Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009284.1 Hibiscus syriacus cultivar Beakdansim tig00112971_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: 142908
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2221 original size:59 final size:58
Alignment explanation
Indices: 2073--2249 Score: 170
Period size: 59 Copynumber: 3.1 Consensus size: 58
2063 ATCCTTAAAG
* *
2073 TATGACATTCATTTTAAATTAGT-CCCTAA-TTTTTACATATTTCAATTTC-TCCCTAAAC
1 TATGACATTCATTATAAATTA-TCCCCAAACTTTTTA-ATATTTCAATTTCATCCC-AAAC
* * * * *
2131 TAT--TA-TCATTCTAAATTAATCCTCAAACTTTTGAATATTTCAATTTCATACCAAAC
1 TATGACATTCATTATAAATT-ATCCCCAAACTTTTTAATATTTCAATTTCATCCCAAAC
*
2187 TATGACATTCATTATAAATTGATCCCCAAACTTTTTAA-ACATTCTAATTTCATCCCAAAC
1 TATGACATTCATTATAAATT-ATCCCCAAACTTTTTAATA-TTTC-AATTTCATCCCAAAC
2247 TAT
1 TAT
2250 ATGTATATAT
Statistics
Matches: 97, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
55 12 0.12
56 26 0.27
57 8 0.08
58 5 0.05
59 29 0.30
60 17 0.18
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (58 bp):
TATGACATTCATTATAAATTATCCCCAAACTTTTTAATATTTCAATTTCATCCCAAAC
Found at i:6372 original size:59 final size:58
Alignment explanation
Indices: 6275--6386 Score: 206
Period size: 59 Copynumber: 1.9 Consensus size: 58
6265 AAAATGAAAA
6275 AAAAACAAATAAGTAAATTCTTGTTTATAGGTACAGATGATGCTTTTCCAATGACTGAC
1 AAAAACAAATAAGTAAATTCTTGTTTATAGGTACAGATGATG-TTTTCCAATGACTGAC
*
6334 AAAAACAAATAAGTAAATTCTTGTTTATAGGTATAGATGATGTTTTCCAATGA
1 AAAAACAAATAAGTAAATTCTTGTTTATAGGTACAGATGATGTTTTCCAATGA
6387 TATGTCTCAC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
58 11 0.21
59 41 0.79
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (58 bp):
AAAAACAAATAAGTAAATTCTTGTTTATAGGTACAGATGATGTTTTCCAATGACTGAC
Found at i:9071 original size:27 final size:27
Alignment explanation
Indices: 9025--9078 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
9015 ACCATCTCAA
* *
9025 CCTTTTTCTCTTATATATAGTGACATT
1 CCTTTTTCTCTTATACATAGTCACATT
*
9052 CCTTTTTCTCTTATCCATAGTCACATT
1 CCTTTTTCTCTTATACATAGTCACATT
9079 TAAGAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.50
Consensus pattern (27 bp):
CCTTTTTCTCTTATACATAGTCACATT
Found at i:14016 original size:29 final size:30
Alignment explanation
Indices: 13960--14017 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
13950 ACAAGTGACT
** *
13960 TAATTGATAACAATTAAAAGTTATATGGTC
1 TAATTGATAACAATTAAAAAATAGATGGTC
*
13990 TAATTTATAA-AATTAAAAAATAGATGGT
1 TAATTGATAACAATTAAAAAATAGATGGT
14018 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (30 bp):
TAATTGATAACAATTAAAAAATAGATGGTC
Found at i:14609 original size:6 final size:6
Alignment explanation
Indices: 14593--14738 Score: 77
Period size: 6 Copynumber: 23.5 Consensus size: 6
14583 AATCAAAGGA
* *
14593 AAAACAT AAAAAT AAAAAT AAAAAT -AAAAT AATAAT AATAAT AATAAAAT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -A-AAAAT
* * * * *
14643 CAAAAG AAAAA- AATAAT -AAAAT AATAAAAT CAAAAGAG AGAAAA- AAAGAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT -A-AAAAT -AAAA-AT A-AAAAT AAA-AAT
* * *
14694 AAAAAT AAAAAT AGAAAT AATAAAT -AAAAT AATAAG AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT AAA
14739 TCAAAGGAGA
Statistics
Matches: 110, Mismatches: 16, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
5 19 0.17
6 60 0.55
7 17 0.15
8 14 0.13
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:14628 original size:3 final size:3
Alignment explanation
Indices: 14598--14669 Score: 55
Period size: 3 Copynumber: 25.3 Consensus size: 3
14588 AAGGAAAAAC
* * *
14598 ATA AAA ATA AAA ATA AAA ATA A-A ATA ATA ATA ATA ATA ATA A-A ATCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* *
14645 A-A AGA A-A AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
14670 AATCAAAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
2 10 0.18
3 44 0.79
4 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (3 bp):
ATA
Found at i:14804 original size:101 final size:98
Alignment explanation
Indices: 14582--14824 Score: 227
Period size: 100 Copynumber: 2.4 Consensus size: 98
14572 AGTATTAAAT
* * *
14582 AAATCAAAGGAAAAACATAAAAATAAAAAT-AAAAATAAA-ATAATAATAATAATAATAAAATCA
1 AAATCAAA-GAAAAACAT--AAATAAAAATAAAAAATAAATAAAATAATAAGAAAAATAAAATCA
14645 AAAGAAAAAAATAATAAAATAATAAAATCAAAAGAG
63 AAAGAAAAAAATAATAAAATAATAAAATCAAAAGAG
**
14681 AGAAAAAAAG-AAAA-A-AAATAAAAATAGAAATAATAAATAAAATAATAAGAAAAAT-AAATCA
1 A-AATCAAAGAAAAACATAAATAAAAATA-AAA-AATAAATAAAATAATAAGAAAAATAAAATCA
*
14742 AAGGAGAAAAAGATTAA-AAAATAGATTAAAAT-AAAA-A-
63 AA--AGAAAAA-AATAATAAAATA-A-TAAAATCAAAAGAG
* *
14779 AAATCAAAGAAAAACATGAAATAAAATAAAAAAAATTAATAAAATA
1 AAATCAAAGAAAAACAT-AAATAAAA-ATAAAAAATAAATAAAATA
14825 TTAAATAAAT
Statistics
Matches: 119, Mismatches: 10, Indels: 29
0.75 0.06 0.18
Matches are distributed among these distances:
94 10 0.08
96 3 0.03
97 21 0.18
98 23 0.19
99 17 0.14
100 26 0.22
101 17 0.14
102 2 0.02
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (98 bp):
AAATCAAAGAAAAACATAAATAAAAATAAAAAATAAATAAAATAATAAGAAAAATAAAATCAAAA
GAAAAAAATAATAAAATAATAAAATCAAAAGAG
Found at i:15850 original size:14 final size:14
Alignment explanation
Indices: 15831--15859 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15821 GTTTGTTATT
15831 GGTTTGTTGGTGTC
1 GGTTTGTTGGTGTC
15845 GGTTTGTTGGTGTC
1 GGTTTGTTGGTGTC
15859 G
1 G
15860 AAAACCACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.45, T:0.48
Consensus pattern (14 bp):
GGTTTGTTGGTGTC
Found at i:28991 original size:58 final size:58
Alignment explanation
Indices: 28901--29015 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
28891 GTGTGAAAAT
* *
28901 TATAAATTTGAATTTAAGATTCCCTCGGGGTCATGTTGTGTGATTGATTATAGTAAAG
1 TATAAATTTGAATTTAAAATTCCCTCGGGGTCATGTTGTGTGATTGATTACAGTAAAG
* *
28959 TATAAATTTGAATTTAAAATTCCTTTGGGGTCATGTTGTGTGATTGATTACAGTAAA
1 TATAAATTTGAATTTAAAATTCCCTCGGGGTCATGTTGTGTGATTGATTACAGTAAA
29016 ATCTCTAGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (58 bp):
TATAAATTTGAATTTAAAATTCCCTCGGGGTCATGTTGTGTGATTGATTACAGTAAAG
Found at i:30575 original size:248 final size:248
Alignment explanation
Indices: 29890--30652 Score: 955
Period size: 248 Copynumber: 3.0 Consensus size: 248
29880 TCCATCCGAG
*
29890 ACCCGACCAGACCAAAATAAATTTTCA-CCGACCCGACCCGAATATATGAATTAGAAACCCGACC
1 ACCCGACCAGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAG-AA----ACC
* *
29954 CGACCCGAAATAATAATAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAGGAAAA--
61 CGACCCGAAATAATAA-AAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAA-AAAAATT
*
30017 A-ATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGG
124 ATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTT---
*
30081 TCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCAACCCGACCCGAATATCACACTTAAAAAAA
186 T-GGGTCGGGTATTTTTCACCCTAAACCCG-A---AACTCGACCCGAATATCACACTT-AAAAAA
*
30146 ACCG
245 ACCA
* * * * *
30150 ACACGACCCGACCAAAATAATGTTTCACCCGACCCGACCTGAATATATGAATTAGAAATCCGACC
1 ACCCGACCAGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
* **
30215 AGAACCGACTCGAAATAAAAAAA-A-AATTATTCAATAAAAACAGTGACTTAATTGAAAAAAATT
66 CGAA---A-T---AATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATT
* *
30278 ATATATTGATGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGG
124 ATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGG
30343 GTCGGGTATTTTTCACCCTAAACCCG-AACTCGACCCGAATATCACACTTAAAAAAACCA
189 GTCGGGTATTTTTCACCCTAAACCCGAAACTCGACCCGAATATCACACTTAAAAAAACCA
*
30402 ACCCGACCAGATCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
1 ACCCGACCAGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
*
30467 CGAAATAATAAAAAAATATTTTTATTCAACAAAAACAGTGACTTAATTGGAAAAAAATTATATAT
66 CGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATT-GAAAAAAATTATATAT
* * * ** * ***
30532 AGAGGGGTATTTTTGTAATTATTCTTAAATATATAAAGTAAAATTATATATATTTTCAGATTAAG
130 AGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGGGTCGGG
* * *
30597 TATTTTCCACCCCAAACCCGAACTCGACTCGACCCAAATATCACACTTAAAAAAAC
195 TATTTTTCACCCTAAACCCGAA----ACTCGACCCGAATATCACACTTAAAAAAAC
30653 TGACTCGACC
Statistics
Matches: 444, Mismatches: 40, Indels: 45
0.84 0.08 0.09
Matches are distributed among these distances:
245 10 0.02
246 1 0.00
247 26 0.06
248 89 0.20
249 2 0.00
252 71 0.16
253 51 0.11
256 10 0.02
258 28 0.06
259 6 0.01
260 55 0.12
261 28 0.06
262 62 0.14
263 5 0.01
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (248 bp):
ACCCGACCAGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
CGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATATA
GAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGGGTCGGGT
ATTTTTCACCCTAAACCCGAAACTCGACCCGAATATCACACTTAAAAAAACCA
Found at i:32187 original size:23 final size:23
Alignment explanation
Indices: 32161--32207 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
32151 ACAATCTCCC
32161 CCATATCAAATTTAAGAAATTAA
1 CCATATCAAATTTAAGAAATTAA
32184 CCATATCAAATTTAAGAAATTAA
1 CCATATCAAATTTAAGAAATTAA
32207 C
1 C
32208 TTCCAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (23 bp):
CCATATCAAATTTAAGAAATTAA
Found at i:34969 original size:2 final size:2
Alignment explanation
Indices: 34962--34992 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34952 CAGAAAATAA
34962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34993 AAAGACTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35146 original size:19 final size:20
Alignment explanation
Indices: 35119--35163 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
35109 ATTAGCAACA
*
35119 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
35138 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
35158 TAATAA
1 TAATAA
35164 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:35147 original size:20 final size:20
Alignment explanation
Indices: 35122--35161 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
35112 AGCAACATAA
*
35122 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
35142 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
35162 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:35204 original size:20 final size:21
Alignment explanation
Indices: 35175--35214 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
35165 TAATAGAATA
*
35175 AAAAATTGATTCTATCTAATT
1 AAAAATTGATCCTATCTAATT
35196 AAAAA-TGATCCTATCTAAT
1 AAAAATTGATCCTATCTAAT
35215 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAATTGATCCTATCTAATT
Found at i:35256 original size:20 final size:20
Alignment explanation
Indices: 35228--35266 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35218 TAATAGAATA
* *
35228 AAAATTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
35248 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
35267 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:35257 original size:52 final size:52
Alignment explanation
Indices: 35120--35267 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
35110 TTAGCAACAT
35120 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
35171 AATAAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
35224 AATAAAAATTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATA
35268 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 3 0.03
52 45 0.48
53 46 0.49
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.34
Consensus pattern (52 bp):
AATAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:37921 original size:19 final size:20
Alignment explanation
Indices: 37894--37938 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
37884 ATTAGCAACA
*
37894 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
37913 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
37933 TAATAA
1 TAATAA
37939 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:37922 original size:20 final size:20
Alignment explanation
Indices: 37897--37936 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
37887 AGCAACATAA
*
37897 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
37917 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
37937 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:37979 original size:20 final size:21
Alignment explanation
Indices: 37950--37989 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
37940 TAATAGAATA
*
37950 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
37971 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
37990 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:38028 original size:20 final size:20
Alignment explanation
Indices: 38003--38041 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
37993 TAATAGAATA
*
38003 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
38023 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
38042 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:38032 original size:52 final size:52
Alignment explanation
Indices: 37895--38042 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
37885 TTAGCAACAT
37895 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
37946 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
37999 AATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
38043 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 3 0.03
52 45 0.48
53 46 0.49
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:45533 original size:22 final size:22
Alignment explanation
Indices: 45508--45576 Score: 111
Period size: 22 Copynumber: 3.0 Consensus size: 22
45498 TATATATATA
*
45508 TATATATATATGTGTGTGTGTG
1 TATATATATATATGTGTGTGTG
45530 TATATATATATATATGTGTGTGTG
1 --TATATATATATATGTGTGTGTG
45554 TATATATATATATGTGTGTGTG
1 TATATATATATATGTGTGTGTG
45576 T
1 T
45577 GTGTTTGTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 23 0.52
24 21 0.48
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (22 bp):
TATATATATATATGTGTGTGTG
Found at i:45533 original size:24 final size:24
Alignment explanation
Indices: 45506--45578 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
45496 TATATATATA
45506 TATATATATATATGTGTGTGTGTG
1 TATATATATATATGTGTGTGTGTG
*
45530 TATATATATATATATGTGTGTGTG
1 TATATATATATATGTGTGTGTGTG
45554 TATATATATATATGTGTGTGTGTG
1 TATATATATATATGTGTGTGTGTG
45578 T
1 T
45579 GTTTGTGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (24 bp):
TATATATATATATGTGTGTGTGTG
Found at i:45533 original size:26 final size:26
Alignment explanation
Indices: 45504--45580 Score: 131
Period size: 26 Copynumber: 3.0 Consensus size: 26
45494 TATATATATA
45504 TATATATATATATATGTGTGTGTGTG
1 TATATATATATATATGTGTGTGTGTG
45530 TATATATATATATA--TGTGTGTGTG
1 TATATATATATATATGTGTGTGTGTG
*
45554 TATATATATATATGTGTGTGTGTGTG
1 TATATATATATATATGTGTGTGTGTG
45580 T
1 T
45581 TTGTGTAAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 23 0.48
26 25 0.52
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (26 bp):
TATATATATATATATGTGTGTGTGTG
Found at i:45538 original size:2 final size:2
Alignment explanation
Indices: 45481--45518 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
45471 TTAACAATAA
45481 AT AT AT AT AT 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 AT AT AT AT AT
45519 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65142 original size:18 final size:18
Alignment explanation
Indices: 65104--65143 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
65094 TGTGCTGTCA
*
65104 TCAGCAGTGATTTGCTCT
1 TCAGCAGTGATTTACTCT
65122 TCAGCTAGTGATTTACT-T
1 TCAGC-AGTGATTTACTCT
65140 TCAG
1 TCAG
65144 ATCCTGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (18 bp):
TCAGCAGTGATTTACTCT
Found at i:65307 original size:18 final size:18
Alignment explanation
Indices: 65269--65308 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
65259 ACTTTGAGCA
*
65269 TCAGCAGTGATTTGCTCT
1 TCAGCAGTGATTTACTCT
65287 TCAGCTAGTGATTTACT-T
1 TCAGC-AGTGATTTACTCT
65305 TCAG
1 TCAG
65309 ATCCTGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (18 bp):
TCAGCAGTGATTTACTCT
Found at i:65392 original size:165 final size:165
Alignment explanation
Indices: 65102--65415 Score: 522
Period size: 165 Copynumber: 1.9 Consensus size: 165
65092 ACTGTGCTGT
65102 CATCAGCAGTGATTTGCTCTTCAGCTAGTGATTTACTTTCAGATCCTGTGTCATTGTTGATGTCC
1 CATCAGCAGTGATTTGCTCTTCAGCTAGTGATTTACTTTCAGATCCTGTGTCATTGTTGATGTCC
* ** * *
65167 GATTTGCCAAGGAATGCATCATCATCATTAGATTCTTTATTTCCATTCTTTGCAGAGGAATCCAT
66 AATTCACCAAGGAATGCATCATCATCATTAGATTCTTCATTCCCATTCTTTGCAGAGGAATCCAT
*
65232 ATGACCTTCTGCAGGGAGATCTGGAATACTTTGAG
131 ATGACCTTCCGCAGGGAGATCTGGAATACTTTGAG
65267 CATCAGCAGTGATTTGCTCTTCAGCTAGTGATTTACTTTCAGATCCTGTGTCATTGTTGATGTCC
1 CATCAGCAGTGATTTGCTCTTCAGCTAGTGATTTACTTTCAGATCCTGTGTCATTGTTGATGTCC
* * * *
65332 AATTCATCAAGGAATGCATCATCATCATTAGATTCTTCATTCCCCTT-TTCTTCTGAGGAATCCA
66 AATTCACCAAGGAATGCATCATCATCATTAGATTCTTCATTCCCATTCTT-TGCAGAGGAATCCA
65396 TATGACCTTCCGCAGGGAGA
130 TATGACCTTCCGCAGGGAGA
65416 ACCAAAACGT
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
164 2 0.01
165 136 0.99
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (165 bp):
CATCAGCAGTGATTTGCTCTTCAGCTAGTGATTTACTTTCAGATCCTGTGTCATTGTTGATGTCC
AATTCACCAAGGAATGCATCATCATCATTAGATTCTTCATTCCCATTCTTTGCAGAGGAATCCAT
ATGACCTTCCGCAGGGAGATCTGGAATACTTTGAG
Found at i:67796 original size:22 final size:24
Alignment explanation
Indices: 67771--67824 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
67761 GAATAAATTC
*
67771 AAATAAATTTAACCAA-TATT-TA
1 AAATAAATTTAACCAACTATTCAA
*
67793 AAATAAA--AAACCAACTATTCAA
1 AAATAAATTTAACCAACTATTCAA
67815 AAATAAATTT
1 AAATAAATTT
67825 TCAAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
20 6 0.24
21 4 0.16
22 15 0.60
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAAATTTAACCAACTATTCAA
Found at i:67827 original size:14 final size:15
Alignment explanation
Indices: 67810--67850 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
67800 AAACCAACTA
67810 TTCAAAAATAAAT-T
1 TTCAAAAATAAATAT
67824 TTCAAAAA-ATAATAT
1 TTCAAAAATA-AATAT
*
67839 TTAAAAAATAAA
1 TTCAAAAATAAA
67851 GAAAACAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 1 0.04
14 11 0.48
15 10 0.43
16 1 0.04
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
TTCAAAAATAAATAT
Found at i:67831 original size:15 final size:15
Alignment explanation
Indices: 67813--67850 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
67803 CCAACTATTC
67813 AAAAATAAAT-TTTCA
1 AAAAATAAATATTT-A
67828 AAAAAT-AATATTTA
1 AAAAATAAATATTTA
67842 AAAAATAAA
1 AAAAATAAA
67851 GAAAACAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATAAATATTTA
Found at i:69275 original size:20 final size:20
Alignment explanation
Indices: 69250--69289 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
69240 CAATCGAGTA
*
69250 TATAAAATTCGAGTCAAGTT
1 TATAAAATTCAAGTCAAGTT
*
69270 TATAAAATTCAAGTCGAGTT
1 TATAAAATTCAAGTCAAGTT
69290 GCTTGGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
TATAAAATTCAAGTCAAGTT
Found at i:71261 original size:47 final size:47
Alignment explanation
Indices: 71189--71278 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
71179 ATAACTTTTA
*
71189 CTGAGAACAACTCTTATTCGGGACAAC-TTCTATCAAGAACAACCATG
1 CTGAGAACAACTCTTATTCGGGACAACATT-TACCAAGAACAACCATG
* * *
71236 CTGAGAACAACTCTTGTTTGTGACAACATTTACCAAGAACAAC
1 CTGAGAACAACTCTTATTCGGGACAACATTTACCAAGAACAAC
71279 TGTGTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
47 36 0.95
48 2 0.05
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (47 bp):
CTGAGAACAACTCTTATTCGGGACAACATTTACCAAGAACAACCATG
Found at i:72200 original size:16 final size:16
Alignment explanation
Indices: 72179--72210 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
72169 AAAAGTGATG
72179 ATATGTCATATGTCAC
1 ATATGTCATATGTCAC
72195 ATATGTCATATGTCAC
1 ATATGTCATATGTCAC
72211 TAAAAGTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
ATATGTCATATGTCAC
Found at i:79735 original size:34 final size:32
Alignment explanation
Indices: 79673--79742 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
79663 CCTTACAAAC
* *
79673 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
79705 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
79739 TCCC
1 TCCC
79743 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:80051 original size:21 final size:21
Alignment explanation
Indices: 80025--80066 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
80015 CCAGAATGGG
*
80025 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
80046 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
80067 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:80266 original size:30 final size:31
Alignment explanation
Indices: 80219--80309 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
80209 AAATTTTGAA
80219 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
80248 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
80279 TAAATTCAATTCAAGTCAAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
80310 CCTTAAATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:80495 original size:23 final size:23
Alignment explanation
Indices: 80468--80515 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
80458 AAGCTCCCCC
80468 TTTTTCATTAAGAAATTGAATTT
1 TTTTTCATTAAGAAATTGAATTT
*
80491 TTTTTTATTAAGAAATTGAATTT
1 TTTTTCATTAAGAAATTGAATTT
80514 TT
1 TT
80516 CAAACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTTTCATTAAGAAATTGAATTT
Found at i:82566 original size:34 final size:32
Alignment explanation
Indices: 82504--82573 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
82494 CCTTACAAAC
* *
82504 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
82536 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
82570 TCCC
1 TCCC
82574 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:82876 original size:21 final size:21
Alignment explanation
Indices: 82850--82891 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
82840 CCCAGAATGG
*
82850 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
82871 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
82892 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:83021 original size:19 final size:19
Alignment explanation
Indices: 82997--83063 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
82987 GAGCCTCGGG
*
82997 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
83016 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
83035 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
83054 TTACTATTCA
1 TTACTGTTCA
83064 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:83175 original size:30 final size:31
Alignment explanation
Indices: 83128--83218 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
83118 AAATTTTGAA
83128 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
83157 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
83188 TAAATTCAATTCAAGTCAAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
83219 CCTTAAATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:83821 original size:20 final size:21
Alignment explanation
Indices: 83793--83836 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
83783 CAACGATCTG
*
83793 AAAGTAAAATCAAGATTTG-A
1 AAAGAAAAATCAAGATTTGCA
**
83813 AAAGAAAAATTTAGATTTGCA
1 AAAGAAAAATCAAGATTTGCA
83834 AAA
1 AAA
83837 TTACTTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.25
Consensus pattern (21 bp):
AAAGAAAAATCAAGATTTGCA
Found at i:87491 original size:20 final size:21
Alignment explanation
Indices: 87466--87504 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
87456 TTTTGGTACA
*
87466 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
87486 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
87505 ACAGGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:94773 original size:2 final size:2
Alignment explanation
Indices: 94766--94800 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
94756 TGGTTTTCGA
94766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
94801 GTTTTTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94860 original size:29 final size:28
Alignment explanation
Indices: 94816--94881 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
94806 TTTGAAAACA
94816 TTTTT-AAACTATATATAT-ATATAATATG
1 TTTTTAAAACTATATATATAATAT-ATA-G
94844 TTTTTGAAAACT-TATATATAATATATAG
1 TTTTT-AAAACTATATATATAATATATAG
94872 TTTTTAAAAC
1 TTTTTAAAAC
94882 ATTTTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
27 5 0.14
28 11 0.31
29 10 0.29
30 9 0.26
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (28 bp):
TTTTTAAAACTATATATATAATATATAG
Found at i:94899 original size:39 final size:39
Alignment explanation
Indices: 94844--95126 Score: 340
Period size: 39 Copynumber: 7.1 Consensus size: 39
94834 ATATAATATG
**
94844 TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
* *
94883 TTTTTGAAAAAATATATATATTATATAGTTTTTAAAACG
1 TTTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
***
94922 TTTTTGAAACCTTATATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
*
94961 TTTTTGAAAAAATATATATATTATATAGCTTTTTAAAACA
1 TTTTTGAAAAAATATATATAATATATAG-TTTTTAAAACA
** *
95001 TTTTTGAAAACTTATATATAATATATAATTTTTAAAACA
1 TTTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
*
95040 TTTTTGAATATATATATATATATATATATTATAGTTTTTAAAAATA
1 TTTTTGAA-A-A-A-ATATATATA-ATA-TATAGTTTTT-AAAACA
*
95086 TTTTTG--AAAATATATAT--TATATAGTTTTTGAAACA
1 TTTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
95121 CTTTTT
1 -TTTTT
95127 ATTTATTTTT
Statistics
Matches: 212, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
35 4 0.02
36 15 0.07
37 2 0.01
39 112 0.53
40 44 0.21
41 2 0.01
42 1 0.00
43 9 0.04
44 3 0.01
45 9 0.04
46 11 0.05
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (39 bp):
TTTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
Found at i:94938 original size:78 final size:78
Alignment explanation
Indices: 94844--95126 Score: 412
Period size: 78 Copynumber: 3.6 Consensus size: 78
94834 ATATAATATG
94844 TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGAAAAAATATATATATTATAT
1 TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGAAAAAATATATATATTATAT
*
94909 AGTTTTTAAAACG
66 AGTTTTTAAAACA
*
94922 TTTTTGAAACCTTATATATAATATATAGTTTTTAAAACATTTTTGAAAAAATATATATATTATAT
1 TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGAAAAAATATATATATTATAT
94987 AGCTTTTTAAAACA
66 AG-TTTTTAAAACA
*
95001 TTTTTGAAAACTTATATATAATATATAATTTTTAAAACATTTTTGAATATATATATATATATATA
1 TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGAA-A-A-A-ATATATATAT-
*
95066 TATTATAGTTTTTAAAAATA
61 TA-TATAGTTTTT-AAAACA
*
95086 TTTTTGAAAA--TATATAT--TATATAGTTTTTGAAACACTTTTT
1 TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACA-TTTTT
95127 ATTTATTTTT
Statistics
Matches: 189, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
78 66 0.35
79 55 0.29
80 1 0.01
81 17 0.09
82 6 0.03
83 17 0.09
84 7 0.04
85 20 0.11
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (78 bp):
TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGAAAAAATATATATATTATAT
AGTTTTTAAAACA
Found at i:95744 original size:15 final size:16
Alignment explanation
Indices: 95713--95767 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
95703 GAAATCGTCG
*
95713 ACCCGGAAGTTCCGGGT
1 ACCCGGAA-ATCCGGGT
95730 ACCCGGAAA-CCGGGT
1 ACCCGGAAATCCGGGT
* *
95745 ACCCGAAAATCCGAGT
1 ACCCGGAAATCCGGGT
95761 ACCCGGA
1 ACCCGGA
95768 TTTGCACACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 14 0.42
16 11 0.33
17 8 0.24
ACGTcount: A:0.27, C:0.33, G:0.29, T:0.11
Consensus pattern (16 bp):
ACCCGGAAATCCGGGT
Found at i:96285 original size:167 final size:168
Alignment explanation
Indices: 96097--96431 Score: 647
Period size: 167 Copynumber: 2.0 Consensus size: 168
96087 CACAGAACGG
96097 TAAACCGAGAGAACATCACAACATCACAACCAAAGAACATCCGAGAGCCATCGAGGCATAACAGT
1 TAAACCGAGAGAACATCACAACATCACAACCAAAGAACATCCGAGAGCCATCGAGGCATAACAGT
96162 GACAACAACGGTGCCAAAGAAAGAAAAAAATAAAACCATCCACATCG-AA-ACAAGCAAACAACA
66 GACAACAACGGTGCCAAAGAAAGAAAAAAATAAAACCATCCACATCGAAACACAAGCAAACAACA
96225 AGGAAAAGTATAAAAGGCAAGTGGGGGAAGCCATCGGGC
131 AGGAAAAGTATAAAAGGCAAGT-GGGGAAGCCATCGGGC
96264 TAAACCGAGAGAACATCACAACATCACAACCAAAGAACATCCGAGAGCCATCGAGGCATAACAGT
1 TAAACCGAGAGAACATCACAACATCACAACCAAAGAACATCCGAGAGCCATCGAGGCATAACAGT
96329 GACAACAACGGTGCCAAAGAAAGAAAAAAATAAAACCATCCACATCGAAACACAAGCAAACAACA
66 GACAACAACGGTGCCAAAGAAAGAAAAAAATAAAACCATCCACATCGAAACACAAGCAAACAACA
96394 AGGAAAAGTATAAAAGGCAAGTGGGGAAGCCATCGGGC
131 AGGAAAAGTATAAAAGGCAAGTGGGGAAGCCATCGGGC
96432 GCCGACGAAC
Statistics
Matches: 166, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
167 112 0.67
168 18 0.11
169 36 0.22
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.09
Consensus pattern (168 bp):
TAAACCGAGAGAACATCACAACATCACAACCAAAGAACATCCGAGAGCCATCGAGGCATAACAGT
GACAACAACGGTGCCAAAGAAAGAAAAAAATAAAACCATCCACATCGAAACACAAGCAAACAACA
AGGAAAAGTATAAAAGGCAAGTGGGGAAGCCATCGGGC
Found at i:97114 original size:22 final size:22
Alignment explanation
Indices: 97058--97116 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
97048 AATTTGGTCC
* *
97058 TTTTAATTTTTAATTGTTCATT
1 TTTTAATTTTTTATTGATCATT
97080 TTTT-ATTTATTTATT-ATCATT
1 TTTTAATTT-TTTATTGATCATT
97101 TTTTAATCTTTTTATT
1 TTTTAAT-TTTTTATT
97117 TGTTATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 13 0.41
22 17 0.53
23 2 0.06
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTAATTTTTTATTGATCATT
Found at i:97181 original size:17 final size:18
Alignment explanation
Indices: 97146--97188 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
97136 TCTTTATTGA
* *
97146 TTTATTTTTCCTTTTTTC
1 TTTATTTTTCATTTATTC
*
97164 -TTATTTTTGATTTATTC
1 TTTATTTTTCATTTATTC
97181 TTTATTTT
1 TTTATTTT
97189 CCCCCTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTATTTTTCATTTATTC
Found at i:97188 original size:26 final size:24
Alignment explanation
Indices: 97163--97223 Score: 50
Period size: 25 Copynumber: 2.4 Consensus size: 24
97153 TTCCTTTTTT
97163 CTTATTTTTGATTTATTCTTTATTTT
1 CTTATTTTTGATTTA-TCTTT-TTTT
****
97189 CCCCCTTTTGATTTATCTTTTTATT
1 CTTATTTTTGATTTATCTTTTT-TT
*
97214 ATTATTTTTG
1 CTTATTTTTG
97224 CTTTTACATT
Statistics
Matches: 25, Mismatches: 9, Indels: 3
0.68 0.24 0.08
Matches are distributed among these distances:
24 2 0.08
25 12 0.48
26 11 0.44
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (24 bp):
CTTATTTTTGATTTATCTTTTTTT
Found at i:97561 original size:13 final size:13
Alignment explanation
Indices: 97543--97573 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
97533 TTGACCGTAA
97543 CCGACTCCCGAAC
1 CCGACTCCCGAAC
97556 CCGACTCCCGAAC
1 CCGACTCCCGAAC
97569 CCGAC
1 CCGAC
97574 ACATTTCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.55, G:0.16, T:0.06
Consensus pattern (13 bp):
CCGACTCCCGAAC
Found at i:97918 original size:59 final size:59
Alignment explanation
Indices: 97834--97955 Score: 167
Period size: 59 Copynumber: 2.1 Consensus size: 59
97824 TAAAGTATAT
* * *
97834 AAATGGTTCACGATTATAGGGTGTTACTTTATTGAGTTTC-TTGACTATT-AAAGTTACA
1 AAATGGTCCACGATTATAAGATGTTACTTTATTGAG-TTCATTGACTATTAAAAGTTACA
* *
97892 AAATGGTCCATCGATTATAAGATGTTATTTTGTTGAGTTCATTGACTATTAAAAGTTACA
1 AAATGGTCCA-CGATTATAAGATGTTACTTTATTGAGTTCATTGACTATTAAAAGTTACA
97952 AAAT
1 AAAT
97956 AGTCATTTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 12 0.21
59 31 0.55
60 13 0.23
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (59 bp):
AAATGGTCCACGATTATAAGATGTTACTTTATTGAGTTCATTGACTATTAAAAGTTACA
Found at i:102227 original size:21 final size:21
Alignment explanation
Indices: 102203--102247 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
102193 TGTCTCGAAG
102203 GACCACGTAGATGTCCCAAAA
1 GACCACGTAGATGTCCCAAAA
102224 GACCACGTAGATGTCCCAAAA
1 GACCACGTAGATGTCCCAAAA
102245 GAC
1 GAC
102248 TACATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.20, T:0.13
Consensus pattern (21 bp):
GACCACGTAGATGTCCCAAAA
Found at i:102284 original size:18 final size:18
Alignment explanation
Indices: 102261--102312 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
102251 ATATAATATA
102261 TATGTCCCGAGGGACCAC
1 TATGTCCCGAGGGACCAC
102279 TATGTCCCGAGGGACCAC
1 TATGTCCCGAGGGACCAC
*
102297 TATGTCCCGAAGGACC
1 TATGTCCCGAGGGACC
102313 TCGTAGACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAGGGACCAC
Found at i:104267 original size:30 final size:30
Alignment explanation
Indices: 104221--104294 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 30
104211 TGATTGAAAA
*
104221 GTAAATTTTGAAAGTTT-AGAGATT-AAAGT
1 GTAAATTTTAAAAGTTTAAG-GATTAAAAGT
104250 GTAAATTTGTAAAAGTTTAAGGATTAAAAGT
1 GTAAATTT-TAAAAGTTTAAGGATTAAAAGT
104281 GTAAATTTTCAAAA
1 GTAAATTTT-AAAA
104295 ATTATATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 8 0.20
30 13 0.32
31 19 0.47
ACGTcount: A:0.45, C:0.01, G:0.18, T:0.36
Consensus pattern (30 bp):
GTAAATTTTAAAAGTTTAAGGATTAAAAGT
Found at i:106935 original size:3 final size:3
Alignment explanation
Indices: 106922--106968 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
106912 TGTTTTAAAA
106922 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
106969 CATTTACCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:110715 original size:23 final size:23
Alignment explanation
Indices: 110671--110715 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
110661 TTGATTCATT
**
110671 TAATTGATTTTATTAATGAAATC
1 TAATTGATTTTATTAAAAAAATC
110694 TAATTG-TTATTATTAAAAAAAT
1 TAATTGATT-TTATTAAAAAAAT
110716 ACAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (23 bp):
TAATTGATTTTATTAAAAAAATC
Found at i:114885 original size:26 final size:26
Alignment explanation
Indices: 114856--114917 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
114846 TCAGTTAGTG
114856 GTGTGTTTCGATGTGTCGCATTAACA
1 GTGTGTTTCGATGTGTCGCATTAACA
* *
114882 GTGTGTTTCAATGTGTCGCATTAGCA
1 GTGTGTTTCGATGTGTCGCATTAACA
114908 GTGTGTTTCG
1 GTGTGTTTCG
114918 GTAGGTGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.40
Consensus pattern (26 bp):
GTGTGTTTCGATGTGTCGCATTAACA
Found at i:120030 original size:22 final size:22
Alignment explanation
Indices: 119977--120030 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
119967 GTTAAGTGCC
* **
119977 CCCGACTCCCTCTCCCTCTCCCT
1 CCCGAC-CCCCCTCCCAATCCCT
120000 CCC-ATCCCCCCTCCCAATCCCT
1 CCCGA-CCCCCCTCCCAATCCCT
120022 CCCGACCCC
1 CCCGACCCC
120031 ATTCCCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.09, C:0.69, G:0.04, T:0.19
Consensus pattern (22 bp):
CCCGACCCCCCTCCCAATCCCT
Found at i:139410 original size:2 final size:2
Alignment explanation
Indices: 139403--139473 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
139393 TAATTTATCT
139403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139445 TA 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 TA T
139474 GCATATGGTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.