Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019868.1 Corchorus olitorius cultivar O-4 contig19901, 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: 43796
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:10808 original size:3 final size:3
Alignment explanation
Indices: 10794--10837 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
10784 ACAATTAATT
*
10794 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10838 TATATCTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:22107 original size:3 final size:3
Alignment explanation
Indices: 22099--22148 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
22089 GGAATCGAAG
* *
22099 GAA GAA GAA GAA GAA GAA GGA G-G GAA GAA GAA -AA GAA -AA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
22144 AAA GA
1 GAA GA
22149 GTTCAGCCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 5 0.13
3 34 0.87
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:22509 original size:38 final size:37
Alignment explanation
Indices: 22458--22625 Score: 220
Period size: 38 Copynumber: 4.6 Consensus size: 37
22448 GTCAGTAGGT
*
22458 AACTTAATTCAGGGTAATTAAGCAAGTTAGTAATAAGC
1 AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAA-C
22496 AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAAGC
1 AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAA-C
* *
22534 AACTTAATTCAGGGTAATTAAGCGAGTTAGTAAT--C
1 AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAAC
* * *
22569 AACTTAATACAAGGTAATTAAGCAAGTCA--ACA-AAT
1 AACTTAATTCAGGGTAATTAAGCAAGTCAGTA-ATAAC
22604 AACTTAATTCAGGGTAATTAAG
1 AACTTAATTCAGGGTAATTAAG
22626 TAAATAACTT
Statistics
Matches: 117, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
33 1 0.01
34 1 0.01
35 46 0.39
38 69 0.59
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (37 bp):
AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAAC
Found at i:22630 original size:27 final size:27
Alignment explanation
Indices: 22600--22682 Score: 139
Period size: 27 Copynumber: 3.1 Consensus size: 27
22590 GCAAGTCAAC
22600 AAATAACTTAATTCAGGGTAATTAAGT
1 AAATAACTTAATTCAGGGTAATTAAGT
*
22627 AAATAACTTAATTAAGGGTAATTAAGT
1 AAATAACTTAATTCAGGGTAATTAAGT
* *
22654 AAATAACTTAATTCAGGGTAGTTGAGT
1 AAATAACTTAATTCAGGGTAATTAAGT
22681 AA
1 AA
22683 GTCAGTCACC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.33
Consensus pattern (27 bp):
AAATAACTTAATTCAGGGTAATTAAGT
Found at i:23191 original size:35 final size:34
Alignment explanation
Indices: 23060--23188 Score: 177
Period size: 34 Copynumber: 3.8 Consensus size: 34
23050 GTTTCAAGTT
* *
23060 TAGTTTTCCATTTGGGAAAGTTCCCACCAGGTTT
1 TAGTTTTCAATTTGGGAAAGTTCCCACCAGGTTC
* * *
23094 TAGTTTCCAAATTGGGAAAGTTCCCACCAGGTTT
1 TAGTTTTCAATTTGGGAAAGTTCCCACCAGGTTC
* * *
23128 TAGTTTTTAAATTGGGAAAGTTCCCATCAGGTTC
1 TAGTTTTCAATTTGGGAAAGTTCCCACCAGGTTC
23162 TAGTTTTCAATTTAGGGAAAGTTCCCA
1 TAGTTTTCAATTT-GGGAAAGTTCCCA
23189 TCATTTTCAG
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
34 72 0.85
35 13 0.15
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (34 bp):
TAGTTTTCAATTTGGGAAAGTTCCCACCAGGTTC
Found at i:23201 original size:34 final size:33
Alignment explanation
Indices: 23058--23207 Score: 169
Period size: 34 Copynumber: 4.5 Consensus size: 33
23048 CAGTTTCAAG
*
23058 TTTAGTTTTCCATTTGGGAAAGTTCCCACCAGGT
1 TTTAGTTTTCAATTTGGGAAAGTTCCCACCA-GT
* *
23092 TTTAGTTTCCAAATTGGGAAAGTTCCCACCAGGT
1 TTTAGTTTTCAATTTGGGAAAGTTCCCACCA-GT
* * *
23126 TTTAGTTTTTAAATTGGGAAAGTTCCCATCAGGT
1 TTTAGTTTTCAATTTGGGAAAGTTCCCACCA-GT
* *
23160 TCTAGTTTTCAATTTAGGGAAAGTTCCCATCA-T
1 TTTAGTTTTCAATTT-GGGAAAGTTCCCACCAGT
23193 TTTCAGTTTT-AATTT
1 TTT-AGTTTTCAATTT
23208 TCAAAGTGGG
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
33 8 0.08
34 80 0.77
35 16 0.15
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.41
Consensus pattern (33 bp):
TTTAGTTTTCAATTTGGGAAAGTTCCCACCAGT
Found at i:27399 original size:2 final size:2
Alignment explanation
Indices: 27394--27420 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27384 TATATGTGTG
27394 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
27421 TCTACCGTTC
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:28497 original size:12 final size:11
Alignment explanation
Indices: 28476--28505 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
28466 GTGCATTAAA
28476 GAAAAAAAAAG
1 GAAAAAAAAAG
28487 GAAAAAGAAAAG
1 GAAAAA-AAAAG
28499 GAAAAAA
1 GAAAAAA
28506 TGATGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAG
Found at i:29788 original size:36 final size:37
Alignment explanation
Indices: 29748--29827 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
29738 GTTGCTTCTA
29748 TTCAGTTAG-TTTCACA-TTGACCCAAGGCGGTCTTTC
1 TTCAGTTAGTTTTCA-AGTTGACCCAAGGCGGTCTTTC
* * * *
29784 TTCAGTT-GTTTTCAAGTTGATCCAGGGTGGTTTTTC
1 TTCAGTTAGTTTTCAAGTTGACCCAAGGCGGTCTTTC
29820 TTCAGTTA
1 TTCAGTTA
29828 CATGACCTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 2 0.05
36 35 0.95
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.42
Consensus pattern (37 bp):
TTCAGTTAGTTTTCAAGTTGACCCAAGGCGGTCTTTC
Found at i:30018 original size:29 final size:29
Alignment explanation
Indices: 29957--30018 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
29947 TCCATCCTCT
* * ** *
29957 AATTGATCTAGGGCGATCTTTCTTTAGTT
1 AATTGATCCAGGGCGATCTCTCTACAGTG
29986 AATTGATCCAGGGCGATCTCTCTACAGTG
1 AATTGATCCAGGGCGATCTCTCTACAGTG
30015 AATT
1 AATT
30019 TCAACTGACC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (29 bp):
AATTGATCCAGGGCGATCTCTCTACAGTG
Found at i:30106 original size:8 final size:8
Alignment explanation
Indices: 30093--30131 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
30083 TAGGGCGATC
30093 ATTATTCA
1 ATTATTCA
30101 ATTATTCA
1 ATTATTCA
*
30109 ATTCTTCA
1 ATTATTCA
30117 ATTATTCA
1 ATTATTCA
*
30125 ATGATTC
1 ATTATTC
30132 CATTTACTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (8 bp):
ATTATTCA
Found at i:30173 original size:8 final size:8
Alignment explanation
Indices: 30160--30216 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 8
30150 AGGGTGGTTT
30160 TTCTTCAA
1 TTCTTCAA
30168 TTCTTCAA
1 TTCTTCAA
* *
30176 TTATTCCA
1 TTCTTCAA
*
30184 TGCTTCAA
1 TTCTTCAA
*
30192 TCCTTCAA
1 TTCTTCAA
* *
30200 CTATTCAA
1 TTCTTCAA
*
30208 TGCTTCAA
1 TTCTTCAA
30216 T
1 T
30217 CACCCAGGGT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.44
Consensus pattern (8 bp):
TTCTTCAA
Found at i:30189 original size:24 final size:24
Alignment explanation
Indices: 30162--30217 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
30152 GGTGGTTTTT
* * *
30162 CTTCAATTCTTCAATTATTCCATG
1 CTTCAATCCTTCAACTATTCAATG
30186 CTTCAATCCTTCAACTATTCAATG
1 CTTCAATCCTTCAACTATTCAATG
30210 CTTCAATC
1 CTTCAATC
30218 ACCCAGGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.41
Consensus pattern (24 bp):
CTTCAATCCTTCAACTATTCAATG
Found at i:30343 original size:36 final size:35
Alignment explanation
Indices: 30251--30493 Score: 174
Period size: 36 Copynumber: 6.8 Consensus size: 35
30241 TAAGTCCAAA
** *
30251 ATGATCGAGGGTGGTCATTCTTCAGTTTATTTCA-G
1 ATGATCGAGGGTGGTTGTTCTTCAGTTTA-GTCAGG
* * *
30286 TTGACCCAGGGTGGTCT-TTCTTCAGTTTGAGTCAGG
1 ATGATCGAGGGTGGT-TGTTCTTCAGTTT-AGTCAGG
* **
30322 GTGATCGAGGGTGGTTGTTCTTCAGTTTAGTCCAAA
1 ATGATCGAGGGTGGTTGTTCTTCAGTTTAGT-CAGG
* *
30358 ATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCA-G
1 ATGATCGAGGGTGGTTGTTCTTCAGTTTA-GTCAGG
* * * * **
30393 CTGGA-CCAAGGTGGTCT-TTCTTCAATTT-GTGTTGG
1 AT-GATCGAGGGTGGT-TGTTCTTCAGTTTAGT-CAGG
*
30428 AATGATCGAGGGTGGTTGTTCTTCAGTTTAGTCCGG
1 -ATGATCGAGGGTGGTTGTTCTTCAGTTTAGTCAGG
* *
30464 AATGATTGAGGGTGGTCGTTCTTCAGTTTA
1 -ATGATCGAGGGTGGTTGTTCTTCAGTTTA
30494 TTTCATTTCA
Statistics
Matches: 164, Mismatches: 30, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
33 1 0.01
35 53 0.32
36 107 0.65
37 3 0.02
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (35 bp):
ATGATCGAGGGTGGTTGTTCTTCAGTTTAGTCAGG
Found at i:30360 original size:107 final size:107
Alignment explanation
Indices: 30243--30498 Score: 390
Period size: 107 Copynumber: 2.4 Consensus size: 107
30233 TCTTTACTTA
* * *
30243 AGTCCAAAATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTTTCT
1 AGTCCAAAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGCTGGA-CCAAGGTGGTCTTTCT
* *
30307 TCAGTTTGAGTCAGG-GTGATCGAGGGTGGTTGTTCTTCAGTTT
65 TCAATTTGAGT-AGGAATGATCGAGGGTGGTTGTTCTTCAGTTT
30350 AGTCCAAAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGCTGGACCAAGGTGGTCTTTCTT
1 AGTCCAAAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGCTGGACCAAGGTGGTCTTTCTT
* *
30415 CAATTTGTGTTGGAATGATCGAGGGTGGTTGTTCTTCAGTTT
66 CAATTTGAGTAGGAATGATCGAGGGTGGTTGTTCTTCAGTTT
** *
30457 AGTCCGGAATGATTGAGGGTGGTCGTTCTTCAGTTTATTTCA
1 AGTCCAAAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCA
30499 TTTCAGTTGA
Statistics
Matches: 137, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
106 2 0.01
107 132 0.96
108 3 0.02
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (107 bp):
AGTCCAAAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGCTGGACCAAGGTGGTCTTTCTT
CAATTTGAGTAGGAATGATCGAGGGTGGTTGTTCTTCAGTTT
Found at i:33910 original size:28 final size:27
Alignment explanation
Indices: 33870--34010 Score: 148
Period size: 28 Copynumber: 5.1 Consensus size: 27
33860 GAGTAAAAAA
*
33870 AAAAAGAAAATTTGAGTAATTAAGGAAT
1 AAAAAGAAAATTTG-GTAATTAAAGAAT
33898 AAAAAGAAAATTTGGGTAATTAAAGAAT
1 AAAAAGAAAATTT-GGTAATTAAAGAAT
*
33926 AAAAAGAAAATTTGGTTAATTAAAGAGT
1 AAAAAGAAAATTTGG-TAATTAAAGAAT
*
33954 -AAAAGGAAA-TTGGTAATTAAA-AGAT
1 AAAAAGAAAATTTGGTAATTAAAGA-AT
*
33979 AAACAATG--AATTTGGTAATTAAAAGAGT
1 AAA-AA-GAAAATTTGGTAATT-AAAGAAT
34007 AAAA
1 AAAA
34011 TTAGTAATTT
Statistics
Matches: 99, Mismatches: 5, Indels: 19
0.80 0.04 0.15
Matches are distributed among these distances:
24 1 0.01
25 9 0.09
26 8 0.08
27 22 0.22
28 57 0.58
29 2 0.02
ACGTcount: A:0.56, C:0.01, G:0.18, T:0.26
Consensus pattern (27 bp):
AAAAAGAAAATTTGGTAATTAAAGAAT
Found at i:34107 original size:64 final size:60
Alignment explanation
Indices: 34039--34186 Score: 188
Period size: 63 Copynumber: 2.4 Consensus size: 60
34029 GGGTAAAATG
* *
34039 AATTTGGACAATTAAAGAGTAAGAGAAAATTTGGTAATTTAAGAATAAAAGAGTAAAGAAAGAA
1 AATTTGGATAATTAAAGAGTAAGAG-AAA-TTGGTAATTAAAGAATAAAAGAGT-AA-AAAGAA
* * *
34103 AATTTGGTTAATTAAAGAGTACAGTGAAATTGGTAATTAAAGAGTAAAAGAGTAAAAAGAA
1 AATTTGGATAATTAAAGAGTA-AGAGAAATTGGTAATTAAAGAATAAAAGAGTAAAAAGAA
*
34164 AATTTGGGTAATTAAAAGAGTAA
1 AATTTGGATAATT-AAAGAGTAA
34187 AAAAAAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
61 19 0.25
62 10 0.13
63 22 0.29
64 22 0.29
65 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.21, T:0.26
Consensus pattern (60 bp):
AATTTGGATAATTAAAGAGTAAGAGAAATTGGTAATTAAAGAATAAAAGAGTAAAAAGAA
Found at i:34120 original size:30 final size:31
Alignment explanation
Indices: 34084--34217 Score: 113
Period size: 30 Copynumber: 4.4 Consensus size: 31
34074 AATTTAAGAA
*
34084 TAAAAGAGTAAAGAAAGAAAATTTGGTTAAT
1 TAAAAGAGTAAAGAAAGAAAATTTGGGTAAT
* *
34115 T-AAAGAGTACAG--TG-AAA-TT-GGTAAT
1 TAAAAGAGTAAAGAAAGAAAATTTGGGTAAT
34140 T-AAAGAGTAAAAGAGTAAAAAGAAAATTTGGGTAAT
1 TAAAAGAGT--AA-AG---AAAGAAAATTTGGGTAAT
* *
34176 TAAAAGAGTAAA-AAAAAAAAATTGGGTAAT
1 TAAAAGAGTAAAGAAAGAAAATTTGGGTAAT
34206 TAAAAGAGTAAA
1 TAAAAGAGTAAA
34218 AGGAAATTGG
Statistics
Matches: 84, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
25 13 0.15
26 2 0.02
27 4 0.05
28 3 0.04
30 38 0.45
31 1 0.01
33 1 0.01
34 4 0.05
35 4 0.05
36 7 0.08
37 7 0.08
ACGTcount: A:0.56, C:0.01, G:0.20, T:0.23
Consensus pattern (31 bp):
TAAAAGAGTAAAGAAAGAAAATTTGGGTAAT
Found at i:34218 original size:30 final size:30
Alignment explanation
Indices: 34147--34218 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
34137 AATTAAAGAG
* *
34147 TAAAAGAGT-AAAAAGAAAATTTGGGTAAT
1 TAAAAGAGTAAAAAAAAAAAATTGGGTAAT
34176 TAAAAGAGTAAAAAAAAAAAATTGGGTAAT
1 TAAAAGAGTAAAAAAAAAAAATTGGGTAAT
34206 TAAAAGAGTAAAA
1 TAAAAGAGTAAAA
34219 GGAAATTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 9 0.22
30 31 0.77
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (30 bp):
TAAAAGAGTAAAAAAAAAAAATTGGGTAAT
Found at i:34330 original size:53 final size:53
Alignment explanation
Indices: 34249--34354 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
34239 TAAAAGGAAG
* * *
34249 TTGGTTAATTTAGTTAATTAAAAAGTAAAATGAAATTGGATAATTAAAGAGTAA
1 TTGGTAAATTTAGGTAATTAAAAAGTAAAATGAAATTGG-TAATCAAAGAGTAA
* *
34303 TTGGTAAATTT-GGTAATTAAGAAGTAAAATGAATTTGGTAATCAAAGAGTAA
1 TTGGTAAATTTAGGTAATTAAAAAGTAAAATGAAATTGGTAATCAAAGAGTAA
34355 AGTAAAATGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 13 0.28
53 24 0.51
54 10 0.21
ACGTcount: A:0.46, C:0.01, G:0.19, T:0.34
Consensus pattern (53 bp):
TTGGTAAATTTAGGTAATTAAAAAGTAAAATGAAATTGGTAATCAAAGAGTAA
Found at i:34337 original size:25 final size:25
Alignment explanation
Indices: 34263--34475 Score: 99
Period size: 30 Copynumber: 7.6 Consensus size: 25
34253 TTAATTTAGT
* *
34263 TAATTAAAAAGTAAAATGAAATTGG
1 TAATTAAGAAGTAAAATGAATTTGG
*
34288 ATAATTAA-AGAGT-AATTGGTAAATTTGG
1 -TAATTAAGA-AGTAAAAT-G--AATTTGG
34316 TAATTAAGAAGTAAAATGAATTTGG
1 TAATTAAGAAGTAAAATGAATTTGG
*
34341 TAATCAAAGAGTAAAGTAAAATGAATTTGG
1 TAAT--TA-AG--AAGTAAAATGAATTTGG
* *
34371 TAATTGAAG-AGTAAGAGGAAATTGGTTAATTTGG
1 TAATT-AAGAAGT---A--AAA-T-G-AATT-TGG
34405 TAATTAAGAAGTAAAATGAATTTGG
1 TAATTAAGAAGTAAAATGAATTTGG
* *
34430 TAAGTAAAGAGTAAAGTAAAATGAGTTTGG
1 TAA-T-TA-AG--AAGTAAAATGAATTTGG
*
34460 TAATTAAAAAGTAAAA
1 TAATTAAGAAGTAAAA
34476 GTAAATTGGT
Statistics
Matches: 147, Mismatches: 13, Indels: 55
0.68 0.06 0.26
Matches are distributed among these distances:
25 32 0.22
26 14 0.10
27 15 0.10
28 19 0.13
29 5 0.03
30 43 0.29
31 2 0.01
32 1 0.01
33 5 0.03
34 11 0.07
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (25 bp):
TAATTAAGAAGTAAAATGAATTTGG
Found at i:34360 original size:30 final size:30
Alignment explanation
Indices: 34324--34532 Score: 185
Period size: 34 Copynumber: 6.7 Consensus size: 30
34314 GGTAATTAAG
*
34324 AAGTAAAATGAATTTGGTAATCAAAGAGTA
1 AAGTAAAATGAATTTGGTAATTAAAGAGTA
*
34354 AAGTAAAATGAATTTGGTAATTGAAGAGTA
1 AAGTAAAATGAATTTGGTAATTAAAGAGTA
* *
34384 AGAGGAAATTGGTTAATTTGGTAATT--A-AG--
1 A-AGTAAAAT-G--AATTTGGTAATTAAAGAGTA
*
34413 AAGTAAAATGAATTTGGTAAGTAAAGAGTA
1 AAGTAAAATGAATTTGGTAATTAAAGAGTA
* *
34443 AAGTAAAATGAGTTTGGTAATTAAAAAGTAA
1 AAGTAAAATGAATTTGGTAATTAAAGAGT-A
* *
34474 AAGTAAATTGGTTAATTTGGTAATTAAAAAGTAA
1 AAGTAAAAT-G--AATTTGGTAATTAAAGAGT-A
*
34508 AAGTAAATTGGTTAATTTGGTAATT
1 AAGTAAAAT-G--AATTTGGTAATT
34533 TAAAATGAAC
Statistics
Matches: 154, Mismatches: 12, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
25 11 0.07
27 2 0.01
28 8 0.05
29 1 0.01
30 55 0.36
31 17 0.11
32 3 0.02
34 57 0.37
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (30 bp):
AAGTAAAATGAATTTGGTAATTAAAGAGTA
Found at i:34407 original size:89 final size:89
Alignment explanation
Indices: 34301--34621 Score: 402
Period size: 89 Copynumber: 3.6 Consensus size: 89
34291 ATTAAAGAGT
* *
34301 AATTGGTAAATTTGGTAATTAAGAAGTAAAATG-AATTTGGTAATCAAAGAGTAAAGTAAAATGA
1 AATTGGTTAATTTGGTAATTAAAAAGTAAAATGAAATTTGGTAAT-AAAGAGTAAAGTAAAATGA
* *
34365 ATTTGGTAATTGAAGAGTAAGAGGA
65 ATTTGGTAATTAAAGAGTAAAAGGA
*
34390 AATTGGTTAATTTGGTAATTAAGAAGTAAAATG-AATTTGGTAAGTAAAGAGTAAAGTAAAATGA
1 AATTGGTTAATTTGGTAATTAAAAAGTAAAATGAAATTTGGTAA-TAAAGAGTAAAGTAAAATGA
* * *
34454 GTTTGGTAATTAAAAAGTAAAAGTA
65 ATTTGGTAATTAAAGAGTAAAAGGA
** **
34479 AATTGGTTAATTTGGTAATTAAAAAGTAAAA-GTAAA-TTGGTTAAT-TTG-GTAATTTAAAATG
1 AATTGGTTAATTTGGTAATTAAAAAGTAAAATG-AAATTTGG-TAATAAAGAGTAAAGTAAAATG
* *
34540 AACTTGGTAATCAAAGAGTAAAAGGA
64 AATTTGGTAATTAAAGAGTAAAAGGA
* *
34566 AGTTGGTTAATTTGGTTAATTAAAAAGTAAAATGAAATTGGGTAATTAAAGAGTAA
1 AATTGGTTAATTTGG-TAATTAAAAAGTAAAATGAAATTTGGTAA-TAAAGAGTAA
34622 TTGGTAAAAT
Statistics
Matches: 202, Mismatches: 20, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
87 46 0.23
88 24 0.12
89 121 0.60
90 7 0.03
91 4 0.02
ACGTcount: A:0.46, C:0.01, G:0.21, T:0.32
Consensus pattern (89 bp):
AATTGGTTAATTTGGTAATTAAAAAGTAAAATGAAATTTGGTAATAAAGAGTAAAGTAAAATGAA
TTTGGTAATTAAAGAGTAAAAGGA
Found at i:34572 original size:53 final size:54
Alignment explanation
Indices: 34490--34591 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 54
34480 ATTGGTTAAT
* * *
34490 TTGGTAATTAAAAAGTAAAAGTAAATTGGTTAATTTGG-TAATTTAAAATGAAC
1 TTGGTAATCAAAAAGTAAAAGGAAATTGGTTAATTTGGTTAATTAAAAATGAAC
* *
34543 TTGGTAATCAAAGAGTAAAAGGAAGTTGGTTAATTTGGTTAATTAAAAA
1 TTGGTAATCAAAAAGTAAAAGGAAATTGGTTAATTTGGTTAATTAAAAA
34592 GTAAAATGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 34 0.79
54 9 0.21
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (54 bp):
TTGGTAATCAAAAAGTAAAAGGAAATTGGTTAATTTGGTTAATTAAAAATGAAC
Found at i:34595 original size:35 final size:34
Alignment explanation
Indices: 34543--34612 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
34533 TAAAATGAAC
* * *
34543 TTGGTAATCAAAGAGTAAAAGGAAGTTGGTTAAT
1 TTGGTAATCAAAAAGTAAAAGGAAATTGGGTAAT
* *
34577 TTGGTTAATTAAAAAGTAAAATGAAATTGGGTAAT
1 TTGG-TAATCAAAAAGTAAAAGGAAATTGGGTAAT
34612 T
1 T
34613 AAAGAGTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 4 0.13
35 26 0.87
ACGTcount: A:0.43, C:0.01, G:0.23, T:0.33
Consensus pattern (34 bp):
TTGGTAATCAAAAAGTAAAAGGAAATTGGGTAAT
Found at i:37165 original size:22 final size:22
Alignment explanation
Indices: 37132--37173 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
37122 TTCATTTAGG
37132 TTTGAAAACTCCTCTTATTTTTT
1 TTTGAAAACTCCTCTT-TTTTTT
37155 TTTG-AAACTCCTCTTTTTT
1 TTTGAAAACTCCTCTTTTTT
37174 ATTTGAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTGAAAACTCCTCTTTTTTTT
Found at i:37178 original size:20 final size:22
Alignment explanation
Indices: 37132--37180 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
37122 TTCATTTAGG
*
37132 TTTGAAAACTCCTCTTATTTTTT
1 TTTG-AAACTCCTCTTATTTTTA
37155 TTTGAAACTCCTC-T-TTTTTA
1 TTTGAAACTCCTCTTATTTTTA
37175 TTTGAA
1 TTTGAA
37181 TTCTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 9 0.36
23 4 0.16
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTGAAACTCCTCTTATTTTTA
Found at i:38449 original size:14 final size:14
Alignment explanation
Indices: 38430--38456 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38420 TCAAATGCGT
38430 GAAATCTAAAACAG
1 GAAATCTAAAACAG
38444 GAAATCTAAAACA
1 GAAATCTAAAACA
38457 AGGATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (14 bp):
GAAATCTAAAACAG
Found at i:40434 original size:39 final size:39
Alignment explanation
Indices: 40376--40514 Score: 251
Period size: 39 Copynumber: 3.6 Consensus size: 39
40366 CATTAACTTG
*
40376 CAAGGACCTAAGCAAGTTTGCTTAAACGGAAATTCTAAA
1 CAAGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTAAA
40415 CAAGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTAAA
1 CAAGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTAAA
* *
40454 CAAGGACCTAAGCAGGTTTACTTAAATGGAAATTCTAAA
1 CAAGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTAAA
40493 CAAGGACCTAAGCAGGTTTGCT
1 CAAGGACCTAAGCAGGTTTGCT
40515 ATGACAAAGC
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 96 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (39 bp):
CAAGGACCTAAGCAGGTTTGCTTAAACGGAAATTCTAAA
Done.