Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009207.1 Hibiscus syriacus cultivar Beakdansim tig00112793_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 66797
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1198 original size:18 final size:18
Alignment explanation
Indices: 1155--1192 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1145 AAGGAGCTTA
1155 CTCGATCTAATCTGTACT
1 CTCGATCTAATCTGTACT
1173 CTCGATCTAATCTGTACT
1 CTCGATCTAATCTGTACT
1191 CT
1 CT
1193 GTATCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (18 bp):
CTCGATCTAATCTGTACT
Found at i:5101 original size:24 final size:24
Alignment explanation
Indices: 5019--5106 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
5009 ATTTCCGACT
*
5019 TGAATTCTGTTCTGATA-CATTACC
1 TGAATTCTGTTCTGATATC-TTATC
* *
5043 TGAATTCTGTTCTGATTTCTTATA
1 TGAATTCTGTTCTGATATCTTATC
* * *
5067 TGGATTTTGTTCTGATATCTGATC
1 TGAATTCTGTTCTGATATCTTATC
*
5091 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
5107 TTATGATATC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 51 0.98
25 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTTATC
Found at i:8123 original size:182 final size:180
Alignment explanation
Indices: 7809--8459 Score: 852
Period size: 182 Copynumber: 3.5 Consensus size: 180
7799 GTCAAGAGAT
* * * * *
7809 AATTTGAGGACAATACGGTTCTTTCGTGATGAGGAAGTTTGATTGTTTGAGGGTGACATTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
* *
7874 TTCGTGATTAGGAGATCGGGTCGGTTTGATGTTGAAGACGACACTGCTCATCTGCGATGAAGAGA
66 TTCGTGATGAGGAGATCGGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
**
7939 TCGGGTTATTTTTTATTATGAGGTTGTTCCTTCGTGATGAGGAATTCGGGCC
131 TCGGGTTATTTTCAATTATGA-GTTGTTCCTTCGTGATGAGGAA-TCGGGCC
*
7991 AATCTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
* *
8056 TTCGTGATGAGGAGATCGGGTCGGTTTGATGTTGAAGACGATACTGCTCATCCGCGATAAAGAGA
66 TTCGTGATGAGGAGATCGGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
* * * *
8121 TCGGGTTATTTTCAATTATGACGTTGTTTCTTCTTGATGAGGGAATCAGGTC
131 TCGGGTTATTTTCAATTATGA-GTTGTTCCTTCGTGATGA-GGAATCGGGCC
* * * * * * *
8173 AATTTGAGGATAATATGTTTCCTTCGTGATGAGAAAGTTTGATTGTCTGAGGGTGACGCTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
* *
8238 TTCGTGATGAGGAGATCTGGTCGATTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
66 TTCGTGATGAGGAGATCGGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
* * *
8303 TCGGGTCATTTTCGATTATGAATCTGTTCCTTCGTGATGAGGAAATCGGGTCAATC
131 TCGGGTTATTTTCAATTATGAGT-TGTTCCTTCGTGATGAGG-AATCGGG-C---C
* * *
8359 AAGAGATAATTTGGGGACAATACGGTTCCTTCGTGATTAGGAAGTCTGATTATCTGAGAGTGACA
1 -------AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACA
* *
8424 CTGCTCTTTCGTGATGAGGAGATCTGGTCGGTTTGA
59 CTGCTCCTTCGTGATGAGGAGATCGGGTCGGTTTGA
8460 AATTCAACTG
Statistics
Matches: 407, Mismatches: 48, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
181 3 0.01
182 317 0.78
183 4 0.01
186 1 0.00
193 82 0.20
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (180 bp):
AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
TTCGTGATGAGGAGATCGGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
TCGGGTTATTTTCAATTATGAGTTGTTCCTTCGTGATGAGGAATCGGGCC
Found at i:8376 original size:375 final size:378
Alignment explanation
Indices: 7578--8459 Score: 1247
Period size: 375 Copynumber: 2.4 Consensus size: 378
7568 CTGCTCACGA
* **
7578 TGTTCCTTCGTGATGAGGAAATCTGGTCAATCAAGAGATAATTTGGGG-CAATACGGTTCCTTTA
1 TGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATACGGTTCCTTCG
*
7642 TGATGAGGAAGTCTGATTGCCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGTT
66 TGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGTT
* *
7707 TGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCATTTTCGATTATGACGATG
131 TGATGTTGAAGACGACACTGCTCATCCGCGATAAAGAGATCGGGTCATTTTCAATTATGACGATG
* *
7772 TTCCTTCGTGATGAGGAAATCGGGTCAGTCAAGAGATAATTTGAGGACAATACGGTTCTTTCGTG
196 TTCCTTCGTGATGAGGAAATCGAG--AGTC-----A-AATTTGAGGACAATACGGTTCCTTCGTG
* * * * *
7837 ATGAGGAAGTTTGATTGTTTGAGGGTGACATTGCTCCTTCGTGATTAGGAGATCGGGTCGGTTTG
253 ATGAGAAAGTTTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCGGGTCGATTTG
* * ** *
7902 ATGTTGAAGACGACACTGCTCATCTGCGATGAAGAGATCGGGTTATTTTTTATTATGAGGT
318 ATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCATTTTCGATTATGAGAT
* *
7963 TGTTCCTTCGTGATGAGGAATTCGGG-C---C-------AATCTGGGGACAATACGGTTCCTTCG
1 TGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATACGGTTCCTTCG
*
8017 TGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCGGGTCGGTT
66 TGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGTT
* * *
8082 TGATGTTGAAGACGATACTGCTCATCCGCGATAAAGAGATCGGGTTATTTTCAATTATGACGTTG
131 TGATGTTGAAGACGACACTGCTCATCCGCGATAAAGAGATCGGGTCATTTTCAATTATGACGATG
* * * * * *
8147 TTTCTTCTTGATGAGGGAATC-AG-GTC-AATTTGAGGATAATATGTTTCCTTCGTGATGAGAAA
196 TTCCTTCGTGATGAGGAAATCGAGAGTCAAATTTGAGGACAATACGGTTCCTTCGTGATGAGAAA
* *
8209 GTTTGATTGTCTGAGGGTGACGCTGCTCCTTCGTGATGAGGAGATCTGGTCGATTTGATGTTGAA
261 GTTTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCGGGTCGATTTGATGTTGAA
8274 GACGACACTGCTCATCCGCGATGAAGAGATCGGGTCATTTTCGATTATGA-AT
326 GACGACACTGCTCATCCGCGATGAAGAGATCGGGTCATTTTCGATTATGAGAT
8326 CTGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATACGGTTCCTTC
1 -TGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATACGGTTCCTTC
* * * *
8391 GTGATTAGGAAGTCTGATTATCTGAGAGTGACACTGCTCTTTCGTGATGAGGAGATCTGGTCGGT
65 GTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGT
8456 TTGA
130 TTGA
8460 AATTCAACTG
Statistics
Matches: 445, Mismatches: 39, Indels: 36
0.86 0.08 0.07
Matches are distributed among these distances:
363 1 0.00
364 161 0.36
365 1 0.00
368 1 0.00
371 3 0.01
374 9 0.02
375 243 0.55
381 1 0.00
384 1 0.00
385 24 0.05
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (378 bp):
TGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGGACAATACGGTTCCTTCG
TGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGGTCGGTT
TGATGTTGAAGACGACACTGCTCATCCGCGATAAAGAGATCGGGTCATTTTCAATTATGACGATG
TTCCTTCGTGATGAGGAAATCGAGAGTCAAATTTGAGGACAATACGGTTCCTTCGTGATGAGAAA
GTTTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCGGGTCGATTTGATGTTGAA
GACGACACTGCTCATCCGCGATGAAGAGATCGGGTCATTTTCGATTATGAGAT
Found at i:8790 original size:84 final size:83
Alignment explanation
Indices: 8654--8890 Score: 269
Period size: 84 Copynumber: 2.8 Consensus size: 83
8644 GTCATCGTGT
* * * * *
8654 TGAATGGAATCAAACTCGAAGGTGTTCGTTGACGGATAACCCTTCTCGCCTTGAGTTATGTTGTA
1 TGAAT-GAATCGAACTTGAAGGT-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTA
*
8719 GATTTGACATG-TCCTTGAGC
64 AATTTGACATGCT-CTTGAGC
* *
8739 TGAATAGAATCGAACTTGAAGGTTTGGTTGACAGATAACCCTTATCACCTTGAGTTATGCTGTAA
1 TGAAT-GAATCGAACTTGAAGGTTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAA
** *
8804 ATTTGGTATGCTTTTGAGC
65 ATTTGACATGCTCTTGAGC
* * * * *
8823 TGAGTGTAGTCGAGCTTGAAGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
1 TGAATG-AATCGAACTTGAAGG-TTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTA
8888 AAT
64 AAT
8891 AGTTCCTTTA
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
83 1 0.01
84 67 0.52
85 62 0.48
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (83 bp):
TGAATGAATCGAACTTGAAGGTTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
TTTGACATGCTCTTGAGC
Found at i:9454 original size:32 final size:32
Alignment explanation
Indices: 9413--9532 Score: 177
Period size: 32 Copynumber: 3.8 Consensus size: 32
9403 TTCGCATCAG
* *
9413 GATGTTGAATCCCCAAAGATGCCCCAATATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTT
* *
9445 GATGTTGAATCTCCAAATATGCCCTAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTT
* *
9477 GATGTTGAATCTTCAAAGATGCACCAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTT
*
9509 GATGTTGAATCTTCAAAGATGCCC
1 GATGTTGAATCTCCAAAGATGCCC
9533 TCTATTGTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 79 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTT
Found at i:14093 original size:63 final size:63
Alignment explanation
Indices: 14014--14194 Score: 290
Period size: 63 Copynumber: 2.9 Consensus size: 63
14004 TATGATGATC
* * * *
14014 ATGCGAACATGCAAATACATATATAAAAGTGATGATCCTTTGACATGCAATGCATTATGCAGA
1 ATGCGAAAATGCAAATACAGATGTAAAATTGATGATCCTTTGACATGCAATGCATTATGCAGA
*
14077 ATGCGAAAATGCAAATACAGATGCAAAATTGATGATCCTTTGACATGCAATGCATTATGCAGA
1 ATGCGAAAATGCAAATACAGATGTAAAATTGATGATCCTTTGACATGCAATGCATTATGCAGA
* *
14140 ATGCGAAAATGCAAAATGCAGATGTAAAATTGATGATCCTTTGAAATGCAATGCA
1 ATGCGAAAATGC-AAATACAGATGTAAAATTGATGATCCTTTGACATGCAATGCA
14195 ACAAGGACGA
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 70 0.64
64 39 0.36
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (63 bp):
ATGCGAAAATGCAAATACAGATGTAAAATTGATGATCCTTTGACATGCAATGCATTATGCAGA
Found at i:15599 original size:16 final size:16
Alignment explanation
Indices: 15580--15610 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15570 TTGAAAAAGT
15580 AAAATAAAATAAAAAC
1 AAAATAAAATAAAAAC
*
15596 AAAATGAAATAAAAA
1 AAAATAAAATAAAAA
15611 TGAAAAGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAATAAAATAAAAAC
Found at i:15988 original size:21 final size:20
Alignment explanation
Indices: 15961--16058 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
15951 AATCAGTGTC
15961 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
15982 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
16002 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
16022 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
16043 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
16059 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:16011 original size:41 final size:41
Alignment explanation
Indices: 15902--16058 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
15892 AAATGACCAA
* **
15902 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
15941 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
15982 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
16023 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
16059 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:16068 original size:20 final size:20
Alignment explanation
Indices: 16045--16215 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
16035 GCGAATATGA
16045 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
16065 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
16085 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
16105 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
16125 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
16145 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
16165 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
16185 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
16205 AAATCGCAACG
1 AAATCGCAACG
16216 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:16110 original size:60 final size:58
Alignment explanation
Indices: 16025--16234 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
16015 CGATTTTCCA
* ** * *
16025 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
16085 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
16145 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
16205 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
16235 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:16216 original size:20 final size:20
Alignment explanation
Indices: 16079--16234 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
16069 CGCAATGCGT
*
16079 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
16099 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
16119 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
16139 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
16159 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
16179 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
16199 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
16219 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
16235 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:16216 original size:40 final size:40
Alignment explanation
Indices: 16045--16234 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
16035 GCGAATATGA
* *
16045 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
16085 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
16125 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
16165 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
16205 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
16235 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:16955 original size:24 final size:24
Alignment explanation
Indices: 16916--16962 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16906 AAATTTGGTC
16916 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
16940 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
16963 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:17153 original size:12 final size:12
Alignment explanation
Indices: 17136--17160 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17126 ATATAATCCT
17136 GAAGAAGAAAAA
1 GAAGAAGAAAAA
17148 GAAGAAGAAAAA
1 GAAGAAGAAAAA
17160 G
1 G
17161 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:19462 original size:19 final size:19
Alignment explanation
Indices: 19440--19694 Score: 272
Period size: 19 Copynumber: 14.7 Consensus size: 19
19430 CGGAAATTAC
*
19440 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
19459 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
19473 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
19493 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
19507 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
19526 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
19545 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
19559 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
19578 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
19597 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
19616 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
19630 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
19649 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
19663 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
19682 AATCGCATTGCGA
1 AATCGCAATGCGA
19695 TTTTCATTTC
Statistics
Matches: 201, Mismatches: 9, Indels: 52
0.77 0.03 0.20
Matches are distributed among these distances:
14 50 0.25
15 3 0.01
16 13 0.06
17 12 0.06
18 4 0.02
19 106 0.53
20 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:19492 original size:34 final size:33
Alignment explanation
Indices: 19440--19529 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 33
19430 CGGAAATTAC
*
19440 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAA
* *
19473 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAA
19507 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
19530 GCAATGCGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 22 0.42
34 29 0.56
35 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAA
Found at i:19527 original size:33 final size:33
Alignment explanation
Indices: 19440--19604 Score: 158
Period size: 33 Copynumber: 4.8 Consensus size: 33
19430 CGGAAATTAC
* *
19440 AATCGCAACGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAA
*
19473 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAAC-ATGAA
19507 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATGAA
* * *
19545 AATCGCAACGAGAGAATCG-CAAT-GCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGC-AACATGAA
19578 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
19605 TGCGAAATGA
Statistics
Matches: 109, Mismatches: 11, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
31 1 0.01
32 8 0.07
33 44 0.40
34 29 0.27
35 2 0.02
37 1 0.01
38 15 0.14
39 8 0.07
40 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAA
Found at i:19555 original size:52 final size:52
Alignment explanation
Indices: 19468--19694 Score: 347
Period size: 52 Copynumber: 4.3 Consensus size: 52
19458 AAATCCCAAC
19468 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
19521 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
19573 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
19628 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
19677 ATGAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
19695 TTTTCATTTC
Statistics
Matches: 161, Mismatches: 3, Indels: 21
0.87 0.02 0.11
Matches are distributed among these distances:
47 10 0.06
48 1 0.01
49 5 0.03
50 3 0.02
52 107 0.66
53 16 0.10
54 3 0.02
55 5 0.03
56 1 0.01
57 10 0.06
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:19591 original size:71 final size:71
Alignment explanation
Indices: 19507--19688 Score: 311
Period size: 71 Copynumber: 2.6 Consensus size: 71
19497 GCAACGAGAG
*
19507 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
19572 AATGAA
66 AATGAA
19578 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
19643 AATGAA
66 AATGAA
*
19649 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
19689 TTGCGATTTT
Statistics
Matches: 109, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
66 28 0.26
67 1 0.01
69 2 0.02
71 78 0.72
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:19634 original size:33 final size:33
Alignment explanation
Indices: 19526--19688 Score: 263
Period size: 33 Copynumber: 4.8 Consensus size: 33
19516 GCGAAATGAA
*
19526 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
19559 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
19595 AAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 --AATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
19630 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
19663 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
19689 TTGCGATTTT
Statistics
Matches: 123, Mismatches: 2, Indels: 10
0.91 0.01 0.07
Matches are distributed among these distances:
33 85 0.69
35 5 0.04
36 6 0.05
38 27 0.22
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:19794 original size:19 final size:19
Alignment explanation
Indices: 19684--19786 Score: 144
Period size: 19 Copynumber: 5.6 Consensus size: 19
19674 GAAATGAAAA
19684 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
19703 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
19723 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
19739 TCG--TTGCGAATTTCATT
1 TCGCATTGCGATTTTCATT
19756 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
19775 TCGCATTGCGAT
1 TCGCATTGCGAT
19787 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:19912 original size:14 final size:14
Alignment explanation
Indices: 19893--19929 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19883 CATCAATTAC
19893 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
19907 ACAAATCATCTTTT
1 ACAAATCAACTTTT
19921 ACAAATCAA
1 ACAAATCAA
19930 TTAAATAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:21917 original size:14 final size:14
Alignment explanation
Indices: 21898--21954 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21888 GCGAAATGAA
*
21898 AATCGCAACGACAG
1 AATCGCAACGAAAG
21912 AATCGCAATACGAAATG
1 AATCGC-A-ACGAAA-G
21929 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
21945 AATCGCAACG
1 AATCGCAACG
21955 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
15 1 0.03
16 6 0.16
17 7 0.19
18 1 0.03
19 6 0.16
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:21926 original size:33 final size:33
Alignment explanation
Indices: 21879--21971 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
21869 GCGAAACCAA
*
21879 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
21912 AATCGCAATACGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
21945 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
21972 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:21976 original size:19 final size:19
Alignment explanation
Indices: 21842--21976 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
21832 TAGTTTACTT
* *
21842 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
21862 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
21881 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
21900 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
**
21914 TCGCAATACGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
21933 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
21947 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
21966 TCGCAATGCGA
1 TCGCAACGCGA
21977 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:21994 original size:19 final size:19
Alignment explanation
Indices: 21972--22030 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
21962 AAAATCGCAA
21972 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
21991 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
22005 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
22024 TGCGATT
1 TGCGATT
22031 CTCTCGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.07, C:0.17, G:0.31, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:22040 original size:14 final size:14
Alignment explanation
Indices: 22021--22077 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
22011 TTTGGTTTCG
22021 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
22035 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
22054 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
22068 CGTTGCGATT
1 CGTTGCGATT
22078 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:22059 original size:19 final size:19
Alignment explanation
Indices: 22002--22123 Score: 84
Period size: 19 Copynumber: 6.9 Consensus size: 19
21992 GCGATCTTGT
**
22002 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTCATTTCG
*
22021 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
22035 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
22054 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
22068 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
22087 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
22107 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
22124 ATCTCGTTGC
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
14 20 0.25
16 5 0.06
17 5 0.06
19 35 0.44
20 15 0.19
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:22086 original size:66 final size:70
Alignment explanation
Indices: 21972--22142 Score: 190
Period size: 66 Copynumber: 2.4 Consensus size: 70
21962 AAAATCGCAA
** * * **
21972 TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGTTGCGATTTTGGTTTCGCGTT-G-C-G-ATTCT
1 TGCGATTTTCATTTCGCGTTGCGATCTTCTCGTTGCGATTGTCATTTCGCGTTCGACAGCATTCT
22033 CTCGT
66 CTCGT
22038 TGCGATTTTCATTTCGCGTTGCGAT-TCTCTCGTTGCGATTGTCATTTCGCGTTGCGACAGTCAT
1 TGCGATTTTCATTTCGCGTTGCGATCT-TCTCGTTGCGATTGTCATTTCGCGTT-CGACAG-CAT
22102 TCTCTCGT
63 TCTCTCGT
*
22110 TGCGATTTTCATTTATCTCGTTGCGACTCTTCT
1 TGCGATTTTCA-TT-TCGCGTTGCGA-TCTTCT
22143 GCAAATTGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
65 1 0.01
66 45 0.52
68 1 0.01
69 1 0.01
70 1 0.01
72 21 0.24
73 2 0.02
74 10 0.11
75 4 0.05
76 1 0.01
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.44
Consensus pattern (70 bp):
TGCGATTTTCATTTCGCGTTGCGATCTTCTCGTTGCGATTGTCATTTCGCGTTCGACAGCATTCT
CTCGT
Found at i:22115 original size:39 final size:33
Alignment explanation
Indices: 21972--22123 Score: 180
Period size: 33 Copynumber: 4.4 Consensus size: 33
21962 AAAATCGCAA
** *
21972 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTC-TCTCGT
**
22005 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
22038 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
22071 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
22110 TGCGATTTTCATTT
1 TGCGATTTTCATTT
22124 ATCTCGTTGC
Statistics
Matches: 107, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
33 79 0.74
34 2 0.02
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.21
ACGTcount: A:0.09, C:0.22, G:0.24, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:22257 original size:33 final size:33
Alignment explanation
Indices: 22215--22285 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
22205 AATACTAACT
22215 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
22248 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
22281 TGAAA
1 TGAAA
22286 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:22519 original size:22 final size:22
Alignment explanation
Indices: 22467--22521 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
22457 TGGTTGTGAG
**
22467 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
22489 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
22511 GGATTTCTTCG
1 GGATTTCTTCG
22522 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:22693 original size:20 final size:20
Alignment explanation
Indices: 22668--22861 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
22658 CTTTAAATAT
22668 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
22688 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
22710 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
* *
22729 CGCGTTGCGATATACAGATA
1 CGCGTTGCGATTTACGGATA
* **
22749 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
22769 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22789 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
22809 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
22829 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
22849 CGCGTTGCGATTT
1 CGCGTTGCGATTT
22862 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:22855 original size:60 final size:60
Alignment explanation
Indices: 22668--22861 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
22658 CTTTAAATAT
* ** *
22668 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* * *** * *
22729 CGCGTTGCGATATACAGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
22789 CACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
22849 CGCGTTGCGATTT
1 CGCGTTGCGATTT
22862 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:23360 original size:28 final size:29
Alignment explanation
Indices: 23290--23389 Score: 130
Period size: 29 Copynumber: 3.5 Consensus size: 29
23280 ACCGTTGACC
* *
23290 GGTGCTATTCTGGTAAATAATTTGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGATTTT
23319 GGTGCTATTCTGGTAAATAATTCGATTTT
1 GGTGCTATTCTGGTAAATAATTCGATTTT
* ** *
23348 -GTGCTATTCTGGTAATTAATTCGAAATG
1 GGTGCTATTCTGGTAAATAATTCGATTTT
*
23376 GGTGCTATTTTGGT
1 GGTGCTATTCTGGT
23390 GATTATTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
28 24 0.38
29 39 0.62
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGATTTT
Found at i:23394 original size:29 final size:29
Alignment explanation
Indices: 23348--23414 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
23338 ATTCGATTTT
* * *
23348 GTGCTATTCTGGTAATTAATTCGAAATGG
1 GTGCTATTTTGGTAATTAATTCAAAAAGG
* * *
23377 GTGCTATTTTGGTGATTATTTTAAAAAGG
1 GTGCTATTTTGGTAATTAATTCAAAAAGG
23406 GTGCTATTT
1 GTGCTATTT
23415 GTGTAAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.43
Consensus pattern (29 bp):
GTGCTATTTTGGTAATTAATTCAAAAAGG
Found at i:30658 original size:18 final size:18
Alignment explanation
Indices: 30635--30673 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
30625 TGACCGGTCA
30635 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
30653 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
30671 CGA
1 CGA
30674 TCGTTGACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.10
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:30732 original size:29 final size:29
Alignment explanation
Indices: 30690--30772 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
30680 ACCGTTGATC
30690 GGTGCTATTCTGGTAAATAATTC-AGTTTT
1 GGTGCTATTCTGGTAAATAATTCGA-TTTT
*
30719 GGTGCTATTTTGGTAAATAATTCGATTTT
1 GGTGCTATTCTGGTAAATAATTCGATTTT
*
30748 GGTGCTATTCTGGTAATTAATTCGA
1 GGTGCTATTCTGGTAAATAATTCGA
30773 AATGGGCTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 49 0.98
30 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGATTTT
Found at i:36480 original size:1 final size:1
Alignment explanation
Indices: 36474--36512 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
36464 GGCATTCATC
36474 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
36513 GATAGGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47790 original size:19 final size:19
Alignment explanation
Indices: 47748--47792 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
47738 CCCTTTAAAA
* *
47748 TATATAATTTAAAATTAAT
1 TATATAATATAAAAATAAT
47767 TATATAATATAAAAAT-AT
1 TATATAATATAAAAATAAT
47785 TGATATAA
1 T-ATATAA
47793 GTTTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TATATAATATAAAAATAAT
Found at i:48313 original size:15 final size:15
Alignment explanation
Indices: 48293--48340 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
48283 ACATTACCCA
48293 CCCCGCATCCGCCCG
1 CCCCGCATCCGCCCG
*
48308 CCCCGCATCCGCCTG
1 CCCCGCATCCGCCCG
* *
48323 CCCCACATCCGCTCG
1 CCCCGCATCCGCCCG
48338 CCC
1 CCC
48341 AGCTAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.08, C:0.65, G:0.17, T:0.10
Consensus pattern (15 bp):
CCCCGCATCCGCCCG
Found at i:49207 original size:2 final size:2
Alignment explanation
Indices: 49200--49226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49190 ATCACATGGT
49200 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
49227 CATTATACAT
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:51592 original size:33 final size:33
Alignment explanation
Indices: 51545--51648 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
51535 ACAAAGTTTA
* *
51545 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
51577 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
51610 CGATAAATTCAAATACTTAAAAACTTACAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
51643 CGATAA
1 CGATAA
51649 TTGAAACAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 4 0.06
33 64 0.94
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:51668 original size:21 final size:21
Alignment explanation
Indices: 51643--51684 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
51633 CTTACAAGTT
51643 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
51664 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
51685 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:57956 original size:13 final size:13
Alignment explanation
Indices: 57938--57962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57928 TCCTACATTG
57938 GTAGGATAACAAT
1 GTAGGATAACAAT
57951 GTAGGATAACAA
1 GTAGGATAACAA
57963 ACATGGGAAT
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:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (13 bp):
GTAGGATAACAAT
Found at i:58662 original size:21 final size:21
Alignment explanation
Indices: 58619--58666 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
58609 AATCGAGGAA
58619 AAAAATAAAAAAAACGTACCAC
1 AAAAATAAAAAAAACGTA-CAC
*
58641 AAAAATAAAAAAACATGT-CAC
1 AAAAATAAAAAAA-ACGTACAC
58662 AAAAA
1 AAAAA
58667 CATATCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 13 0.54
23 3 0.12
ACGTcount: A:0.71, C:0.15, G:0.04, T:0.10
Consensus pattern (21 bp):
AAAAATAAAAAAAACGTACAC
Found at i:60488 original size:19 final size:20
Alignment explanation
Indices: 60460--60501 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
60450 TAGAATTATT
*
60460 ATAATATTTTAAAATTAATA
1 ATAATATTTTAAAATAAATA
*
60480 ATAAT-TTTTATAATAAATA
1 ATAATATTTTAAAATAAATA
60499 ATA
1 ATA
60502 TTAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATATTTTAAAATAAATA
Found at i:63335 original size:99 final size:101
Alignment explanation
Indices: 63163--63362 Score: 386
Period size: 100 Copynumber: 2.0 Consensus size: 101
63153 ATTCAAAGAA
63163 AATTTAAAGCTTTCATTAAAGTAAAAGCAGTTTAGTTACATAATTTGACCACAATAACCAAAATC
1 AATTTAAAGCTTTCATTAAAGTAAAAGCAGTTTAGTTACATAATTTGACCACAATAACCAAAATC
63228 GATCAGAG-CATATTTAACTCAATCAATTAGTACAT
66 GATCAGAGCCATATTTAACTCAATCAATTAGTACAT
63263 AATTTAAAGCTTTCATTAAAGTAAAAGCAGTTTAG-TACATAATTTGACCACAATAACCAAAATC
1 AATTTAAAGCTTTCATTAAAGTAAAAGCAGTTTAGTTACATAATTTGACCACAATAACCAAAATC
63327 GATCAGAGCCATATTTAACTCAATCAATTAGTACAT
66 GATCAGAGCCATATTTAACTCAATCAATTAGTACAT
63363 GCCAACTATA
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
99 37 0.37
100 62 0.63
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (101 bp):
AATTTAAAGCTTTCATTAAAGTAAAAGCAGTTTAGTTACATAATTTGACCACAATAACCAAAATC
GATCAGAGCCATATTTAACTCAATCAATTAGTACAT
Found at i:64058 original size:23 final size:23
Alignment explanation
Indices: 64032--64100 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
64022 CACCACAGCT
*
64032 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
64055 CGTAGAATTGCAACGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
64078 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
64101 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:64639 original size:13 final size:13
Alignment explanation
Indices: 64621--64652 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
64611 TACTAGCAAC
64621 TTAAACGAACTTA
1 TTAAACGAACTTA
64634 TTAAACGAACTTA
1 TTAAACGAACTTA
64647 TTAAAC
1 TTAAAC
64653 CCATATTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (13 bp):
TTAAACGAACTTA
Found at i:65840 original size:23 final size:23
Alignment explanation
Indices: 65814--65882 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
65804 GTCACCACAG
*
65814 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
65837 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
65860 CTTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
65883 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:66062 original size:20 final size:21
Alignment explanation
Indices: 66037--66086 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
66027 ATTTCACATT
*
66037 TTCACATAAACACGTAG-TTC
1 TTCACATAAACACGTAGATTA
*
66057 TTCACAT-AGCACGTAGATTA
1 TTCACATAAACACGTAGATTA
66077 TGTCACATAA
1 T-TCACATAA
66087 GTTGAATCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 8 0.32
20 10 0.40
21 6 0.24
22 1 0.04
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (21 bp):
TTCACATAAACACGTAGATTA
Done.