Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014950.1 Corchorus olitorius cultivar O-4 contig14983, 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: 57185
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:2195 original size:30 final size:29
Alignment explanation
Indices: 2158--2227 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 29
2148 TGATGCAGAA
2158 TTTTTTTTTTTTATAAATGACGCAAAAAAAC
1 TTTTTTTTTTTTATAAA--ACGCAAAAAAAC
**
2189 TTTTTTTTTTTTTATAAAACGCAAAAACTC
1 -TTTTTTTTTTTTATAAAACGCAAAAAAAC
2219 TTTTTTTTT
1 TTTTTTTTT
2228 GTGACGCAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 9 0.25
30 10 0.28
32 17 0.47
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTTTTTTTTTTATAAAACGCAAAAAAAC
Found at i:2672 original size:15 final size:16
Alignment explanation
Indices: 2652--2689 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
2642 AGGTTGACAT
2652 AAAACAATTAAAC-AG
1 AAAACAATTAAACTAG
2667 AAAACAATTAAACTAG
1 AAAACAATTAAACTAG
2683 AAAACAA
1 AAAACAA
2690 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.68, C:0.13, G:0.05, T:0.13
Consensus pattern (16 bp):
AAAACAATTAAACTAG
Found at i:4403 original size:25 final size:27
Alignment explanation
Indices: 4366--4421 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 27
4356 AGAAGAGAAG
*
4366 AAAAGAAGAAAAGAA-TTGAAAAAG-A
1 AAAAGAAGAAAAGAAGCTGAAAAAGTA
4391 AAAAGAA-AGAAAGAAGCTGAAAAAGTA
1 AAAAGAAGA-AAAGAAGCTGAAAAAGTA
4418 AAAA
1 AAAA
4422 TGGAGGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 1 0.04
25 13 0.48
26 8 0.30
27 5 0.19
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (27 bp):
AAAAGAAGAAAAGAAGCTGAAAAAGTA
Found at i:5931 original size:54 final size:54
Alignment explanation
Indices: 5808--6300 Score: 446
Period size: 54 Copynumber: 9.2 Consensus size: 54
5798 CGATCTTTTA
* * * * * *
5808 AAGTTTTCAGAGATCTAAGTTGA-CATT-CATGGCCCAGTACGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTTAGATGACCCTGTGCGGTCTTTCATAG
* * *
5860 AAGTTTTCAGAGGTTTAAGTTGATCTTTAGATAACCCTGTGCGGTCATTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTTAGATGACCCTGTGCGGTCTTTCATAG
* *
5914 AAGTTTTTAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTTAGATGACCCTGTGCGGTCTTTCATAG
* * * *
5968 AAGCTTTT-AGAGATTTAAGTTGATCTTCATATAACCCTGTGCGGTCATTCATAG
1 AAG-TTTTCAGAGATTTAAGTTGATCTTTAGATGACCCTGTGCGGTCTTTCATAG
* * * *
6022 AAGTTTTCAGAGATTTAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCGTAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTTAGATGACCCTGTGCGGTCTTTCATAG
** * * *
6076 AAGTTTTCAGAGATCAAAATTAAT-TTTATGATGATCCTGTGCGGTCTTTCATA-
1 AAGTTTTCAGAGATTTAAGTTGATCTTTA-GATGACCCTGTGCGGTCTTTCATAG
* * * *** *
6129 AAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCC-GATGTTATCTTTTGA-AG
1 AAGTTTTCAGAGATTTAAGTTGATCTTTAGATGACCCTG-TGCGGTC-TTTCATAG
* ** ** * *
6183 AAGTTTTTAGAGATCAAAGTTGATCCCTAGATGACCCAGTGCGGTCATTCCA-AG
1 AAGTTTTCAGAGATTTAAGTTGATCTTTAGATGACCCTGTGCGGTC-TTTCATAG
* * ** * * * *
6237 AAGTTTTTAGAGA-TCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAAG
1 AAGTTTTCAGAGATTTA-AGTTGATCTTTAGATGACCCTGTGCGGTC-TTTCATAG
6292 AAGTTTTCA
1 AAGTTTTCA
6301 ATGATCAAAG
Statistics
Matches: 372, Mismatches: 57, Indels: 21
0.83 0.13 0.05
Matches are distributed among these distances:
52 22 0.06
53 43 0.12
54 292 0.78
55 15 0.04
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (54 bp):
AAGTTTTCAGAGATTTAAGTTGATCTTTAGATGACCCTGTGCGGTCTTTCATAG
Found at i:6002 original size:108 final size:108
Alignment explanation
Indices: 5808--6640 Score: 491
Period size: 108 Copynumber: 7.7 Consensus size: 108
5798 CGATCTTTTA
* * *
5808 AAGTTTTCAGAGATCTAAGTTGA-CATTC--ATGGCCCAGTACGGTCTTTCATAGAAGTTTTCAG
1 AAGTTTTCAGAGATCTAAGTTGATC-TTCAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAG
* ** *
5870 AGGTTTAAGTTGATCTTTAGATAACCCTGTGCGGTCATTCATAG
65 AGATCAAAGTTGATCTTCAGATAACCCTGTGCGGTCATTCATAG
* *
5914 AAGTTTTTAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAGCTTTT-AG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAG-TTTTCAG
** *
5978 AGATTTAAGTTGATCTTCATATAACCCTGTGCGGTCATTCATAG
65 AGATCAAAGTTGATCTTCAGATAACCCTGTGCGGTCATTCATAG
* * * *
6022 AAGTTTTCAGAGATTTAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCGTAGAAGTTTTCAGA
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
* * * * * *
6087 GATCAAAATTAAT-TTTATGATGATCCTGTGCGGTCTTTCATA-
66 GATCAAAGTTGATCTTCA-GATAACCCTGTGCGGTCATTCATAG
* * *** * *
6129 AAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCC-GATGTTATCTTTTGA-AGAAGTTTTTA
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTG-TGCGGTC-TTTCATAGAAGTTTTCA
* * *
6192 GAGATCAAAGTTGATC-CCTAGATGACCCAGTGCGGTCATTCCA-AG
64 GAGATCAAAGTTGATCTTC-AGATAACCCTGTGCGGTCATT-CATAG
* * * * * *
6237 AAGTTTTTAGAGATC-AGAGTTGATC-CCTAGATGATCCAGTGCGGTCATTCCAAAGAAGTTTTC
1 AAGTTTTCAGAGATCTA-AGTTGATCTTC-AGATGACCCTGTGCGGTC-TTTCATAGAAGTTTTC
* * * **
6300 A-ATGATCAAAGTTGAT-TCTCGGATGATCCACTGCGGTCATTTCA-AG
63 AGA-GATCAAAGTTGATCT-TCAGATAACCCTGTGCGGTCA-TTCATAG
* ** ** * * * *
6346 AAGTGTTT-AGATATCGGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA-AGAAGTTTTCT
1 AAGT-TTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTC-TTTCATAGAAGTTTTCA
** * * * * ** * * *
6409 TTGATCAGAGGTGATC-CCAGATGA-TATAGTACTGTCATTC-TAAT
64 GAGATCAAAGTTGATCTTCAGATAACCCT-GTGCGGTCATTCAT-AG
*** ** * *
6453 AAGTTTTCTTTGATC-AGAGTTGATCTT-AGATGACCAAGTGCGGTCATTCCA-AGAAGTTTTTA
1 AAGTTTTCAGAGATCTA-AGTTGATCTTCAGATGACCCTGTGCGGTC-TTTCATAGAAGTTTTCA
* * * * * * *
6515 GAGAACAGAGTTGATC-CCTAGATGATCCGGTGCGGTCATTCCAAAG
64 GAGATCAAAGTTGATCTTC-AGATAACCCTGTGCGGTCATT-CATAG
* * * *
6561 AAGTTTTCA-ATGATC-AGAGTTGAT-TCCCAGATGATCCAGTGCAGTCATTTCA-AGAAGTTTT
1 AAGTTTTCAGA-GATCTA-AGTTGATCT-TCAGATGACCCTGTGCGGTC-TTTCATAGAAGTTTT
*
6622 CAGTGAT-AAGAGTTGATCT
62 CAGAGATCAA-AGTTGATCT
6641 CAAATGATCT
Statistics
Matches: 586, Mismatches: 102, Indels: 74
0.77 0.13 0.10
Matches are distributed among these distances:
106 76 0.13
107 131 0.22
108 240 0.41
109 131 0.22
110 8 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (108 bp):
AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
GATCAAAGTTGATCTTCAGATAACCCTGTGCGGTCATTCATAG
Found at i:6260 original size:215 final size:216
Alignment explanation
Indices: 5808--6261 Score: 489
Period size: 215 Copynumber: 2.1 Consensus size: 216
5798 CGATCTTTTA
* * * *
5808 AAGTTTTCAGAGA-TCTAAGTTGA-CATTC--ATGGCCCAGTACGGTCTTTCATAGAAGTTTTCA
1 AAGTTTTCAGAGATTC-AAGTTGATC-TTCAAATGACCCTGTGCAGTCTTTCATAGAAGTTTTCA
* ** * * * * *
5869 GAGGTTTAAGTTGATCTTTAGATAACCCTGTGCGGTCATTCATAGAAGTTTTTAGAGATTTAAGT
64 GAGATCAAAATTAATCTTTAGATAACCCTGTGCGGTCATTCATAGAAGCTTTCAGAGATCTAAGT
* * ** * *
5934 TGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAGCTTTTAGAGATTTAAGTTGATCTTCATA
129 TGATCTTAAGATGACCCTGTGCGATCTTTCATAGAAGCTTTTAGAGATCAAAGTTGATCCTCAGA
*
5999 TAACCCTGTGCGGTCATTCATAG
194 TAACCCAGTGCGGTCATTCATAG
* *
6022 AAGTTTTCAGAGATTTAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCGTAGAAGTTTTCAGA
1 AAGTTTTCAGAGATTCAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCATAGAAGTTTTCAGA
* * *
6087 GATCAAAATTAAT-TTTATGATGATCCTGTGCGGTCTTTCATA-AAGCTTTCAGAGATCTAAGTT
66 GATCAAAATTAATCTTTA-GATAACCCTGTGCGGTCATTCATAGAAGCTTTCAGAGATCTAAGTT
** * *
6150 GATCTTAAGATGACCC-GATGTTATCTTTTGA-AGAAGTTTTTAGAGATCAAAGTTGATCC-CTA
130 GATCTTAAGATGACCCTG-TGCGATC-TTTCATAGAAGCTTTTAGAGATCAAAGTTGATCCTC-A
*
6212 GATGACCCAGTGCGGTCATTCCA-AG
192 GATAACCCAGTGCGGTCATT-CATAG
*
6237 AAGTTTTTAGAGA-TCAGAGTTGATC
1 AAGTTTTCAGAGATTCA-AGTTGATC
6262 CCTAGATGAT
Statistics
Matches: 199, Mismatches: 31, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
214 27 0.14
215 107 0.54
216 65 0.33
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (216 bp):
AAGTTTTCAGAGATTCAAGTTGATCTTCAAATGACCCTGTGCAGTCTTTCATAGAAGTTTTCAGA
GATCAAAATTAATCTTTAGATAACCCTGTGCGGTCATTCATAGAAGCTTTCAGAGATCTAAGTTG
ATCTTAAGATGACCCTGTGCGATCTTTCATAGAAGCTTTTAGAGATCAAAGTTGATCCTCAGATA
ACCCAGTGCGGTCATTCATAG
Found at i:6379 original size:54 final size:53
Alignment explanation
Indices: 6180--7095 Score: 821
Period size: 54 Copynumber: 17.0 Consensus size: 53
6170 TTATCTTTTG
* * *
6180 AAGAAGTTTTTAGA-GATCAAAGTTGATCCCTAGATGACCCAGTGCGGTCATTCC
1 AAGAAG-TTTTA-ATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
*
6234 AAGAAGTTTTTAGA-GATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCC
1 AAGAAG-TTTTA-ATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* * * * * *
6288 AAAGAAGTTTTCAATGATCAAAGTTGATTCTCGGATGATCCACTGCGGTCATTTC
1 -AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
*
6343 AAGAAGTGTTTAGAT-ATCGGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
1 AAGAAGT-TTTA-ATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
** * ** * * *
6397 AAGAAGTTTTCTTTGATCAGAGGTGAT-CCCAGATGATATAGTACTGTCATTCT
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* ** **
6450 AATAAGTTTTCTTTGATCAGAGTTGAT-CTTAGATGA-CCAAGTGCGGTCATTCC
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCC-AGTGCGGTCATTCC
* * *
6503 AAGAAGTTTTTAGA-GAACAGAGTTGATCCCTAGATGATCCGGTGCGGTCATTCC
1 AAGAAG-TTTTA-ATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* * *
6557 AAAGAAGTTTTCAATGATCAGAGTTGATTCCCAGATGATCCAGTGCAGTCATTTC
1 -AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* * * * * * **
6612 AAGAAGTTTTCAGTGATAAGAGTTGAT-CTCAAATGATCTAGCGCATTCATTCC
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
**
6665 AAGAAGTTTTCTTTGATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTCC
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* ** * * *
6718 AAAAAGTTTTCTTTGATCAGAGTTGAT--CCGGGTGATCCAGTGCGGTCATACC
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* * * *
6770 AAGAAGTTTTCCATGATCAGAGTTGATCCCTAGATGATCTAGTGCGGTCATTTC
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* * ** *
6824 AAGAAGTTTTCAATGGTCAAAGTTGAT-CCCAGAACAATCCAGTGCGGTCATTTC
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAG-ATGATCCAGTGCGGTCATTCC
* * * * *
6878 AAGAAGTTTTCAATGGTCAGAGTTGATTCCCAGAAGATCTAGTGCGGTCATTCT
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* * * * * *
6932 AAGAAGTTTTTTATGGTCATAGTTGATTCCTAGATGATCTAGTGCGGTCATTCC
1 AAGAAG-TTTTAATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
* * * * * *
6986 AAGAATTTTTCAATGATCAGATTTGATCTCCAGATGATCCATTGTGGTAATTCC
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
*** * * *
7040 AAGAAGTTTTCAATGATCAGAGTTGATCTTTAAATAATCCAGTGCGGTCTTTCC
1 AAGAAGTTTT-AATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
7094 AA
1 AA
7096 TGATCAGAGT
Statistics
Matches: 725, Mismatches: 116, Indels: 42
0.82 0.13 0.05
Matches are distributed among these distances:
52 46 0.06
53 183 0.25
54 399 0.55
55 97 0.13
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (53 bp):
AAGAAGTTTTAATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
Found at i:6669 original size:162 final size:159
Alignment explanation
Indices: 6180--7067 Score: 952
Period size: 162 Copynumber: 5.5 Consensus size: 159
6170 TTATCTTTTG
* * *
6180 AAGAAGTTTTTAGAGATCAAAGTTGATCCCTAGATGACCCAGTGCGGTCATTCCAAGAAGTTTTT
1 AAGAAGTTTTTAGAGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
* * *
6245 AGA-GATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAAGAAGTTTTCAATGATCAA
65 A-ATGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTTCTAAGAAGTTTTC-ATGATCAG
* * * *
6309 AGTTGATTCTCGGATGATCCACTGCGGTCATTTC
127 AGTTGA-TCTCAGATGATCTAGTGCGGTCATTCC
* * *
6343 AAGAAGTGTTTAGATATCGGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
1 AAGAAGTTTTTAGAGATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
** * ** * * * *
6408 TTTGATCAGAGGTGATCCCAGATGATATAGTACTGTCA-TTCTAATAAGTTTTCTTTGATCAGAG
65 AATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTCTAAGAAGTTTTC-ATGATCAGAG
* * *
6472 TTGATCTTAGATGACCAAGTGCGGTCATTCC
129 TTGATCTCAGATGATCTAGTGCGGTCATTCC
* *
6503 AAGAAGTTTTTAGAGAACAGAGTTGATCCCTAGATGATCCGGTGCGGTCATTCCAAAGAAGTTTT
1 AAGAAGTTTTTAGAGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTCC-AAGAAGTTTT
* *
6568 CAATGATCAGAGTTGATTCCCAGATGATCCAGTGCAGTCATTTC-AAGAAGTTTTCAGTGATAAG
64 CAATGATCAGAGTTGA-TCCCAGATGATCCAGTGCGGTCATTTCTAAGAAGTTTTCA-TGATCAG
* * **
6632 AGTTGATCTCAAATGATCTAGCGCATTCATTCC
127 AGTTGATCTCAGATGATCTAGTGCGGTCATTCC
** *
6665 AAGAAGTTTTCT-TTGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAAAAGTTTTC
1 AAGAAGTTTT-TAGAGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
** * * * *
6729 TTTGATCAGAGTTGAT-CCGGGTGATCCAGTGCGGTCA-TACCAAGAAGTTTTCCATGATCAGAG
65 AATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTCTAAGAAGTTTT-CATGATCAGAG
* *
6792 TTGATCCCTAGATGATCTAGTGCGGTCATTTC
129 TTGATCTC-AGATGATCTAGTGCGGTCATTCC
* * * ** *
6824 AAGAAGTTTTCA-ATGGTCAAAGTTGATCCCAGAACAATCCAGTGCGGTCATTTCAAGAAGTTTT
1 AAGAAGTTTTTAGA-GATCAGAGTTGATCCCAG-ATGATCCAGTGCGGTCATTCCAAGAAGTTTT
* * * * * *
6888 CAATGGTCAGAGTTGATTCCCAGAAGATCTAGTGCGGTCA-TTCTAAGAAGTTTTTTATGGTCAT
64 CAATGATCAGAGTTGA-TCCCAGATGATCCAGTGCGGTCATTTCTAAGAAG-TTTTCATGATCAG
6952 AGTTGAT-TCCTAGATGATCTAGTGCGGTCATTCC
127 AGTTGATCT-C-AGATGATCTAGTGCGGTCATTCC
* * * *
6986 AAGAA-TTTTTCA-ATGATCAGATTTGATCTCCAGATGATCCATTGTGGTAATTCCAAGAAGTTT
1 AAGAAGTTTTT-AGA-GATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGAAGTTT
7049 TCAATGATCAGAGTTGATC
63 TCAATGATCAGAGTTGATC
7068 TTTAAATAAT
Statistics
Matches: 607, Mismatches: 98, Indels: 42
0.81 0.13 0.06
Matches are distributed among these distances:
157 2 0.00
158 43 0.07
159 50 0.08
160 129 0.21
161 76 0.13
162 222 0.37
163 82 0.14
164 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (159 bp):
AAGAAGTTTTTAGAGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
ATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTTCTAAGAAGTTTTCATGATCAGAGTT
GATCTCAGATGATCTAGTGCGGTCATTCC
Found at i:6887 original size:108 final size:107
Alignment explanation
Indices: 6180--7095 Score: 910
Period size: 108 Copynumber: 8.5 Consensus size: 107
6170 TTATCTTTTG
* *
6180 AAGAAGTTTTTAGA-GATCAAAGTTGATCCCTAG-ATGACCCAGTGCGGTCATTCCAAGAAGTTT
1 AAGAAGTTTTCA-ATGATCAAAGTTGATCCC-AGAATGATCCAGTGCGGTCATTCCAAGAAGTTT
*
6243 TTAGA-GATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCC
64 TCA-ATGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTCC
* * * *
6288 AAAGAAGTTTTCAATGATCAAAGTTGATTCTC-GGATGATCCACTGCGGTCATTTCAAGAAGTGT
1 -AAGAAGTTTTCAATGATCAAAGTTGA-TCCCAGAATGATCCAGTGCGGTCATTCCAAGAAGT-T
*
6352 TT-AGAT-ATCGGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCC
63 TTCA-ATGATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTCC
** * * ** * * * *
6397 AAGAAGTTTTCTTTGATCAGAGGTGATCCCAG-ATGATATAGTACTGTCATTCTAATAAGTTTTC
1 AAGAAGTTTTCAATGATCAAAGTTGATCCCAGAATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
** **
6461 TTTGATCAGAGTTGATCTTAGATGA-CCAAGTGCGGTCATTCC
66 AATGATCAGAGTTGATCCCAGATGATCC-AGTGCGGTCATTCC
* * * *
6503 AAGAAGTTTTTAGA-GAACAGAGTTGATCCCTAG-ATGATCCGGTGCGGTCATTCCAAAGAAGTT
1 AAGAAGTTTTCA-ATGATCAAAGTTGATCCC-AGAATGATCCAGTGCGGTCATTCC-AAGAAGTT
* *
6566 TTCAATGATCAGAGTTGATTCCCAGATGATCCAGTGCAGTCATTTC
63 TTCAATGATCAGAGTTGA-TCCCAGATGATCCAGTGCGGTCATTCC
* * * * **
6612 AAGAAGTTTTCAGTGAT-AAGAGTTGATCTCA-AATGATCTAGCGCATTCATTCCAAGAAGTTTT
1 AAGAAGTTTTCAATGATCAA-AGTTGATCCCAGAATGATCCAGTGCGGTCATTCCAAGAAGTTTT
**
6675 CTTTGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCC
65 CAATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCC
* ** * ** *
6718 AAAAAGTTTTCTTTGATCAGAGTTGAT-CC-GGGTGATCCAGTGCGGTCATACCAAGAAGTTTTC
1 AAGAAGTTTTCAATGATCAAAGTTGATCCCAGAATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
* * *
6781 CATGATCAGAGTTGATCCCTAGATGATCTAGTGCGGTCATTTC
66 AATGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTCC
* ** *
6824 AAGAAGTTTTCAATGGTCAAAGTTGATCCCAGAACAATCCAGTGCGGTCATTTCAAGAAGTTTTC
1 AAGAAGTTTTCAATGATCAAAGTTGATCCCAGAATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
* * * *
6889 AATGGTCAGAGTTGATTCCCAGAAGATCTAGTGCGGTCATTCT
66 AATGATCAGAGTTGA-TCCCAGATGATCCAGTGCGGTCATTCC
** * * * * *
6932 AAGAAGTTTTTTATGGTCATAGTTGATTCCTAG-ATGATCTAGTGCGGTCATTCCAAGAATTTTT
1 AAGAAGTTTTCAATGATCAAAGTTGA-TCCCAGAATGATCCAGTGCGGTCATTCCAAGAAGTTTT
* * * *
6996 CAATGATCAGATTTGATCTCCAGATGATCCATTGTGGTAATTCC
65 CAATGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCC
* ** * *
7040 AAGAAGTTTTCAATGATCAGAGTTGATCTTTA-AATAATCCAGTGCGGTCTTTCCAA
1 AAGAAGTTTTCAATGATCAAAGTTGATC-CCAGAATGATCCAGTGCGGTCATTCCAA
7096 TGATCAGAGT
Statistics
Matches: 666, Mismatches: 113, Indels: 57
0.80 0.14 0.07
Matches are distributed among these distances:
105 46 0.07
106 138 0.21
107 82 0.12
108 253 0.38
109 136 0.20
110 11 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (107 bp):
AAGAAGTTTTCAATGATCAAAGTTGATCCCAGAATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
AATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCC
Found at i:8934 original size:27 final size:28
Alignment explanation
Indices: 8895--8947 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
8885 ATTAGGTTGG
8895 TTTTGGACTTGCACTTGGACATTTTAAC
1 TTTTGGACTTGCACTTGGACATTTTAAC
* *
8923 TTTT-GACTTGCATTTGGACCTTTTA
1 TTTTGGACTTGCACTTGGACATTTTA
8948 GCCTTGGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (28 bp):
TTTTGGACTTGCACTTGGACATTTTAAC
Found at i:8960 original size:27 final size:27
Alignment explanation
Indices: 8897--8965 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
8887 TAGGTTGGTT
* *
8897 TTGGACTTGCACTTGGACATTTTAACT
1 TTGGACTTGCATTTGGACATTTTAACC
* * *
8924 TTTGACTTGCATTTGGACCTTTTAGCC
1 TTGGACTTGCATTTGGACATTTTAACC
* *
8951 TTGGATTTGCTTTTG
1 TTGGACTTGCATTTG
8966 CGGCATAATG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.17, G:0.20, T:0.46
Consensus pattern (27 bp):
TTGGACTTGCATTTGGACATTTTAACC
Found at i:11420 original size:29 final size:29
Alignment explanation
Indices: 11338--11495 Score: 137
Period size: 29 Copynumber: 5.5 Consensus size: 29
11328 CTTGGCTTCT
* *
11338 CATTTTGGTCATTTTTCATGACCA-GGGG
1 CATTTTGGTCATTTTACATGTCCAGGGGG
* *
11366 CATTTTGGTCAATTTACAAT-ACCAGGGGG
1 CATTTTGGTCATTTTAC-ATGTCCAGGGGG
*
11395 CATTTTGGTCATTTTACATGTTCA--GGG
1 CATTTTGGTCATTTTACATGTCCAGGGGG
* * *
11422 CAGTCTGGTCATTCTT-CTAGGTCCAGGGGGG
1 CATTTTGGTCATT-TTAC-ATGTCCA-GGGGG
* * * *
11453 CATTGTGATCATTTTTCATGTTCAGGGGG
1 CATTTTGGTCATTTTACATGTCCAGGGGG
11482 CATTTTGGTCATTT
1 CATTTTGGTCATTT
11496 CAAGTTTATT
Statistics
Matches: 105, Mismatches: 16, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
27 15 0.14
28 28 0.27
29 41 0.39
30 7 0.07
31 14 0.13
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (29 bp):
CATTTTGGTCATTTTACATGTCCAGGGGG
Found at i:17289 original size:28 final size:28
Alignment explanation
Indices: 17226--17300 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
17216 AGGATCAACT
* * *
17226 AGGGGAATTTTAGTCA-TTTGCATATTC
1 AGGGGCATTTTGGTCATTTTGCACATTC
*
17253 AGGGGCATTTTGGTCATTTTTCACATTC
1 AGGGGCATTTTGGTCATTTTGCACATTC
*
17281 GGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
17301 AAGTTCACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 14 0.33
28 28 0.67
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCACATTC
Found at i:21774 original size:32 final size:32
Alignment explanation
Indices: 21635--21766 Score: 201
Period size: 32 Copynumber: 4.1 Consensus size: 32
21625 CGTTTCGACA
* *
21635 GGTAATCAGTAATCAAATTCAAAGGATAGAAT
1 GGTAATCAGTAATCAAATTCAAAGGGTAAAAT
* *
21667 TGTAATCAGTAATCAAATTCAAAGGGCAAAAT
1 GGTAATCAGTAATCAAATTCAAAGGGTAAAAT
21699 GGTAATCAGTAATCAAATTCAAAGGGTAAAAT
1 GGTAATCAGTAATCAAATTCAAAGGGTAAAAT
* * *
21731 TGTAATTAGTAATCAAATTCAAAGAGTAAAAT
1 GGTAATCAGTAATCAAATTCAAAGGGTAAAAT
21763 GGTA
1 GGTA
21767 GTTAGTAACT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 90 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (32 bp):
GGTAATCAGTAATCAAATTCAAAGGGTAAAAT
Found at i:21792 original size:64 final size:64
Alignment explanation
Indices: 21635--21809 Score: 187
Period size: 64 Copynumber: 2.8 Consensus size: 64
21625 CGTTTCGACA
* * *
21635 GGTAATCAGTAATCAAATTC-AAAGGATAGAATTGTAATCAGTAATCAAATTCAAAGGGCAAAAT
1 GGTAATCAGTAATCAAATTCAAAAAG-TAAAATTGTAATCAGTAATCAAATTCAAAGAGCAAAAT
** * *
21699 GGTAATCAGTAATCAAATTCAAAGGGTAAAATTGTAATTAGTAATCAAATTCAAAGAGTAAAAT
1 GGTAATCAGTAATCAAATTCAAAAAGTAAAATTGTAATCAGTAATCAAATTCAAAGAGCAAAAT
* * * * *
21763 GGTAGTTAGTAA-CTAAGGTT-AAAAAGTAAAATGGTAA-CGGTAATCAA
1 GGTAATCAGTAATC-AA-ATTCAAAAAGTAAAATTGTAATCAGTAATCAA
21810 TAATGAGTAA
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
63 9 0.09
64 80 0.84
65 6 0.06
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (64 bp):
GGTAATCAGTAATCAAATTCAAAAAGTAAAATTGTAATCAGTAATCAAATTCAAAGAGCAAAAT
Found at i:21834 original size:42 final size:42
Alignment explanation
Indices: 21782--22029 Score: 249
Period size: 42 Copynumber: 5.9 Consensus size: 42
21772 TAACTAAGGT
* * *
21782 TAAAAAGTAAAATGGTAACGGTAATCAATAATGAGTAAAGAG
1 TAAAAGGTAAAATGGTAACGGTAATCAGTAAAGAGTAAAGAG
21824 TAAAAGGTAAAATGGTAACGGTAATCAGTAAAGAGTAAAGAG
1 TAAAAGGTAAAATGGTAACGGTAATCAGTAAAGAGTAAAGAG
* * *
21866 TAATCA-GTAAAATGGTAA-TGAAATCAGTAAAGAGTAAAGAG
1 TAA-AAGGTAAAATGGTAACGGTAATCAGTAAAGAGTAAAGAG
* *
21907 GAAAAGGTAAAATGGTAATGGTAATCAGTAAAGAGTAAAGAG
1 TAAAAGGTAAAATGGTAACGGTAATCAGTAAAGAGTAAAGAG
* * * *
21949 TAATCAA--TAAAA-AGTAATGGTATTCAGCAAAGAGTAAAGAG
1 TAA--AAGGTAAAATGGTAACGGTAATCAGTAAAGAGTAAAGAG
* * **
21990 CAATCA-GTAAAA-GAGTAAAAAGTAATCAGTAAAGAGTAAA
1 TAA-AAGGTAAAATG-GT-AACGGTAATCAGTAAAGAGTAAA
22030 ATGGTAATTA
Statistics
Matches: 176, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.01
41 68 0.39
42 84 0.48
43 20 0.11
44 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.20
Consensus pattern (42 bp):
TAAAAGGTAAAATGGTAACGGTAATCAGTAAAGAGTAAAGAG
Found at i:21924 original size:83 final size:83
Alignment explanation
Indices: 21787--22029 Score: 294
Period size: 83 Copynumber: 2.9 Consensus size: 83
21777 AAGGTTAAAA
* * * * *
21787 AGTAAAATGGTAACGGTAATCAATAATGAGTAAAGAGTAAAAGGTAAAATGGTAACGGTAATCAG
1 AGTAAAATGGTAA-TGTAATCAGTAAAGAGTAAAGAGCAAAAGGTAAAATGGTAAAGGTAATCAG
21852 TAAAGAGTAAAGAGTAATC
65 TAAAGAGTAAAGAGTAATC
* * *
21871 AGTAAAATGGTAATGAAATCAGTAAAGAGTAAAGAGGAAAAGGTAAAATGGTAATGGTAATCAGT
1 AGTAAAATGGTAATGTAATCAGTAAAGAGTAAAGAGCAAAAGGTAAAATGGTAAAGGTAATCAGT
21936 AAAGAGTAAAGAGTAATC
66 AAAGAGTAAAGAGTAATC
* * * * * *
21954 AATAAAA-AGTAATGGTATTCAGCAAAGAGTAAAGAGCAATCA-GTAAAA-GAGTAAAAAGTAAT
1 AGTAAAATGGTAAT-GTAATCAGTAAAGAGTAAAGAGCAA-AAGGTAAAATG-GT-AAAGGTAAT
22016 CAGTAAAGAGTAAA
62 CAGTAAAGAGTAAA
22030 ATGGTAATTA
Statistics
Matches: 140, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
82 6 0.04
83 99 0.71
84 35 0.25
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.20
Consensus pattern (83 bp):
AGTAAAATGGTAATGTAATCAGTAAAGAGTAAAGAGCAAAAGGTAAAATGGTAAAGGTAATCAGT
AAAGAGTAAAGAGTAATC
Found at i:22061 original size:32 final size:32
Alignment explanation
Indices: 22024--22140 Score: 139
Period size: 32 Copynumber: 3.7 Consensus size: 32
22014 ATCAGTAAAG
* *
22024 AGTAAAATGGTAATTAGTAATTAAATTCAAAG
1 AGTAAAATGGTAATCAGTAATTAAATTCAAAA
* * *
22056 AGTAAAATGGTCATCAGTAATGAAGTTCAAAA
1 AGTAAAATGGTAATCAGTAATTAAATTCAAAA
*
22088 AGTAAAATGGTAATCAGAGTAGTTAAATTCAAAA
1 AGTAAAATGGTAATC--AGTAATTAAATTCAAAA
*
22122 AGT--AATGGTAATCAATAAT
1 AGTAAAATGGTAATCAGTAAT
22141 AGTAAAAACG
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
30 4 0.06
32 51 0.71
34 17 0.24
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (32 bp):
AGTAAAATGGTAATCAGTAATTAAATTCAAAA
Found at i:22178 original size:32 final size:31
Alignment explanation
Indices: 22145--22249 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 31
22135 AATAATAGTA
*
22145 AAAACGGTAATCAGTAATCCAATTCAAGAGT
1 AAAATGGTAATCAGTAATCCAATTCAAGAGT
22176 AAAATGGTAATCAGT-A---AA---AAGAGT
1 AAAATGGTAATCAGTAATCCAATTCAAGAGT
22200 AAAAATGGTAATCAGTAATCCAATTCAAAGAGT
1 -AAAATGGTAATCAGTAATCCAATTC-AAGAGT
22233 AAAATGGTAATCAGTAA
1 AAAATGGTAATCAGTAA
22250 AAAGAGTAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
24 6 0.09
25 15 0.23
26 1 0.02
27 2 0.03
29 2 0.03
30 1 0.02
31 14 0.22
32 17 0.27
33 6 0.09
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (31 bp):
AAAATGGTAATCAGTAATCCAATTCAAGAGT
Found at i:22210 original size:25 final size:25
Alignment explanation
Indices: 22170--22303 Score: 128
Period size: 26 Copynumber: 5.0 Consensus size: 25
22160 AATCCAATTC
22170 AAGAGT-AAAATGGTAATCAGTAAA
1 AAGAGTAAAAATGGTAATCAGTAAA
22194 AAGAGTAAAAATGGTAATCAGTAATCCAATTCA
1 AAGAGTAAAAATGGTAATCAG---T--AA---A
22227 AAGAGT-AAAATGGTAATCAGTAAA
1 AAGAGTAAAAATGGTAATCAGTAAA
22251 AAGAGTAAAAAATGGTAATCAGTAAAA
1 AAGAGT-AAAAATGGTAATCAGT-AAA
* *
22278 AAGAGTAGGAAAAGGGTAATAAGTAA
1 AAGAGTA--AAAATGGTAATCAGTAA
22304 TCTAATTAAA
Statistics
Matches: 94, Mismatches: 2, Indels: 25
0.78 0.02 0.21
Matches are distributed among these distances:
24 13 0.14
25 14 0.15
26 16 0.17
27 13 0.14
28 14 0.15
29 1 0.01
30 2 0.02
32 14 0.15
33 7 0.07
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.20
Consensus pattern (25 bp):
AAGAGTAAAAATGGTAATCAGTAAA
Found at i:22210 original size:56 final size:57
Alignment explanation
Indices: 22141--22275 Score: 245
Period size: 57 Copynumber: 2.4 Consensus size: 57
22131 AATCAATAAT
*
22141 AGTAAAAACGGTAATCAGTAATCCAATTC-AAGAGTAAAATGGTAATCAGTAAAAAG
1 AGTAAAAATGGTAATCAGTAATCCAATTCAAAGAGTAAAATGGTAATCAGTAAAAAG
22197 AGTAAAAATGGTAATCAGTAATCCAATTCAAAGAGTAAAATGGTAATCAGTAAAAAG
1 AGTAAAAATGGTAATCAGTAATCCAATTCAAAGAGTAAAATGGTAATCAGTAAAAAG
22254 AGTAAAAAATGGTAATCAGTAA
1 AGT-AAAAATGGTAATCAGTAA
22276 AAAAGAGTAG
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
56 28 0.37
57 30 0.39
58 18 0.24
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (57 bp):
AGTAAAAATGGTAATCAGTAATCCAATTCAAAGAGTAAAATGGTAATCAGTAAAAAG
Found at i:24972 original size:14 final size:13
Alignment explanation
Indices: 24925--24974 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
24915 CGAAAAGTAT
24925 TTTTCAAAAAT-G
1 TTTTCAAAAATGG
*
24937 TTTTCAAGAAAAGG
1 TTTTCAA-AAATGG
24951 TTTTCAAAAATGAG
1 TTTTCAAAAATG-G
24965 TTTTCAAAAA
1 TTTTCAAAAA
24975 GATTTTGAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 7 0.21
13 7 0.21
14 19 0.58
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAATGG
Found at i:24974 original size:26 final size:26
Alignment explanation
Indices: 24916--24980 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 26
24906 TGGTCAAAAC
24916 GAAAAGTATTTTTCAAAAATGTTTTCAA
1 GAAAAG-A-TTTTCAAAAATGTTTTCAA
*
24944 GAAAAGGTTTTCAAAAATGAGTTTTC-A
1 GAAAAGATTTTCAAAAAT--GTTTTCAA
24971 -AAAAGATTTT
1 GAAAAGATTTT
24981 GAGTTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 20 0.61
27 1 0.03
28 12 0.36
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (26 bp):
GAAAAGATTTTCAAAAATGTTTTCAA
Found at i:29751 original size:14 final size:15
Alignment explanation
Indices: 29732--29761 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29722 CAATTAAAGC
29732 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
29746 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
29761 A
1 A
29762 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:33368 original size:53 final size:53
Alignment explanation
Indices: 33298--33399 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 53
33288 AATAAAGAAA
33298 TTTTTTTTTTATAAAAAACGCAGACAAA-TTTTTTTTATGACGCAAAAACTCTCG
1 TTTTTTTTTTATAAAAAACGCA-A-AAACTTTTTTTTATGACGCAAAAACTCTCG
* *
33352 TTTTTTTTTTA-GAAAAACGCAAAAACTTTTTTTTTATGACGCAGAAAC
1 TTTTTTTTTTATAAAAAACGCAAAAAC-TTTTTTTTATGACGCAAAAAC
33400 AAAAAAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
51 3 0.07
52 1 0.02
53 29 0.66
54 11 0.25
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (53 bp):
TTTTTTTTTTATAAAAAACGCAAAAACTTTTTTTTATGACGCAAAAACTCTCG
Found at i:33499 original size:33 final size:32
Alignment explanation
Indices: 33421--33510 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 32
33411 TTTTATGACG
* * *
33421 CAAAAATATATTTTTTTTTCGATGC-AAAACA
1 CAAAACTAAATTTTTTTTTCGACGCAAAAACA
***
33452 CAAAACTCTTTTTTTCTTTTTCGACGCAAAAACA
1 CAAAACT-AAATTTT-TTTTTCGACGCAAAAACA
33486 CAAAAC-AAA-TTTTTTTTCGACGCAA
1 CAAAACTAAATTTTTTTTTCGACGCAA
33511 GACTCAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
30 13 0.27
31 9 0.18
32 5 0.10
33 10 0.20
34 12 0.24
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.37
Consensus pattern (32 bp):
CAAAACTAAATTTTTTTTTCGACGCAAAAACA
Found at i:33499 original size:34 final size:32
Alignment explanation
Indices: 33431--33502 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 32
33421 CAAAAATATA
* ***
33431 TTTTTTTTTCGATGCAAAACACAAAACTCTTT
1 TTTTTTTTTCGACGCAAAACACAAAACAAATT
33463 TTTTCTTTTTCGACGCAAAAACACAAAACAAATT
1 TTTT-TTTTTCGACGC-AAAACACAAAACAAATT
33497 TTTTTT
1 TTTTTT
33503 CGACGCAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 4 0.12
33 12 0.35
34 18 0.53
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (32 bp):
TTTTTTTTTCGACGCAAAACACAAAACAAATT
Found at i:33605 original size:86 final size:88
Alignment explanation
Indices: 33462--33627 Score: 241
Period size: 86 Copynumber: 1.9 Consensus size: 88
33452 CAAAACTCTT
** *
33462 TTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTTCGACGCAAGACTCAAAA-A-AAAA
1 TTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTTCGACAAAAGACGCAAAACACAAAA
33525 ATTAA-AAACGCAAAACAAAAAGA
66 A-TAAGAAACGCAAAACAAAAAGA
**
33548 TTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTT-TTCAAAACGACGCAAAACACAAA
1 TTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTTCGACAAAA-GACGCAAAACACAAA
33612 AATAAGAAACGCAAAA
65 AATAAGAAACGCAAAA
33628 ACAATTTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
85 3 0.04
86 49 0.69
87 4 0.06
88 15 0.21
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (88 bp):
TTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTTCGACAAAAGACGCAAAACACAAAA
ATAAGAAACGCAAAACAAAAAGA
Found at i:33638 original size:86 final size:86
Alignment explanation
Indices: 33460--33646 Score: 227
Period size: 86 Copynumber: 2.2 Consensus size: 86
33450 CACAAAACTC
** *
33460 TTTTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTTCGACGCAAGACTCAAAAAAAAA
1 TTTTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTTCGACAAAAGACGCAAAAAAAAA
33525 ATTAAAAACGCAAAACAAAAA
66 ATTAAAAACGCAAAACAAAAA
** **
33546 GATTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTT-TTCAAAACGACGCAAAACACA
1 TTTTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTTCGACAAAA-GACGCAAAA-A-A
* *
33610 AAAA-TAAGAAACGCAAAA-ACAAT
63 AAAATTAA-AAACGCAAAACAAAAA
*
33633 TTTTTTTTTTTTTC
1 TTTTTTTCTTTTTC
33647 AGATAAAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
85 3 0.04
86 49 0.58
87 18 0.21
88 15 0.18
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (86 bp):
TTTTTTTCTTTTTCGACGCAAAAACACAAAACAAATTTTTTTTCGACAAAAGACGCAAAAAAAAA
ATTAAAAACGCAAAACAAAAA
Found at i:33743 original size:30 final size:30
Alignment explanation
Indices: 33709--33780 Score: 130
Period size: 29 Copynumber: 2.5 Consensus size: 30
33699 AGTCTATTTT
33709 CCTTCCCCTGGCAAAAACCAGAAAAAGTTC
1 CCTTCCCCTGGCAAAAACCAGAAAAAGTTC
33739 CCTTCCCC-GGCAAAAACCAGAAAAAGTTC
1 CCTTCCCCTGGCAAAAACCAGAAAAAGTTC
33768 CCTT-CCCTGGCAA
1 CCTTCCCCTGGCAA
33781 CGGCGCCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 3 0.07
29 30 0.73
30 8 0.20
ACGTcount: A:0.33, C:0.36, G:0.14, T:0.17
Consensus pattern (30 bp):
CCTTCCCCTGGCAAAAACCAGAAAAAGTTC
Found at i:33991 original size:16 final size:15
Alignment explanation
Indices: 33953--33994 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
33943 ACAGAGGTTG
33953 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
33968 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
33983 ACTAGAAAACAA
1 AC-AGAAAACAA
33995 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:36904 original size:50 final size:50
Alignment explanation
Indices: 36849--36992 Score: 193
Period size: 50 Copynumber: 2.9 Consensus size: 50
36839 TGAAGTTGAT
* *
36849 CGGAAGACGGTCCTTTTAAAATTGAATTGGAAGACAGTTTGAAGGAT-AA
1 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATGAA
* * *
36898 GCGGAAGACGGTCTTTTTAAGTTTGAATTGGAAGACCGTTCGAAGGATGAA
1 -CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATGAA
* * *
36949 CGGAAGATGGTCCTTTTAAGAGTAAATTGGAAGACAGTTC-AAGG
1 CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGG
36993 GAAGGCAACC
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
49 4 0.05
50 76 0.93
51 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.26
Consensus pattern (50 bp):
CGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCGAAGGATGAA
Found at i:40487 original size:16 final size:16
Alignment explanation
Indices: 40462--40494 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40452 GAGAACATGA
*
40462 TTTGAGAAAAACCTTT
1 TTTGAAAAAAACCTTT
40478 TTTGAAAAAAACCTTT
1 TTTGAAAAAAACCTTT
40494 T
1 T
40495 ATTACCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTTGAAAAAAACCTTT
Found at i:41889 original size:13 final size:13
Alignment explanation
Indices: 41871--41896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41861 TACTTAGTCG
41871 AACTTCTTCTTCT
1 AACTTCTTCTTCT
41884 AACTTCTTCTTCT
1 AACTTCTTCTTCT
41897 TTTTCCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (13 bp):
AACTTCTTCTTCT
Found at i:43917 original size:2 final size:2
Alignment explanation
Indices: 43910--43937 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43900 TAAAAATGGA
43910 AT 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 AT
43938 TCGTGCAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44412 original size:27 final size:27
Alignment explanation
Indices: 44342--44448 Score: 124
Period size: 27 Copynumber: 3.8 Consensus size: 27
44332 AACAGTAAAC
* *
44342 TGCAAATAACCAAAATGCCCCCTGGATG
1 TGCAAATGACCAAAATG-CCCCTGGACG
44370 TGCAAAATGACCAAAATGCCCCTGGACG
1 TGC-AAATGACCAAAATGCCCCTGGACG
* * *
44398 TGCAAATGACTAAAATGCCCCTGAACA
1 TGCAAATGACCAAAATGCCCCTGGACG
*
44425 TGCAAATGATCCCAAAATCCCCCT
1 TGCAAATGA--CCAAAATGCCCCT
44449 AAGTGACCCT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
27 30 0.43
28 15 0.22
29 24 0.35
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (27 bp):
TGCAAATGACCAAAATGCCCCTGGACG
Found at i:46906 original size:27 final size:27
Alignment explanation
Indices: 46867--46924 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
46857 GCTTATTAGG
46867 TTAGTTTTGGACTTACACTTGGACATT
1 TTAGTTTTGGACTTACACTTGGACATT
* * * *
46894 TTAGTTTTTGACTTGCATTTGGACCTT
1 TTAGTTTTGGACTTACACTTGGACATT
46921 TTAG
1 TTAG
46925 CCTTGGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (27 bp):
TTAGTTTTGGACTTACACTTGGACATT
Found at i:52229 original size:32 final size:32
Alignment explanation
Indices: 52080--52221 Score: 194
Period size: 32 Copynumber: 4.3 Consensus size: 32
52070 AGAAGAAGAA
52080 GTAAAATGGTAATCAGTAATCAATTAATTCAAAGG
1 GTAAAATGGTAATCAGTAATC-A--AATTCAAAGG
* *
52115 GTAGAATAGTAATCAGTAATCAAATTCAAAGG
1 GTAAAATGGTAATCAGTAATCAAATTCAAAGG
* * *
52147 GCAAAATGGTAGTCAGAAATCAAATTCAAAGG
1 GTAAAATGGTAATCAGTAATCAAATTCAAAGG
* *
52179 GTAAAATGGTAATTAGTAATCAAATTCAAAGA
1 GTAAAATGGTAATCAGTAATCAAATTCAAAGG
52211 GTAAAATGGTA
1 GTAAAATGGTA
52222 GTTAGTAACT
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
32 75 0.79
34 1 0.01
35 19 0.20
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (32 bp):
GTAAAATGGTAATCAGTAATCAAATTCAAAGG
Found at i:52246 original size:32 final size:32
Alignment explanation
Indices: 52078--52254 Score: 142
Period size: 32 Copynumber: 5.4 Consensus size: 32
52068 GAAGAAGAAG
*
52078 AAGTAAAATGGTAATCAGTAATCAATTAATTCAAA
1 AAGTAAAATGGTAATTAGTAATC-A--AATTCAAA
** * * *
52113 GGGTAGAATAGTAATCAGTAATCAAATTCAAA
1 AAGTAAAATGGTAATTAGTAATCAAATTCAAA
** * * * *
52145 GGGCAAAATGGTAGTCAGAAATCAAATTCAAA
1 AAGTAAAATGGTAATTAGTAATCAAATTCAAA
**
52177 GGGTAAAATGGTAATTAGTAATCAAATTCAAA
1 AAGTAAAATGGTAATTAGTAATCAAATTCAAA
* * *
52209 GAGTAAAATGGTAGTTAGTAA-CTAAGGTT-AAA
1 AAGTAAAATGGTAATTAGTAATC-AA-ATTCAAA
52241 AAGTAAAATGGTAA
1 AAGTAAAATGGTAA
52255 CGGTAATCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
31 1 0.01
32 99 0.81
33 2 0.02
34 1 0.01
35 19 0.16
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.25
Consensus pattern (32 bp):
AAGTAAAATGGTAATTAGTAATCAAATTCAAA
Found at i:52247 original size:64 final size:64
Alignment explanation
Indices: 52082--52264 Score: 165
Period size: 64 Copynumber: 2.8 Consensus size: 64
52072 AAGAAGAAGT
* * ** * * *
52082 AAAATGGTAATCAGTAATCAATTAATTCAAAGGGTAGAATAGTAATCAGTAATCAAATTCAAAGG
1 AAAATGGTAGTCAGAAATC-A--AATTCAAAAAGTAAAATGGTAATCAGTAATCAAATTCAAAGA
52147 GC
63 GC
** * *
52149 AAAATGGTAGTCAGAAATCAAATTCAAAGGGTAAAATGGTAATTAGTAATCAAATTCAAAGAGT
1 AAAATGGTAGTCAGAAATCAAATTCAAAAAGTAAAATGGTAATCAGTAATCAAATTCAAAGAGC
* * * *
52213 AAAATGGTAGTTAGTAA-CTAAGGTT-AAAAAGTAAAATGGTAA-CGGTAATCAA
1 AAAATGGTAGTCAGAAATC-AA-ATTCAAAAAGTAAAATGGTAATCAGTAATCAA
52265 TAAAGAGTAA
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
63 9 0.09
64 71 0.71
65 2 0.02
66 1 0.01
67 17 0.17
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (64 bp):
AAAATGGTAGTCAGAAATCAAATTCAAAAAGTAAAATGGTAATCAGTAATCAAATTCAAAGAGC
Found at i:52289 original size:42 final size:40
Alignment explanation
Indices: 52239--52440 Score: 269
Period size: 42 Copynumber: 4.9 Consensus size: 40
52229 ACTAAGGTTA
*
52239 AAAAGTAAAATGGTAACGGTAATCAATAAAGAGTAAAGAGT
1 AAAAGTAAAATGGTAA-GGTAATCAGTAAAGAGTAAAGAGT
52280 AAAAGGTAAAATGGTAATGGTAATCAGTAAAGAGTAAAGAGT
1 AAAA-GTAAAATGGTAA-GGTAATCAGTAAAGAGTAAAGAGT
* * *
52322 AATCAGTAAAATGGTAATGAAATCAGTAAAGAGTAAAGAGT
1 AA-AAGTAAAATGGTAAGGTAATCAGTAAAGAGTAAAGAGT
*
52363 AAAAGGTAAAATGGTAATGGTAATCAGTAAAGAATAAAGAGT
1 AAAA-GTAAAATGGTAA-GGTAATCAGTAAAGAGTAAAGAGT
* * *
52405 AATCAGTAAAATGGTAATGAAATCAGTAAAGAGTAA
1 AA-AAGTAAAATGGTAAGGTAATCAGTAAAGAGTAA
52441 TCAATAAAAA
Statistics
Matches: 143, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
40 1 0.01
41 56 0.39
42 84 0.59
43 2 0.01
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.21
Consensus pattern (40 bp):
AAAAGTAAAATGGTAAGGTAATCAGTAAAGAGTAAAGAGT
Found at i:52455 original size:83 final size:83
Alignment explanation
Indices: 52242--52440 Score: 353
Period size: 83 Copynumber: 2.4 Consensus size: 83
52232 AAGGTTAAAA
* * *
52242 AGTAAAATGGTAACGGTAATCAATAAAGAGTAAAGAGTAAAAGGTAAAATGGTAATGGTAATCAG
1 AGTAAAATGGTAA-TGAAATCAGTAAAGAGTAAAGAGTAAAAGGTAAAATGGTAATGGTAATCAG
*
52307 TAAAGAGTAAAGAGTAATC
65 TAAAGAATAAAGAGTAATC
52326 AGTAAAATGGTAATGAAATCAGTAAAGAGTAAAGAGTAAAAGGTAAAATGGTAATGGTAATCAGT
1 AGTAAAATGGTAATGAAATCAGTAAAGAGTAAAGAGTAAAAGGTAAAATGGTAATGGTAATCAGT
52391 AAAGAATAAAGAGTAATC
66 AAAGAATAAAGAGTAATC
52409 AGTAAAATGGTAATGAAATCAGTAAAGAGTAA
1 AGTAAAATGGTAATGAAATCAGTAAAGAGTAA
52441 TCAATAAAAA
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 98 0.88
84 13 0.12
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (83 bp):
AGTAAAATGGTAATGAAATCAGTAAAGAGTAAAGAGTAAAAGGTAAAATGGTAATGGTAATCAGT
AAAGAATAAAGAGTAATC
Found at i:52475 original size:83 final size:82
Alignment explanation
Indices: 52242--52505 Score: 260
Period size: 83 Copynumber: 3.2 Consensus size: 82
52232 AAGGTTAAAA
* * * * * * * * *
52242 AGTAAAATGGTAACGGTAATCAATAAAGAGTAAAGAGTAAAAGGTAAAATGGTAATGGTAATCAG
1 AGTAAAATGGTAA-TGAAATCAGTAAAGAGTAAACAATAAAAAGTAAAA-GGCAATAGTAAACAG
*
52307 TAAAGAGTAAAGAGTAATC
64 TAAAGAATAAAGAGTAATC
* * * * * *
52326 AGTAAAATGGTAATGAAATCAGTAAAGAGTAAAGAGTAAAAGGTAAAATGGTAATGGTAATCAGT
1 AGTAAAATGGTAATGAAATCAGTAAAGAGTAAACAATAAAAAGTAAAA-GGCAATAGTAAACAGT
52391 AAAGAATAAAGAGTAATC
65 AAAGAATAAAGAGTAATC
* *
52409 AGTAAAATGGTAATGAAATCAGTAAAGAGTAATCAATAAAAAGT-AAAGAGCAATCAGTAAAGAG
1 AGTAAAATGGTAATGAAATCAGTAAAGAGTAAACAATAAAAAGTAAAAG-GCAAT-AGTAAACAG
* ** ** *
52473 TAAAGATTAATTAGTTTTG
64 TAAAGAATAAAGAGTAATC
52492 AGTAAAATGGTAAT
1 AGTAAAATGGTAAT
52506 CAGTAATTAA
Statistics
Matches: 160, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
81 1 0.01
82 7 0.04
83 139 0.87
84 13 0.08
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.23
Consensus pattern (82 bp):
AGTAAAATGGTAATGAAATCAGTAAAGAGTAAACAATAAAAAGTAAAAGGCAATAGTAAACAGTA
AAGAATAAAGAGTAATC
Found at i:57138 original size:21 final size:21
Alignment explanation
Indices: 57099--57147 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
57089 TCAATGCTTT
** *
57099 AGGAATGCAAGAGGGATTTCGA
1 AGGAA-GCAAGAGCCATTTCCA
57121 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCCA
57142 A-GAAGC
1 AGGAAGC
57148 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.39, C:0.16, G:0.31, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCCA
Done.