Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019934.1 Corchorus olitorius cultivar O-4 contig19967, 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: 85664
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:132 original size:29 final size:28
Alignment explanation
Indices: 94--148 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
84 TTATTCCACA
*
94 TTCTTTAGCGTTCTTGAAGATTAGAAATG
1 TTCTTGAGCGTTCTTGAA-ATTAGAAATG
123 TTCTTGAGCGTTCTTGAAATTAGAAA
1 TTCTTGAGCGTTCTTGAAATTAGAAA
149 GTTTGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (28 bp):
TTCTTGAGCGTTCTTGAAATTAGAAATG
Found at i:9114 original size:71 final size:72
Alignment explanation
Indices: 8997--9183 Score: 243
Period size: 71 Copynumber: 2.6 Consensus size: 72
8987 GATTAGTAGC
* * **
8997 AAGGATTGCGCGAAGGACTGCC-AATGTGGGAACTGCCTCGGCTACAATCGCAATGTGGAAGATA
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAACATGGAAGATA
9061 ATCACAT
66 ATCACAT
* * * *
9068 AAGGATTGTGTGAAGGACTGCCAAATGTGGG-ATTGCCTCGGTTACAACCGCAACATGGAAGATT
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAACATGGAAGATA
**
9132 ATCATGT
66 ATCACAT
* * *
9139 AAGGATTGTGCGAAGGACTGCCAAATATGGCAACTGTCTCGGCTA
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTA
9184 TAACTGTGCG
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
71 80 0.82
72 18 0.18
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.22
Consensus pattern (72 bp):
AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAACATGGAAGATA
ATCACAT
Found at i:11212 original size:35 final size:35
Alignment explanation
Indices: 11135--11212 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
11125 AGTATGACAT
*
11135 AGCCCCCAAGCGTTGAATGATGAAGGAATTGCTAG
1 AGCCCCCAAACGTTGAATGATGAAGGAATTGCTAG
* * **
11170 AGTCCCCAAATGTTGAATGATGAAGGGGTTGCT-G
1 AGCCCCCAAACGTTGAATGATGAAGGAATTGCTAG
11204 CAGCCCCCA
1 -AGCCCCCA
11213 GGTGCTGAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (35 bp):
AGCCCCCAAACGTTGAATGATGAAGGAATTGCTAG
Found at i:11222 original size:35 final size:35
Alignment explanation
Indices: 11148--11222 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
11138 CCCCAAGCGT
* *
11148 TGAATGATGAAGGAATTGCTAGAGTCCCCAAATGT
1 TGAATGATGAAGGAATTGCTAGAGCCCCCAAATGC
** **
11183 TGAATGATGAAGGGGTTGCT-GCAGCCCCCAGGTGC
1 TGAATGATGAAGGAATTGCTAG-AGCCCCCAAATGC
11218 TGAAT
1 TGAAT
11223 CTGATGAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (35 bp):
TGAATGATGAAGGAATTGCTAGAGCCCCCAAATGC
Found at i:13865 original size:28 final size:28
Alignment explanation
Indices: 13833--13893 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
13823 TTTTTGTGGG
13833 TATGTGAGGAAGGCCTGGTTCGGCTCAC
1 TATGTGAGGAAGGCCTGGTTCGGCTCAC
13861 TATGTGAGGAAGGCCTGGTTCGGCTCAC
1 TATGTGAGGAAGGCCTGGTTCGGCTCAC
13889 TATGT
1 TATGT
13894 CCGGTCAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (28 bp):
TATGTGAGGAAGGCCTGGTTCGGCTCAC
Found at i:14573 original size:2 final size:2
Alignment explanation
Indices: 14566--14592 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14556 GGCTTTTGCT
14566 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
14593 TATATATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:14774 original size:41 final size:42
Alignment explanation
Indices: 14665--14983 Score: 240
Period size: 41 Copynumber: 7.8 Consensus size: 42
14655 ATAAGGAGAA
* * * * *
14665 ATGCCTTTGTGTCATAAATGTGTTTGAGAACTTT-GAAATAGAG
1 ATGCCTCTGTGTTATAAATGTGTTTGGGGACTTTAG-TAT-GAG
*
14708 GTGTCCT-TGTGTTATAAATGTGTTTGGGGACTTTAGTATG-G
1 ATG-CCTCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGAG
* *
14749 ATGCCTCTTTGTTATAAATGTGTTTGAGGACTTT--TA-GAG
1 ATGCCTCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGAG
** **
14788 A-------GAATTATAGTTGTGTTTGGGGACTTT-GATAT-AG
1 ATGCCTCTGTGTTATAAATGTGTTTGGGGACTTTAG-TATGAG
* * * *
14822 ATGCCTCTGTATTATAAATGTGTTTGAGGACTTTGGAATAGAG
1 ATGCCTCTGTGTTATAAATGTGTTTGGGGACTTTAGTAT-GAG
*
14865 GTGGCC-CTGTGTTATAAATGTGTTTGGGGACTTTAGTATG-G
1 AT-GCCTCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGAG
** * *
14906 ATGCCTCTGTGTTATAAATGTGTTTGAAGACTTTAGAAAGAG
1 ATGCCTCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGAG
* *
14948 AATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTT
1 -A-TGCCTCTGTGTTATAAATGTGTTTGGGGACTTT
14984 TAGTTATTGG
Statistics
Matches: 221, Mismatches: 33, Indels: 43
0.74 0.11 0.14
Matches are distributed among these distances:
32 20 0.09
34 5 0.02
38 1 0.00
39 4 0.02
40 6 0.03
41 84 0.38
42 4 0.02
43 61 0.28
44 36 0.16
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (42 bp):
ATGCCTCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGAG
Found at i:14938 original size:84 final size:84
Alignment explanation
Indices: 14799--14983 Score: 266
Period size: 84 Copynumber: 2.2 Consensus size: 84
14789 GAATTATAGT
* *
14799 TGTGTTTGGGGACTTTGATATAGATGCCTCTGTATTATAAATGTGTTTGAGGACTTTGGAATAGA
1 TGTGTTTGGGGACTTTGATATAGATGCCTCTGTATTATAAATGTGTTTGAAGACTTTAGAA-AGA
*
14864 G-GTGGCCCTGTGTTATAAA
65 GAGTGCCCCTGTGTTATAAA
* *
14883 TGTGTTTGGGGACTTT-AGTATGGATGCCTCTGTGTTATAAATGTGTTTGAAGACTTTAGAAAGA
1 TGTGTTTGGGGACTTTGA-TATAGATGCCTCTGTATTATAAATGTGTTTGAAGACTTTAGAAAGA
* *
14947 GAATTGCCCCTGTGTTATAAT
65 G-AGTGCCCCTGTGTTATAAA
14968 TGTGTTTGGGGACTTT
1 TGTGTTTGGGGACTTT
14984 TAGTTATTGG
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
83 5 0.05
84 55 0.60
85 31 0.34
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.39
Consensus pattern (84 bp):
TGTGTTTGGGGACTTTGATATAGATGCCTCTGTATTATAAATGTGTTTGAAGACTTTAGAAAGAG
AGTGCCCCTGTGTTATAAA
Found at i:18504 original size:141 final size:143
Alignment explanation
Indices: 18328--18609 Score: 408
Period size: 141 Copynumber: 2.0 Consensus size: 143
18318 CGTGAGTATG
* * * * *
18328 AAGATAAAATAATTAAAAAAGTAGTTTATGCTAGTTTTGTTTTTCAAATGGGTAGGTTTTTTTGT
1 AAGATAAAATAATT--AAAAGTAGTTTATGCTAGTTTTCTTTTTAAAACGGGTAGCTTTTTATGT
* *
18393 TAAATGATATAAATAAAAGTT-AACTTTCATATTAATCCTTCAATTGGTAGTTTTTTTTTAAATA
64 TAAATGATATAAATAAAAGTTGAA-TTTCATATTAATCCTTCAATTGGTAATTTTCTTTTAAATA
18457 AGT-AGTTTTTATTTA
128 AGTAAGTTTTTATTTA
*
18472 AAGATAAAATAATT-AAAGTAGTTTATGGTAGTTTTCTTTTTAAAACGGGTAGCTTTTTATGTTA
1 AAGATAAAATAATTAAAAGTAGTTTATGCTAGTTTTCTTTTTAAAACGGGTAGCTTTTTATGTTA
* * * *
18536 ATTGATATAAATAAAAGTTGAATTTCATATTTATCTTTTAATTGGTAATTTTCTTTTAAATAAGT
66 AATGATATAAATAAAAGTTGAATTTCATATTAATCCTTCAATTGGTAATTTTCTTTTAAATAAGT
18601 AAGTTTTTA
131 AAGTTTTTA
18610 CTTTTAGGAT
Statistics
Matches: 124, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
141 100 0.81
142 10 0.08
144 14 0.11
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (143 bp):
AAGATAAAATAATTAAAAGTAGTTTATGCTAGTTTTCTTTTTAAAACGGGTAGCTTTTTATGTTA
AATGATATAAATAAAAGTTGAATTTCATATTAATCCTTCAATTGGTAATTTTCTTTTAAATAAGT
AAGTTTTTATTTA
Found at i:21691 original size:16 final size:17
Alignment explanation
Indices: 21662--21693 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21652 TATTATTAGA
21662 TGTGTGATATATATGTG
1 TGTGTGATATATATGTG
21679 TGTGTGA-ATATATGT
1 TGTGTGATATATATGT
21694 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (17 bp):
TGTGTGATATATATGTG
Found at i:23206 original size:3 final size:3
Alignment explanation
Indices: 23198--23267 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
23188 TGCAACGCAG
23198 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23246 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
23268 CTCGGTCCCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:24232 original size:3 final size:3
Alignment explanation
Indices: 24224--24314 Score: 121
Period size: 3 Copynumber: 29.3 Consensus size: 3
24214 TGGCGGCCTC
* *
24224 TTA TTA TTA TTA TTTA TTTA TAA TT- TATA ATA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA -TTA -TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA
24272 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
24315 GTTACATCCT
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.01
3 69 0.86
4 10 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:25095 original size:14 final size:15
Alignment explanation
Indices: 25068--25100 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
25058 CCGCCGGTGG
25068 CTAAGGAACAACGCC
1 CTAAGGAACAACGCC
*
25083 CTAA-GAACGACGCC
1 CTAAGGAACAACGCC
25097 CTAA
1 CTAA
25101 AAATTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.39, C:0.33, G:0.18, T:0.09
Consensus pattern (15 bp):
CTAAGGAACAACGCC
Found at i:26412 original size:132 final size:130
Alignment explanation
Indices: 26112--26659 Score: 605
Period size: 131 Copynumber: 4.2 Consensus size: 130
26102 TTTTACAACA
*
26112 ATAAAAAGTCGTTGCCTTAGTGA-TTTGATGGTATTTTATC-CAACAACTTTTTTAATTGTTGCC
1 ATAAAAA-T-GTTGCCTAAGTGATTTTGATGGTATTTTA-CACAACAA-TTTTTTAATTGTTGCC
* * * * **
26175 AATGCTTACAGTTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATTATAATTTATTCGTAACAA
62 AATGTTTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCTAAATCATAAACTATTCGTAACAA
*
26240 TTTT
127 CTTT
** * ** *
26244 ATAAAGTTGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAGTCATTGTCAATG
1 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAATTGTTGCCAATG
* * *
26309 TTTACAATTTTCGTAACAACAAAAACAAAATCGCTGCTAAATCATAAACTATTCATATAACAACT
66 TTTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCTAAATCATAAACTATTC--GTAACAACT
26374 TT
129 TT
* *
26376 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACAAAACACTTTTTTAATTGTTGCCAATG
1 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAATTGTTGCCAATG
* ** * * *
26441 TTTACAATATTCGTAACAACAAATTCTTAAGTTGTTG-TGAAATCATAAACTACTCGTAACAACT
66 TTTACAATTTTCGTAACAACAAAAAC-AAAGTCGTTGCT-AAATCATAAACTATTCGTAACAACT
26505 TT
129 TT
* * *
26507 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTGCACAACACTTTTTTAATTTTTGCCAATG
1 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAATTGTTGCCAATG
*** * * * *
26572 TTT---A----C-TAACAACAACTTCTAAGTTGCTGCGAAATCATAAACTATTCGTAACAACTTT
66 TTTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCTAAATCATAAACTATTCGTAACAACTTT
***
26629 ATAAAAACACTGCCTAAGTGATTTTGATGGT
1 ATAAAAATGTTGCCTAAGTGATTTTGATGGT
26660 GTGAGAGCCT
Statistics
Matches: 365, Mismatches: 44, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
122 63 0.17
123 12 0.03
124 1 0.00
128 1 0.00
130 75 0.21
131 97 0.27
132 95 0.26
133 21 0.06
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (130 bp):
ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAATTGTTGCCAATG
TTTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCTAAATCATAAACTATTCGTAACAACTTT
Found at i:26551 original size:131 final size:130
Alignment explanation
Indices: 26112--26659 Score: 621
Period size: 132 Copynumber: 4.2 Consensus size: 130
26102 TTTTACAACA
*
26112 ATAAAAAGTCGTTGCCTTAGTGA-TTTGATGGTATTTTATC-CAACAACTTTTTTAATTGTTGCC
1 ATAAAAA-T-GTTGCCTAAGTGATTTTGATGGTATTTTA-CACAAC-ACTTTTTTAATTGTTGCC
* * * * * **
26175 AATGCTTACAGTTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATTATAATTTATTCGTAACAA
62 AATGTTTACAATATTCGTAACAACAAAAACAAAGTCGCTGCGAAATCATAAACTATTCGTAACAA
*
26240 TTTT
127 CTTT
** * * ** *
26244 ATAAAGTTGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAGTCATTGTCAATG
1 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTGCCAATG
* * * *
26309 TTTACAATTTTCGTAACAACAAAAACAAAATCGCTGCTAAATCATAAACTATTCATATAACAACT
66 TTTACAATATTCGTAACAACAAAAACAAAGTCGCTGCGAAATCATAAACTATTC--GTAACAACT
26374 TT
129 TT
*
26376 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACAAAACACTTTTTTAATTGTTGCCAATG
1 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTGCCAATG
** * * * * *
26441 TTTACAATATTCGTAACAACAAATTCTTAAGTTGTTGTGAAATCATAAACTACTCGTAACAACTT
66 TTTACAATATTCGTAACAACAAAAAC-AAAGTCGCTGCGAAATCATAAACTATTCGTAACAACTT
26506 T
130 T
* *
26507 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTGCACAACACTTTTTTAATTTTTGCCAATG
1 ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTGCCAATG
*** * *
26572 -TT----TA--C-TAACAACAACTTCTAAGTTGCTGCGAAATCATAAACTATTCGTAACAACTTT
66 TTTACAATATTCGTAACAACAAAAACAAAGTCGCTGCGAAATCATAAACTATTCGTAACAACTTT
***
26629 ATAAAAACACTGCCTAAGTGATTTTGATGGT
1 ATAAAAATGTTGCCTAAGTGATTTTGATGGT
26660 GTGAGAGCCT
Statistics
Matches: 364, Mismatches: 47, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
122 64 0.18
123 12 0.03
124 1 0.00
126 2 0.01
130 78 0.21
131 92 0.25
132 94 0.26
133 21 0.06
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (130 bp):
ATAAAAATGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTGCCAATG
TTTACAATATTCGTAACAACAAAAACAAAGTCGCTGCGAAATCATAAACTATTCGTAACAACTTT
Found at i:30933 original size:131 final size:133
Alignment explanation
Indices: 30694--30933 Score: 337
Period size: 131 Copynumber: 1.8 Consensus size: 133
30684 GCACCTTACG
*
30694 CAACGAAAAAAATAGTCGTTATAAAAACAATTTTAATTTCGAAACGATATAAATAAGTTGTTGCA
1 CAACGAAAAAAATA-TCGTTACAAAAACAATTTTAATTTCGAAACGATATAAATAAGTTGTTGCA
* * *
30759 AAAACTTAATCTTTTCACAACCACTTTATTAATTTGTTGTGTAAATGATTTTATTGAGATATTAC
65 AAAACTTAATCTTTTCACAACCACTTTATTAAGTTGCTATGTAAATGATTTTATTGAGATATTAC
30824 ACAA
130 ACAA
*
30828 CAAC-AAAAAAAT-TCGTTACAAAAACAATTTTATTTTCGAAAC-AGTA-AGAATATA-TTGTTG
1 CAACGAAAAAAATATCGTTACAAAAACAATTTTAATTTCGAAACGA-TATA-AATA-AGTTGTTG
* * *
30888 CGAAATCTTATTCTTTTCACAACCACTTTATTAAGTTGCTATGTAA
63 CAAAAACTTAATCTTTTCACAACCACTTTATTAAGTTGCTATGTAA
30934 TTAATTCTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
130 2 0.02
131 80 0.84
132 1 0.01
133 8 0.08
134 4 0.04
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (133 bp):
CAACGAAAAAAATATCGTTACAAAAACAATTTTAATTTCGAAACGATATAAATAAGTTGTTGCAA
AAACTTAATCTTTTCACAACCACTTTATTAAGTTGCTATGTAAATGATTTTATTGAGATATTACA
CAA
Found at i:33246 original size:210 final size:210
Alignment explanation
Indices: 32878--33277 Score: 737
Period size: 210 Copynumber: 1.9 Consensus size: 210
32868 CATGGAAAAG
* * *
32878 TTGTTAACGATTCACATGTGAGGGAACATCCCACATCATGAAAAGATGGGTTGTTAGAGTAGCTT
1 TTGTTAACGATTCACATGTGAGGAAAAATCCCACATCACGAAAAGATGGGTTGTTAGAGTAGCTT
32943 ATATACATGAAGGACCCAAGAAACCATTAGTCTAGGCTTTTGGGTTCAGGTTGGCGTCTGACATG
66 ATATACATGAAGGACCCAAGAAACCATTAGTCTAGGCTTTTGGGTTCAGGTTGGCGTCTGACATG
*
33008 TATATGGGCTACTCGGTGGGCCTTGCTGAAACAGACAGGGCCCGGGTTCCTCTCCCATCAGATCA
131 TATATGGGCTACTCGGTGGGCATTGCTGAAACAGACAGGGCCCGGGTTCCTCTCCCATCAGATCA
33073 TTGGCTTCCTTTAGA
196 TTGGCTTCCTTTAGA
* *
33088 TTGTTAAGGATTCACATGTGAGGAAAAATCCCACATCACGAAGAGATGGGTTGTTAGAGTAGCTT
1 TTGTTAACGATTCACATGTGAGGAAAAATCCCACATCACGAAAAGATGGGTTGTTAGAGTAGCTT
*
33153 ATATACATGAAGGACCCAAGAAACCATTAGTCTAGGCTTTTGGGTTCAGGTTGGTGTCTGACATG
66 ATATACATGAAGGACCCAAGAAACCATTAGTCTAGGCTTTTGGGTTCAGGTTGGCGTCTGACATG
33218 TATATGGGCTACTCGGTGGGCATTGCTGAAACAGACAGGGCCCGGGTTCCTCTCCCATCA
131 TATATGGGCTACTCGGTGGGCATTGCTGAAACAGACAGGGCCCGGGTTCCTCTCCCATCA
33278 AGTGGTATCA
Statistics
Matches: 183, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
210 183 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (210 bp):
TTGTTAACGATTCACATGTGAGGAAAAATCCCACATCACGAAAAGATGGGTTGTTAGAGTAGCTT
ATATACATGAAGGACCCAAGAAACCATTAGTCTAGGCTTTTGGGTTCAGGTTGGCGTCTGACATG
TATATGGGCTACTCGGTGGGCATTGCTGAAACAGACAGGGCCCGGGTTCCTCTCCCATCAGATCA
TTGGCTTCCTTTAGA
Found at i:40320 original size:25 final size:26
Alignment explanation
Indices: 40271--40321 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40261 TTAAGTACAT
***
40271 AAAAACTTTAAGTCTTTTTGTTAAAA
1 AAAAACTTTAAGTCTTTTAACTAAAA
40297 AAAAACTTTAAGTC-TTTAACTAAAA
1 AAAAACTTTAAGTCTTTTAACTAAAA
40322 GACTTTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (26 bp):
AAAAACTTTAAGTCTTTTAACTAAAA
Found at i:41724 original size:7 final size:7
Alignment explanation
Indices: 41687--41759 Score: 50
Period size: 7 Copynumber: 11.0 Consensus size: 7
41677 AAATTTTAAT
41687 ATATATA
1 ATATATA
41694 A-ATAATA
1 ATAT-ATA
41701 ATAT-TA
1 ATATATA
*
41707 GATATATT
1 -ATATATA
41715 ATA-AT-
1 ATATATA
41720 ATATATA
1 ATATATA
41727 ATATA-A
1 ATATATA
41733 A-ATATA
1 ATATATA
*
41739 AAATATA
1 ATATATA
* *
41746 AAAAATA
1 ATATATA
41753 ATATATA
1 ATATATA
41760 TTATTATTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
5 6 0.11
6 12 0.22
7 33 0.61
8 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (7 bp):
ATATATA
Found at i:41731 original size:14 final size:14
Alignment explanation
Indices: 41683--41746 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
41673 TCTTAAATTT
*
41683 TAATAT-ATATAAA
1 TAATATAATATATA
* *
41696 TAATAATATTAGATA
1 TAAT-ATAATATATA
*
41711 TATTATAATATATA
1 TAATATAATATATA
*
41725 TAATATAAAATATA
1 TAATATAATATATA
*
41739 AAATATAA
1 TAATATAA
41747 AAAATAATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
13 4 0.10
14 29 0.73
15 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
TAATATAATATATA
Found at i:41745 original size:33 final size:33
Alignment explanation
Indices: 41683--41745 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
41673 TCTTAAATTT
* *
41683 TAATATATATAAATAATAATATTAGATATATTA
1 TAATATATATAAATAATAATATAAAATATATTA
41716 TAATATATATAATATAA-AATATAAAATATA
1 TAATATATATAA-ATAATAATATAAAATATA
41746 AAAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (33 bp):
TAATATATATAAATAATAATATAAAATATATTA
Found at i:41747 original size:14 final size:14
Alignment explanation
Indices: 41714--41759 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
41704 TTAGATATAT
* *
41714 TATAATATATATAA
1 TATAAAATATAAAA
41728 TATAAAATATAAAA
1 TATAAAATATAAAA
* *
41742 TATAAAAAATAATA
1 TATAAAATATAAAA
41756 TATA
1 TATA
41760 TTATTATTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATAAAATATAAAA
Found at i:42808 original size:15 final size:15
Alignment explanation
Indices: 42788--42817 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42778 TATTAGTTTC
42788 TTTTAATAATTTAAT
1 TTTTAATAATTTAAT
*
42803 TTTTAATATTTTAAT
1 TTTTAATAATTTAAT
42818 CTAAAAAAAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAATAATTTAAT
Found at i:46437 original size:13 final size:13
Alignment explanation
Indices: 46419--46443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46409 TTCAATGTTG
46419 TAAATATTATTTA
1 TAAATATTATTTA
46432 TAAATATTATTT
1 TAAATATTATTT
46444 GAAATTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:47475 original size:2 final size:2
Alignment explanation
Indices: 47470--47504 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
47460 AATATACTCC
*
47470 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47505 TAAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48886 original size:2 final size:2
Alignment explanation
Indices: 48879--48904 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48869 ACCAAAATAA
48879 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
48905 GCTAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49606 original size:3 final size:3
Alignment explanation
Indices: 49600--49638 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
49590 TAATAATAAT
*
49600 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AGC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
49639 GCGCTTGCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.33, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:49788 original size:15 final size:15
Alignment explanation
Indices: 49750--49790 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
49740 ATATCATCAT
*
49750 AATATATCCTTCAAA
1 AATATATTCTTCAAA
* *
49765 AATAAATTCTTTAAA
1 AATATATTCTTCAAA
49780 AATATATTCTT
1 AATATATTCTT
49791 AAATATCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATATTCTTCAAA
Found at i:49798 original size:40 final size:41
Alignment explanation
Indices: 49753--49844 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 41
49743 TCATCATAAT
49753 ATATCCTTCAAAAATAAATTC-TTT-AAAAATATATTCTTAA
1 ATATCCTTCAAAAATAAA-TCATTTAAAAAATATATTCTTAA
* *
49793 ATATCCTTAAAAAATGAATCATTTAAAAAATATATTCTTAA
1 ATATCCTTCAAAAATAAATCATTTAAAAAATATATTCTTAA
*
49834 ATATCTTTCAA
1 ATATCCTTCAA
49845 CAATGGAGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 2 0.04
40 19 0.41
41 25 0.54
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (41 bp):
ATATCCTTCAAAAATAAATCATTTAAAAAATATATTCTTAA
Found at i:50492 original size:3 final size:3
Alignment explanation
Indices: 50484--50600 Score: 218
Period size: 3 Copynumber: 39.3 Consensus size: 3
50474 ATATACTAAC
50484 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
50532 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
50579 AAT AAT AAT AAT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
50601 TTTATTATAA
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 109 0.98
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:52036 original size:20 final size:19
Alignment explanation
Indices: 52011--52050 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52001 TATTTTTACC
*
52011 AAAATAAATTTCAATAAAAT
1 AAAATAAA-TTCAAAAAAAT
*
52031 AAAATATATTCAAAAAAAT
1 AAAATAAATTCAAAAAAAT
52050 A
1 A
52051 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATAAATTCAAAAAAAT
Found at i:53226 original size:13 final size:14
Alignment explanation
Indices: 53208--53244 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
53198 TAAAATTGAC
53208 ATTATTAAAAATT-
1 ATTATTAAAAATTA
53221 ATTATTTAAAAATTA
1 ATTA-TTAAAAATTA
53236 ATTA-TAAAA
1 ATTATTAAAA
53245 GTTTCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 9 0.41
15 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTATTAAAAATTA
Found at i:53231 original size:14 final size:15
Alignment explanation
Indices: 53208--53240 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
53198 TAAAATTGAC
53208 ATTA-TTAAAAATT-
1 ATTATTTAAAAATTA
53221 ATTATTTAAAAATTA
1 ATTATTTAAAAATTA
53236 ATTAT
1 ATTAT
53241 AAAAGTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATTTAAAAATTA
Found at i:53524 original size:20 final size:20
Alignment explanation
Indices: 53501--53539 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53491 ACTATTATTT
53501 TTTTAAATTT-AATATTTTAC
1 TTTT-AATTTCAATATTTTAC
*
53521 TTTTAATTTCAATTTTTTA
1 TTTTAATTTCAATATTTTA
53540 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAATTTCAATATTTTAC
Found at i:53848 original size:22 final size:22
Alignment explanation
Indices: 53733--54228 Score: 95
Period size: 22 Copynumber: 22.6 Consensus size: 22
53723 ATGGTTATTG
* ***
53733 TATCAAAATTCCATAGTTTGGT
1 TATCAAAATTTCATAGGAAGGT
*
53755 TACCAAAATTTCATATGGAA-GT
1 TATCAAAATTTCATA-GGAAGGT
* * *
53777 TATCAAAATTTTATGGGAAAGT
1 TATCAAAATTTCATAGGAAGGT
* *
53799 TATCAAAATTTCATCGGATCGGGT
1 TATCAAAATTTCATAGGA--AGGT
* *
53823 TATTAAAATTTCTTAGGAAGGT
1 TATCAAAATTTCATAGGAAGGT
** * * *
53845 TATTGAAGTTTCATATTG-TGGT
1 TATCAAAATTTCATA-GGAAGGT
* * *
53867 TATCACAATTTTATAGAAAGGT
1 TATCAAAATTTCATAGGAAGGT
***
53889 TAT-AAAA----A-A-GATTAT
1 TATCAAAATTTCATAGGAAGGT
* * *
53904 TA-AAAATTGTCATAGCG-AGGT
1 TATCAAAATTTCATAG-GAAGGT
* * *
53925 TATAAAAATTTCATAGTATGGT
1 TATCAAAATTTCATAGGAAGGT
** *
53947 TATCAAAATTTTTTAGTG-TGGT
1 TATCAAAATTTCATAG-GAAGGT
*
53969 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAGGAAGGT
*** **
53991 TAT-AAAATTCTCAATTTCATTAGCAA
1 TATCAAAATT-TC-ATAGGA--AG-GT
* * *
54017 TACCAAAATTTGATA-GAATGT
1 TATCAAAATTTCATAGGAAGGT
*
54038 TATC-AAATCTCATA-G-AGTGAT
1 TATCAAAATTTCATAGGAAG-G-T
*
54059 TATCAAAATTTCATAGAGATTGGAT
1 TATCAAAATTTCATAG-GA-AGG-T
* **
54084 TATCAAAATTTCGTAGTG-TTGT
1 TATCAAAATTTCATAG-GAAGGT
* *
54106 TATCAAAATTTCAAAGCG-ACGT
1 TATCAAAATTTCATAG-GAAGGT
* *
54128 TATCAAAATTACATA--ATGTGAT
1 TATCAAAATTTCATAGGAAG-G-T
*
54150 TATCAAAATTTCATA-GAGGGGT
1 TATCAAAATTTCATAGGA-AGGT
* * **
54172 CAACAAAATTTTGTA-GAGAGGT
1 TATCAAAATTTCATAGGA-AGGT
* *
54194 AATCAAAATTTCATA-AAGAGGT
1 TATCAAAATTTCATAGGA-AGGT
*
54216 TATCAAATTTTCA
1 TATCAAAATTTCA
54229 AAATGTAATT
Statistics
Matches: 345, Mismatches: 93, Indels: 72
0.68 0.18 0.14
Matches are distributed among these distances:
15 7 0.02
16 1 0.00
17 1 0.00
19 2 0.01
20 11 0.03
21 26 0.08
22 234 0.68
23 10 0.03
24 20 0.06
25 23 0.07
26 4 0.01
27 6 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Found at i:53954 original size:23 final size:22
Alignment explanation
Indices: 53922--54165 Score: 115
Period size: 22 Copynumber: 10.9 Consensus size: 22
53912 GTCATAGCGA
*
53922 GGTTATAAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
** *
53944 GGTTATCAAAATTTTTTAGTGT
1 GGTTATCAAAATTTCATAGTAT
*
53966 GGTTATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGT-AT
*
53988 GGTTAT-AAAATTCTCA-ATTTCATT
1 GGTTATCAAAATT-TCATA-GT-A-T
** * * *
54012 AGCAATACCAAAATTTGATAGAAT
1 -G-GTTATCAAAATTTCATAGTAT
*
54036 -GTTATC-AAATCTCATAG-AGT
1 GGTTATCAAAATTTCATAGTA-T
* *
54056 GATTATCAAAATTTCATAGAGATT
1 GGTTATCAAAATTTCATAG-TA-T
* *
54080 GGATTATCAAAATTTCGTAGTGT
1 GG-TTATCAAAATTTCATAGTAT
* * *
54103 TGTTATCAAAATTTCAAAGCGA-
1 GGTTATCAAAATTTCATAG-TAT
* * * *
54125 CGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAGTAT
*
54147 GATTATCAAAATTTCATAG
1 GGTTATCAAAATTTCATAG
54166 AGGGGTCAAC
Statistics
Matches: 162, Mismatches: 43, Indels: 34
0.68 0.18 0.14
Matches are distributed among these distances:
19 1 0.01
20 10 0.06
21 16 0.10
22 98 0.60
23 4 0.02
24 4 0.02
25 18 0.11
26 4 0.02
27 7 0.04
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:54179 original size:44 final size:44
Alignment explanation
Indices: 54054--54253 Score: 125
Period size: 44 Copynumber: 4.5 Consensus size: 44
54044 ATCTCATAGA
* * * *
54054 GTGATTATCAAAATTTCATAGAGATTGGATTATCAAAATTTCGTAGT
1 GTGATTATCAAAATTTCATAGAG---GGGTTATCAAAATTACATAAT
* * **
54101 GTTG-TTATCAAAATTTCAAAGCGACGTTATCAAAATTACATAAT
1 G-TGATTATCAAAATTTCATAGAGGGGTTATCAAAATTACATAAT
* * ***
54145 GTGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTGTAGA-
1 GTGATTATCAAAATTTCATAGAGGGGTTATCAAAATTACATA-AT
* * * * * * * *
54189 GAGGTAATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAAT
1 GTGATTATCAAAATTTCATAGAGGGGTTATCAAAATTACATAAT
* * *
54233 GTAATTACCAAAATTGCATAG
1 GTGATTATCAAAATTTCATAG
54254 TGGTATTTCT
Statistics
Matches: 114, Mismatches: 35, Indels: 11
0.71 0.22 0.07
Matches are distributed among these distances:
43 3 0.03
44 90 0.79
45 1 0.01
47 18 0.16
48 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (44 bp):
GTGATTATCAAAATTTCATAGAGGGGTTATCAAAATTACATAAT
Found at i:54860 original size:22 final size:22
Alignment explanation
Indices: 54334--54860 Score: 152
Period size: 22 Copynumber: 24.0 Consensus size: 22
54324 TTATGTAGTA
* *
54334 ATCAAAATTT--TAGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
* *
54354 ATCCAAAATTTCATATGAAGGTT
1 AT-CAAAATTTCATAAGGAGGTT
54377 ATCAAAATTTCATAA-GAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * *
54399 ATCAAAATTTCAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
* *
54421 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
** * *
54443 AAAAAAAATTTCATAATGA-CTT
1 -ATCAAAATTTCATAAGGAGGTT
**
54465 ATCAAAAAATCATATATTGGGAGGTT
1 ATCAAAATTTCATA-A---GGAGGTT
*
54491 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
*
54507 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
54529 ATTAAAATTTTAT-AGCGAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* *
54551 ATCACAATTTCAT--GTGA--TC
1 ATCAAAATTTCATAAG-GAGGTT
* *
54570 ATCAAAATTTCA-GAGTGTGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* *
54592 A-CTAACAA-TTCATATGGAAGTT
1 ATC-AA-AATTTCATAAGGAGGTT
* * * * *
54614 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
54636 ATCAATATATCATATGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
54658 ATCAACATCTCATAGTATAGTGTTGGTT
1 ATCAAAATTTC--A-TA-AG-G-AGGTT
* *
54686 ATCAAAATTTCATTAGGAAGTT
1 ATCAAAATTTCATAAGGAGGTT
54708 ATCAAAATTTCAT-AGTGAGGTCT
1 ATCAAAATTTCATAAG-GAGGT-T
* *
54731 -TCAAAA-TTCCTTAGGAAGGTT
1 ATCAAAATTTCATAAGG-AGGTT
* *
54752 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
** ** *
54774 AAAAAAAATTT-ATAAAAATGTT
1 -ATCAAAATTTCATAAGGAGGTT
* * * *
54796 CTCGAAA-TTCTATAA-TATCGTT
1 ATCAAAATTTC-ATAAGGA-GGTT
* *
54818 ATTAAAATTTCAT-TGGAAGGTT
1 ATCAAAATTTCATAAGG-AGGTT
54840 ATCAAAATTTCATAAGGAGGT
1 ATCAAAATTTCATAAGGAGGT
54861 CATAAAAAAT
Statistics
Matches: 366, Mismatches: 92, Indels: 96
0.66 0.17 0.17
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 13 0.04
20 7 0.02
21 43 0.12
22 204 0.56
23 53 0.14
24 3 0.01
25 6 0.02
26 11 0.03
28 13 0.04
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:54868 original size:22 final size:22
Alignment explanation
Indices: 54821--54868 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
54811 TATCGTTATT
* * *
54821 AAAATTTCATTGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATA
54843 AAAATTTCATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAGGTCATA
54865 AAAA
1 AAAA
54869 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATA
Found at i:55105 original size:2 final size:2
Alignment explanation
Indices: 55098--55124 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55088 TCCACAAGAG
55098 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55125 GGGCAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55113 original size:55 final size:55
Alignment explanation
Indices: 55048--55154 Score: 214
Period size: 55 Copynumber: 1.9 Consensus size: 55
55038 TTCAAACGAC
55048 ATATATATATATATATATATATGGGCAAAGAGGGACATATTCCACAAGAGTATAT
1 ATATATATATATATATATATATGGGCAAAGAGGGACATATTCCACAAGAGTATAT
55103 ATATATATATATATATATATATGGGCAAAGAGGGACATATTCCACAAGAGTA
1 ATATATATATATATATATATATGGGCAAAGAGGGACATATTCCACAAGAGTA
55155 AAACATATGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (55 bp):
ATATATATATATATATATATATGGGCAAAGAGGGACATATTCCACAAGAGTATAT
Found at i:56649 original size:19 final size:20
Alignment explanation
Indices: 56621--56661 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
56611 ACTTATTTTT
*
56621 TTTTTTTGGCTTA-TTAGTC
1 TTTTTATGGCTTATTTAGTC
56640 TTTTTATGGCTTATTTAGTC
1 TTTTTATGGCTTATTTAGTC
56660 TT
1 TT
56662 GTTTGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.12, C:0.10, G:0.15, T:0.63
Consensus pattern (20 bp):
TTTTTATGGCTTATTTAGTC
Found at i:56756 original size:31 final size:32
Alignment explanation
Indices: 56718--56795 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 32
56708 CATAAATTTC
* * *
56718 AAATCAAGATATTTTGTTCCCTGAA-TTTCCA
1 AAATCAAGACATTTTGCTCCCTGAACTTCCCA
56749 AAATCAAGACATTTTGCTCCCTGAACTTCCCA
1 AAATCAAGACATTTTGCTCCCTGAACTTCCCA
56781 AAATCAAGACATTTT
1 AAATCAAGACATTTT
56796 ACCCCCTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
31 23 0.53
32 20 0.47
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (32 bp):
AAATCAAGACATTTTGCTCCCTGAACTTCCCA
Found at i:57139 original size:13 final size:13
Alignment explanation
Indices: 57121--57145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57111 ACCACATAAC
57121 CATGTCATTAAAG
1 CATGTCATTAAAG
57134 CATGTCATTAAA
1 CATGTCATTAAA
57146 TATATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
CATGTCATTAAAG
Found at i:59696 original size:41 final size:41
Alignment explanation
Indices: 59651--59734 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
59641 GAAGTTCAAA
59651 GTGTAAGAGATATTGATGATTTTAATCTTGAATTTTGAATT
1 GTGTAAGAGATATTGATGATTTTAATCTTGAATTTTGAATT
59692 GTGTAAGAGATATTGATGATTTTAATCTTGAATTTTGAATT
1 GTGTAAGAGATATTGATGATTTTAATCTTGAATTTTGAATT
59733 GT
1 GT
59735 AAATTTCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.46
Consensus pattern (41 bp):
GTGTAAGAGATATTGATGATTTTAATCTTGAATTTTGAATT
Found at i:82556 original size:70 final size:70
Alignment explanation
Indices: 82438--82594 Score: 251
Period size: 70 Copynumber: 2.2 Consensus size: 70
82428 CCGCAACAAC
*
82438 TCCTGGACAGGACTTGGGTAACTCCTGGACAGGACTTGTCCTATATTTCTGCGCTCCTCAACAGC
1 TCCTGGACAGGACTTGGGTAACTCCTGCACAGGACTTGTCCTATATTTCTGCGCTCCTCAACAGC
82503 CCAAA
66 CCAAA
* * * * *
82508 TCCTAGACAGGACTTGGGTAACTCTTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTCAACAGC
1 TCCTGGACAGGACTTGGGTAACTCCTGCACAGGACTTGTCCTATATTTCTGCGCTCCTCAACAGC
*
82573 CCAAG
66 CCAAA
82578 TCCTGGACAGGACTTGG
1 TCCTGGACAGGACTTGG
82595 CCAAGATCTG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 79 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (70 bp):
TCCTGGACAGGACTTGGGTAACTCCTGCACAGGACTTGTCCTATATTTCTGCGCTCCTCAACAGC
CCAAA
Done.