Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001972.1 Hibiscus syriacus cultivar Beakdansim tig00003989_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: 69092
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:85 original size:31 final size:31
Alignment explanation
Indices: 13--85 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
3 AATATTTTTA
**
13 TTTATTTTAAC--TTAAAAATATATTTTAGT
1 TTTATTTTAACTTTTAAAAATATACATTAGT
* * * *
42 TTGATATCAACTTTTAAAAATATACATTATT
1 TTTATTTTAACTTTTAAAAATATACATTAGT
73 TTTATTTTAACTT
1 TTTATTTTAACTT
86 ATTACATGTA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
29 8 0.24
31 25 0.76
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTATTTTAACTTTTAAAAATATACATTAGT
Found at i:118 original size:30 final size:30
Alignment explanation
Indices: 79--155 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
69 TATTTTTATT
* * * *
79 TTAACTTATTACATGTATTATATTCTTAAC
1 TTAAATTATTAAATATATTATAGTCTTAAC
* *
109 TTAAATTATTAAATATATTGTAGTCTTACC
1 TTAAATTATTAAATATATTATAGTCTTAAC
*
139 TTAAATTATCAAATATA
1 TTAAATTATTAAATATA
156 ATTTACCCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (30 bp):
TTAAATTATTAAATATATTATAGTCTTAAC
Found at i:195 original size:29 final size:30
Alignment explanation
Indices: 149--215 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
139 TTAAATTATC
*
149 AAATATAATTTACCCTTA-TCTAAACATAA
1 AAATATATTTTACCCTTATTCTAAACATAA
** * * *
178 AAATATATTTTATTCTTATTTTTAACTTAA
1 AAATATATTTTACCCTTATTCTAAACATAA
208 AAATATAT
1 AAATATAT
216 ATTTTTTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (30 bp):
AAATATATTTTACCCTTATTCTAAACATAA
Found at i:225 original size:28 final size:30
Alignment explanation
Indices: 175--235 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 30
165 TATCTAAACA
*
175 TAAAAATATATTTTATTCTTATTTTTAACT
1 TAAAAATATATATTATTCTTATTTTTAACT
*
205 TAAAAATATATATT-TT-TTATTTTTAATT
1 TAAAAATATATATTATTCTTATTTTTAACT
233 TAA
1 TAA
236 TTCAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 14 0.48
29 2 0.07
30 13 0.45
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TAAAAATATATATTATTCTTATTTTTAACT
Found at i:271 original size:29 final size:29
Alignment explanation
Indices: 239--336 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 29
229 AATTTAATTC
239 AAATATATTTTAAAGTTAAAATAAAAATA
1 AAATATATTTTAAAGTTAAAATAAAAATA
* * *
268 AAATATATTTTTAGGTTAAAACAAAAATA
1 AAATATATTTTAAAGTTAAAATAAAAATA
* * * *
297 AAATAGA-TTTAATAATTTAAATTAAAATA
1 AAATATATTTTAA-AGTTAAAATAAAAATA
*
326 AAAAATATTTT
1 AAATATATTTT
337 TTATACTAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
28 4 0.07
29 48 0.87
30 3 0.05
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (29 bp):
AAATATATTTTAAAGTTAAAATAAAAATA
Found at i:1537 original size:112 final size:111
Alignment explanation
Indices: 1223--1681 Score: 762
Period size: 112 Copynumber: 4.1 Consensus size: 111
1213 TTGTCGGTTT
* *
1223 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAATAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAATGACAAAACCG
*
1288 GTCTATAAATGACAAAACAGGTAAAGCGCTACTGGATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1334 GTGTCGATACTTTATAAAAA---ATTGATCCATAACAATATAATAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGT-AAAAAATGACAAAACC
1396 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1443 GTGTCGATACTTTATAAAAATGTATCGATCCATAAGAATATAATAGGTTAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGG-TAAAAAATGACAAAACC
* *
1508 GGTCTATAAATGACAAAACCGGTAAAGCGCTACCAGATATATTGAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1555 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAA-ATGACAAAACC
* * * *
1620 GGTCTATAAATGACAAAACAAGTAAATCGCTACCGGATATGTTGATA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1667 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1682 TATAAGTATC
Statistics
Matches: 329, Mismatches: 13, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
108 25 0.08
109 82 0.25
111 26 0.08
112 195 0.59
113 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (111 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1988 original size:177 final size:178
Alignment explanation
Indices: 1552--1996 Score: 703
Period size: 182 Copynumber: 2.5 Consensus size: 178
1542 AGATATATTG
1552 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** ** *
1617 ACCGGTCTATAAATGACAAAACAAGTAAATCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACAAGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
* * *
1682 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAACGCTAAT
131 TATAAGTATCG--A--TTTGGAATTTAAAAGAAAAGAAGTTATAACACCAAT
*
1734 AAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
**
1799 ACCGGTCTCGAAATGACAAAACTGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACAAGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
*
1864 TATAAGTATCG-TTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
131 TATAAGTATCGATTTGGAATTTAAAAGAAAAGAAGTTATAACACCAAT
* *
1911 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
1976 ATCAGTCTCGAAATGACAAAA
66 ACCGGTCTCGAAATGACAAAA
1997 TCGGTAGTAA
Statistics
Matches: 246, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
177 113 0.46
182 133 0.54
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (178 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACAAGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGATTTGGAATTTAAAAGAAAAGAAGTTATAACACCAAT
Found at i:2672 original size:23 final size:23
Alignment explanation
Indices: 2640--2687 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2630 AAATAGGTCA
* *
2640 ATATATGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
2663 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
2686 AT
1 AT
2688 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:3208 original size:85 final size:84
Alignment explanation
Indices: 3012--3456 Score: 385
Period size: 85 Copynumber: 5.2 Consensus size: 84
3002 GATTAAGACT
* * * * * * * *
3012 CCTAATTTTTTCAATTTCACTTTTTATCTTTATAACTGAAGTCTTTAAATTTTTTTATCTGAGTT
1 CCTAATTTTTTTAATCTCACTTTTTACCTTTATAATTG-AGTCCTT-AATTTTTTAATCTCACTT
*
3077 TTTCACCTTTATAATTAAAGTC
64 TTT-ACCTTTATAATTAAAGCC
* * * * * *
3099 TCTAGTTTTTTTCAATCACA-TTTTTACCTTTATAATTGAGTCCCCTAAATTTTTAATCTCACAT
1 CCTAATTTTTTT-AATCTCACTTTTTACCTTTATAATTGAGT-CCTTAATTTTTTAATCTCACTT
* *
3163 TATAGCTTTATAATTAAAGCC
64 TTTACCTTTATAATTAAAGCC
* **
3184 CCTAATTTTTTTAATCTCACTTTTTCCCTTTATAATTGAGATATTTAATTTTTTCAATC-CAACT
1 CCTAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAG-TCCTTAATTTTTT-AATCTC-ACT
*
3248 TTTTACCTTTATAATTGAAGCC
63 TTTTACCTTTATAATTAAAGCC
** * * * *
3270 TATAA-TTTTTTATTCTCACTTTTTACATTTATAATCGAGGTCCCTAATTTTTTCAATCTCACTT
1 CCTAATTTTTTTAATCTCACTTTTTACCTTTATAATTGA-GTCCTTAATTTTTT-AATCTCACTT
* * * * *
3334 TTTATCTTTATAGTTGAGGTC
64 TTTACCTTTATAATTAAAGCC
* * * **
3355 CCTAATTTTTTTAATCTCACTTTCTACCTTTATGATTGAAGCCCTTATATTTTTTAATCTTGCTT
1 CCTAATTTTTTTAATCTCACTTTTTACCTTTATAATTG-AGTCCTTA-ATTTTTTAATCTCACTT
* * *
3420 TTTAGCTTTATAATT-GAGGC
64 TTTACCTTTATAATTAAAGCC
3440 CCTAATTTTTTTCAATC
1 CCTAATTTTTTT-AATC
3457 CAACTATATA
Statistics
Matches: 288, Mismatches: 58, Indels: 25
0.78 0.16 0.07
Matches are distributed among these distances:
84 6 0.02
85 136 0.47
86 106 0.37
87 35 0.12
88 5 0.02
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (84 bp):
CCTAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGTCCTTAATTTTTTAATCTCACTTTT
TACCTTTATAATTAAAGCC
Found at i:3251 original size:128 final size:126
Alignment explanation
Indices: 3014--3456 Score: 385
Period size: 128 Copynumber: 3.4 Consensus size: 126
3004 TTAAGACTCC
* * * * ** * *
3014 TAATTTTTTCAATTTCACTTTTTATCTTTATAACTGAAGTCTTTAAATTTTTTT-ATCTGAGTTT
1 TAATTTTTT-AATCTCACTTTTTAGCTTTATAA-TTAAGCCCCT-AATTTTTTTAATCTCACTTT
* *
3078 TTCACCTTTATAATT-AAAGT-CTCTAGTTTTTTTCAAT-CACATTTTTACCTTTATAATTG-AG
63 TT-ACCTTTATAATTGAGA-TAC-CTA-ATTTTTTCAATCCAC-TTTTTACCTTTATAATTGAAG
*
3139 TCCCC
123 -CCCA
* * *
3144 TAAATTTTTAATCTCACATTATAGCTTTATAATTAAAGCCCCTAATTTTTTTAATCTCACTTTTT
1 TAATTTTTTAATCTCACTTTTTAGCTTTATAATT-AAGCCCCTAATTTTTTTAATCTCACTTTTT
* ** *
3209 CCCTTTATAATTGAGATATTTAATTTTTTCAATCCAACTTTTTACCTTTATAATTGAAGCCTA
65 ACCTTTATAATTGAGATACCTAATTTTTTCAATCC-ACTTTTTACCTTTATAATTGAAGCCCA
* * * * *
3272 TAATTTTTTATTCTCACTTTTTA-CATTTATAATCGAGGTCCCTAATTTTTTCAATCTCACTTTT
1 TAATTTTTTAATCTCACTTTTTAGC-TTTATAAT-TAAGCCCCTAATTTTTTTAATCTCACTTTT
* * * * * * * *
3336 TATCTTTATAGTTGAGGTCCCTAATTTTTTTAATCTCACTTTCTACCTTTATGATTGAAGCCCT
64 TACCTTTATAATTGAGATACCTAATTTTTTCAATC-CACTTTTTACCTTTATAATTGAAGCCCA
** * *
3400 TATATTTTTTAATCTTGCTTTTTAGCTTTATAATTGAGGCCCTAATTTTTTTCAATC
1 TA-ATTTTTTAATCTCACTTTTTAGCTTTATAATTAAGCCCCTAATTTTTTT-AATC
3457 CAACTATATA
Statistics
Matches: 254, Mismatches: 46, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
127 11 0.04
128 163 0.64
129 71 0.28
130 9 0.04
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.51
Consensus pattern (126 bp):
TAATTTTTTAATCTCACTTTTTAGCTTTATAATTAAGCCCCTAATTTTTTTAATCTCACTTTTTA
CCTTTATAATTGAGATACCTAATTTTTTCAATCCACTTTTTACCTTTATAATTGAAGCCCA
Found at i:3473 original size:43 final size:42
Alignment explanation
Indices: 3012--3491 Score: 317
Period size: 43 Copynumber: 11.2 Consensus size: 42
3002 GATTAAGACT
* * * *
3012 CCTAATTTTTTCAATTTCACTTTTTATCTTTATAACTGAAGTC
1 CCTAATTTTTTTAATCTCACTTTTTATCTTTATAATTG-AGGC
** * * * * *
3055 TTTAAATTTTTTT-ATCTGAGTTTTTCACCTTTATAATTAAAGTC
1 CCT-AATTTTTTTAATCTCACTTTTT-ATCTTTATAATT-GAGGC
* * * * *
3099 TCTAGTTTTTTTCAATCACA-TTTTTACCTTTATAATTGAGTCC
1 CCTAATTTTTTT-AATCTCACTTTTTATCTTTATAATTGAG-GC
* * * * * *
3142 CCTAA-ATTTTTAATCTCACATTATAGCTTTATAATTAAAGCC
1 CCTAATTTTTTTAATCTCACTTTTTATCTTTATAATT-GAGGC
** **
3184 CCTAATTTTTTTAATCTCACTTTTTCCCTTTATAATTGAGATA
1 CCTAATTTTTTTAATCTCACTTTTTATCTTTATAATTGAG-GC
** * * *
3227 TTTAATTTTTTCAATC-CAACTTTTTACCTTTATAATTGAAG-
1 CCTAATTTTTTTAATCTC-ACTTTTTATCTTTATAATTGAGGC
* * *
3268 CCTATAATTTTTTATTCTCACTTTTTA-CATTTATAATCGAGGTC
1 CCTA-ATTTTTTTAATCTCACTTTTTATC-TTTATAATTGAGG-C
* *
3312 CCTAATTTTTTCAATCTCACTTTTTATCTTTATAGTTGAGGTC
1 CCTAATTTTTTTAATCTCACTTTTTATCTTTATAATTGAGG-C
* * * *
3355 CCTAATTTTTTTAATCTCACTTTCTACCTTTATGATTGAAGC
1 CCTAATTTTTTTAATCTCACTTTTTATCTTTATAATTGAGGC
* ** *
3397 CCTTATATTTTTTAATCTTGCTTTTTAGCTTTATAATTGAGGC
1 CCTAAT-TTTTTTAATCTCACTTTTTATCTTTATAATTGAGGC
* * * *
3440 CCTAATTTTTTTCAATC-CAACTATATATATTTATAATTTAGGC
1 CCTAATTTTTTT-AATCTC-ACTTTTTATCTTTATAATTGAGGC
*
3483 TTCTAATTT
1 -CCTAATTT
3492 AATCATTTTT
Statistics
Matches: 345, Mismatches: 71, Indels: 41
0.75 0.16 0.09
Matches are distributed among these distances:
41 9 0.03
42 71 0.21
43 220 0.64
44 41 0.12
45 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.50
Consensus pattern (42 bp):
CCTAATTTTTTTAATCTCACTTTTTATCTTTATAATTGAGGC
Found at i:11618 original size:63 final size:65
Alignment explanation
Indices: 11551--11674 Score: 182
Period size: 63 Copynumber: 1.9 Consensus size: 65
11541 TGTACTAAGA
* * *
11551 GTGCATCGATGCATCAAGTGCATTCGAT-TTTTCA-AAATAT-CAGAGTGCATCGATGCATGGTT
1 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ATCCACAGTGCATCGATGCATGGTT
11613 G
65 G
*
11614 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATG
1 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAATCCACAGTGCATCGATGCATG
11675 AAATGCATTC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
63 26 0.48
64 8 0.15
65 20 0.37
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (65 bp):
GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAATCCACAGTGCATCGATGCATGGTTG
Found at i:11786 original size:20 final size:20
Alignment explanation
Indices: 11714--11779 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
11704 GATGCATCAA
11714 TGCATCGATGCATGGATTGG
1 TGCATCGATGCATGGATTGG
* *
11734 TGCATTGATGTATGGATTGG
1 TGCATCGATGCATGGATTGG
11754 TGCATCGATGCATGGATTGG
1 TGCATCGATGCATGGATTGG
11774 TGCATC
1 TGCATC
11780 AGTGCATCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.33
Consensus pattern (20 bp):
TGCATCGATGCATGGATTGG
Found at i:12459 original size:14 final size:15
Alignment explanation
Indices: 12440--12468 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12430 TCAAGCATTT
12440 AACAATCCA-AAACA
1 AACAATCCAGAAACA
12454 AACAATCCAGAAACA
1 AACAATCCAGAAACA
12469 TCAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:13249 original size:15 final size:15
Alignment explanation
Indices: 13226--13255 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13216 ATTTTCATTC
*
13226 TCATTATATAACCCA
1 TCATCATATAACCCA
13241 TCATCATATAACCCA
1 TCATCATATAACCCA
13256 AAACGGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (15 bp):
TCATCATATAACCCA
Found at i:20169 original size:65 final size:64
Alignment explanation
Indices: 19971--20171 Score: 214
Period size: 65 Copynumber: 3.1 Consensus size: 64
19961 TGGACCCTTA
* * * * *
19971 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCA-GAGTGCATTGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATATCCATG-GTGCATCGATGCATGGTTG
* * *
20035 GTGCATCGATGCATCAAATCCATTCGATGTTTTC-ATAAAATCC-TCAGTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAT-ATATCCAT-GGTGCATCGATGCATGGT
20098 AT-
63 -TG
* *
20100 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATA-TCCATGGTGCATCGATGCATGG-TT
20164 G
64 G
20165 GTGCATC
1 GTGCATC
20172 ATTTTGAAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
63 4 0.04
64 50 0.44
65 59 0.52
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATATCCATGGTGCATCGATGCATGGTTG
Found at i:22453 original size:18 final size:18
Alignment explanation
Indices: 22419--22456 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
22409 CATATTATAA
*
22419 TATTATAAATTTAATTTT
1 TATTATAAATATAATTTT
22437 TATT-TAAATATATATTTT
1 TATTATAAATATA-ATTTT
22455 TA
1 TA
22457 ACTTATACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATAAATATAATTTT
Found at i:28289 original size:21 final size:22
Alignment explanation
Indices: 28242--28295 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
28232 GTATGAACAA
28242 TATCGATACCATATGGAAGGAG
1 TATCGATACCATATGGAAGGAG
*
28264 TATCGATACCA-ATGTGGAGG-G
1 TATCGATACCATATG-GAAGGAG
28285 TATCGATACCA
1 TATCGATACCA
28296 GGGAATATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (22 bp):
TATCGATACCATATGGAAGGAG
Found at i:28803 original size:15 final size:14
Alignment explanation
Indices: 28783--28812 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28773 ATAAGCTATT
28783 TATGATAATAAGATA
1 TATGATAA-AAGATA
28798 TATGATAAAAGATA
1 TATGATAAAAGATA
28812 T
1 T
28813 TGTTGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (14 bp):
TATGATAAAAGATA
Found at i:31643 original size:22 final size:22
Alignment explanation
Indices: 31605--31646 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
31595 TTATAAAATT
*
31605 GGATTAAATGGTAATTATGGAA
1 GGATTAAAAGGTAATTATGGAA
31627 GGATTAAAAGAGT-ATTATGG
1 GGATTAAAAG-GTAATTATGG
31647 TAATTTTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (22 bp):
GGATTAAAAGGTAATTATGGAA
Found at i:33220 original size:18 final size:17
Alignment explanation
Indices: 33189--33226 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
33179 ATGATATGTC
*
33189 ATATGTAGTGCTTCGGG
1 ATATGTAGTCCTTCGGG
33206 ATATAGTAGTCCTTCGGG
1 ATAT-GTAGTCCTTCGGG
33224 ATA
1 ATA
33227 AATTCTACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (17 bp):
ATATGTAGTCCTTCGGG
Found at i:35392 original size:13 final size:13
Alignment explanation
Indices: 35374--35398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35364 AATATGTTCA
35374 TTTATGTTCATTC
1 TTTATGTTCATTC
35387 TTTATGTTCATT
1 TTTATGTTCATT
35399 TATGTAATGC
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:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTATGTTCATTC
Found at i:40741 original size:50 final size:50
Alignment explanation
Indices: 40682--40781 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
40672 TTGATGAAAT
40682 TATGTTAGGGGTTTGATTATAGAAGCCGTGAAATATTGTTTAGAGGTGGA
1 TATGTTAGGGGTTTGATTATAGAAGCCGTGAAATATTGTTTAGAGGTGGA
40732 TATGTTAGGGGTTTGATTATAGAAGCCGTGAAATATTGTTTAGAGGTGGA
1 TATGTTAGGGGTTTGATTATAGAAGCCGTGAAATATTGTTTAGAGGTGGA
40782 ATCTATGTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.04, G:0.32, T:0.36
Consensus pattern (50 bp):
TATGTTAGGGGTTTGATTATAGAAGCCGTGAAATATTGTTTAGAGGTGGA
Found at i:58529 original size:19 final size:20
Alignment explanation
Indices: 58492--58529 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
58482 GATTTAACCA
*
58492 TAAAAATAGTGGCTGAAATG
1 TAAAAATAGTGGCTAAAATG
*
58512 TAAAAAT-GTGGGTAAAAT
1 TAAAAATAGTGGCTAAAAT
58530 TGGGGATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (20 bp):
TAAAAATAGTGGCTAAAATG
Found at i:60072 original size:124 final size:124
Alignment explanation
Indices: 59915--60172 Score: 408
Period size: 124 Copynumber: 2.1 Consensus size: 124
59905 GAATTGAACA
* * *
59915 AAATGTTTATGTCGATCTATCTTCTTATGCGATAAAGTCAAGCAAAAGGTTGAACAAGTTCTTCT
1 AAATGTTGATGTCGATCTATCTCCTTATACGATAAAGTCAAGCAAAAGGTTGAACAAGTTCTTCT
* * * *
59980 CATTATGAACTTCTTCTCCCTCATCGAATAAGTTCTTCTCATTATGAACTCTCCATTGG
66 CATTATGAACTTATTCTCCCTCATCAAATAAGTTATTCTCATTATGAACTCTACATTGG
* * * *
60039 AAATGTTGATGTTGATCTATCTCCTTCTACGATAGAGTCAAGCAAAAGGTTGAACAAGTTTTTCT
1 AAATGTTGATGTCGATCTATCTCCTTATACGATAAAGTCAAGCAAAAGGTTGAACAAGTTCTTCT
*
60104 CATTATGAACTTATTCTCCCTCATCAAATGAGTTATTCTCATTATGAACTCTACATTGG
66 CATTATGAACTTATTCTCCCTCATCAAATAAGTTATTCTCATTATGAACTCTACATTGG
60163 AAATGTTGAT
1 AAATGTTGAT
60173 CCCTCGAGTG
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (124 bp):
AAATGTTGATGTCGATCTATCTCCTTATACGATAAAGTCAAGCAAAAGGTTGAACAAGTTCTTCT
CATTATGAACTTATTCTCCCTCATCAAATAAGTTATTCTCATTATGAACTCTACATTGG
Found at i:60338 original size:139 final size:139
Alignment explanation
Indices: 60084--60435 Score: 535
Period size: 139 Copynumber: 2.5 Consensus size: 139
60074 AGTCAAGCAA
* * *
60084 AAGGTTGAACAAGTTTTTCTCATTATGAACTTATTCTCCCTCATCAAATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTATTCTCATTAT
* * * *
60149 GAACTCTACATTGGAAATGTTGATCCCTCGAGTGAGGTGTCGCTAATTCAACTCCATATGTGATG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCGCTAATTCAACTCCATATGCGATG
60214 AATCGAGCT
131 AATCGAGCT
*
60223 AAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTATTCTCATTAT
* * *
60288 GAACTCTCCACTGGAAATGTTGATCCCTTGAGTGAGGGGTCGTTATTTCAACTCCATATGCGATG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCGCTAATTCAACTCCATATGCGATG
*
60353 AATTGAGCT
131 AATCGAGCT
* * * *
60362 AAGGTTGAACAAGTCCTTCTTATTATGAAATTCTTCTCCCTCATCGGATGAG-TACTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTA-TTCTCATTA
*
60426 TGAACCCTCC
65 TGAACTCTCC
60436 TAGAAATAAT
Statistics
Matches: 194, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
138 2 0.01
139 192 0.99
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (139 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTATTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCGCTAATTCAACTCCATATGCGATG
AATCGAGCT
Found at i:62968 original size:6 final size:6
Alignment explanation
Indices: 62947--63000 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
62937 GAACCCTACT
* * * *
62947 TTTTTC TCTCTC TTTTTC TTTTTC -TTTTC TTCTTC -TTTT- TTTCTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
62992 TTTTTC TTT
1 TTTTTC TTT
63001 AAAATAGCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
5 11 0.30
6 26 0.70
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:65875 original size:28 final size:28
Alignment explanation
Indices: 65843--65930 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 28
65833 TTGAAACTAT
** *
65843 AAATGTAACTATACAAAGATGCAAATGC
1 AAATGTAAAAATACAAAGATGAAAATGC
* * *
65871 AAATGCAAAAATGCAAAGTTGAAAATGC
1 AAATGTAAAAATACAAAGATGAAAATGC
*** * *
65899 AAATGTGCGAATGCAAA-ATGAAAATGT
1 AAATGTAAAAATACAAAGATGAAAATGC
65926 AAATG
1 AAATG
65931 CAATGAAGGT
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
27 13 0.27
28 35 0.73
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.20
Consensus pattern (28 bp):
AAATGTAAAAATACAAAGATGAAAATGC
Found at i:67297 original size:19 final size:20
Alignment explanation
Indices: 67270--67312 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
67260 ACAGATATAG
67270 AAAAAAATTG-AAA-GAAAT
1 AAAAAAATTGTAAATGAAAT
*
67288 AAAAAGAATTGTAAATTAAAT
1 AAAAA-AATTGTAAATGAAAT
67309 AAAA
1 AAAA
67313 TTGAATTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 3 0.14
21 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (20 bp):
AAAAAAATTGTAAATGAAAT
Found at i:67326 original size:22 final size:21
Alignment explanation
Indices: 67284--67326 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
67274 AAATTGAAAG
*
67284 AAATAAAAAGAATTGTAAATT
1 AAATAAAAAGAATTCTAAATT
* *
67305 AAATAAAATTGAATTCTCAATT
1 AAATAAAA-AGAATTCTAAATT
67327 TTCAACTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
AAATAAAAAGAATTCTAAATT
Done.