.17
12 21 0.46
13 17 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:82131 original size:28 final size:27
Alignment explanation
Indices: 82100--82167 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
82090 GGCCTTTAGG
*
82100 TTTTATATTTTACATTTTAATCACTG-AT
1 TTTTATATTTT-CATTTTAACCA-TGAAT
*
82128 TTTTATAATTTTCATTTTGACCATGAAT
1 TTTTAT-ATTTTCATTTTAACCATGAAT
82156 TTTATATATTTT
1 TTT-TATATTTT
82168 GTAATTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
28 25 0.71
29 8 0.23
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (27 bp):
TTTTATATTTTCATTTTAACCATGAAT
Found at i:91780 original size:3 final size:3
Alignment explanation
Indices: 91753--91800 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
91743 AATAAAATGA
91753 AAT AA- AAT ATAT AA- AAT ATAT AAT AAT AAT AAT AAT AAT AAT AGAT
1 AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT
91799 AA
1 AA
91801 ACAATAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 4 0.10
3 27 0.68
4 9 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:92063 original size:20 final size:20
Alignment explanation
Indices: 92018--92062 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
92008 ATATTTATAT
92018 AAAAAAGTATAATAAGATAC
1 AAAAAAGTATAATAAGATAC
*
92038 TAAAAAGTATAATAA-ATAC
1 AAAAAAGTATAATAAGATAC
92057 AAAAAA
1 AAAAAA
92063 AAGGGGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAAAGTATAATAAGATAC
Found at i:96090 original size:36 final size:36
Alignment explanation
Indices: 96050--96146 Score: 133
Period size: 36 Copynumber: 2.7 Consensus size: 36
96040 GAGAGTGAGA
*
96050 GAGGTGGCTTATG-TCACGAGGAAAGCGGTGAACCAG
1 GAGGTGACTTATGAT-ACGAGGAAAGCGGTGAACCAG
*
96086 GAGGTGACTTATGATTCGAGGAAAGCGGTGAACCAG
1 GAGGTGACTTATGATACGAGGAAAGCGGTGAACCAG
* * *
96122 AAGGTGACTGATGATTCGAGGAAAG
1 GAGGTGACTTATGATACGAGGAAAG
96147 AGAAAAGTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
36 55 0.98
37 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.37, T:0.19
Consensus pattern (36 bp):
GAGGTGACTTATGATACGAGGAAAGCGGTGAACCAG
Done.