Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001172.1 Hibiscus syriacus cultivar Beakdansim tig00002335_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: 55367
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1193 original size:18 final size:17
Alignment explanation
Indices: 1158--1200 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1148 ACTAAAGTCG
**
1158 AAACTAATTTAATTTAT
1 AAACTAATTTAAAGTAT
1175 AAACGTAATTTAAAGTAT
1 AAAC-TAATTTAAAGTAT
*
1193 AAAATAAT
1 AAACTAAT
1201 ATAAGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (17 bp):
AAACTAATTTAAAGTAT
Found at i:1326 original size:19 final size:19
Alignment explanation
Indices: 1302--1368 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
1292 AAATTTATAA
1302 TGCGATTTTCCAAATTCGT
1 TGCGATTTTCCAAATTCGT
** *
1321 TGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATT--CGT
1342 TGCGATTTATTCCAAATTCGT
1 TGCGA-TT-TTCCAAATTCGT
1363 TGCGAT
1 TGCGAT
1369 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
19 13 0.34
20 1 0.03
21 16 0.42
22 1 0.03
23 7 0.18
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGT
Found at i:1376 original size:19 final size:19
Alignment explanation
Indices: 1310--1376 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 19
1300 AATGCGATTT
1310 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* *
1329 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
1352 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
1371 TCCAAA
1 TCCAAA
1377 ATCGCAACGA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 15 0.38
21 16 0.40
23 9 0.22
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:2296 original size:40 final size:40
Alignment explanation
Indices: 2252--2400 Score: 159
Period size: 40 Copynumber: 3.8 Consensus size: 40
2242 GGACTTCGAC
2252 TATCGCAA-CGAACTTGGACTATCGCAACGAATTTGTAATA
1 TATCGCAACCGAACTTGGACTATCGCAACGAATTTG-AATA
*
2292 TATCGCAACACGAACTTGG---ATCGCAA-TAATTTGGAATA
1 TATCGCAAC-CGAACTTGGACTATCGCAACGAATTT-GAATA
*
2330 AATCGCAACGCGAACTTGGACTATCGCAACGAATTTAGAA-A
1 TATCGCAAC-CGAACTTGGACTATCGCAACGAATTT-GAATA
* *
2371 -ATTGCAACGCGAACTTCGACTATCGCAACG
1 TATCGCAAC-CGAACTTGGACTATCGCAACG
2401 CGAACTTGGA
Statistics
Matches: 95, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
38 26 0.27
39 8 0.08
40 36 0.38
41 8 0.08
42 17 0.18
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (40 bp):
TATCGCAACCGAACTTGGACTATCGCAACGAATTTGAATA
Found at i:2335 original size:38 final size:39
Alignment explanation
Indices: 2272--2386 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 39
2262 AACTTGGACT
* *
2272 ATCGCAACGAATTTGTAATATATCGCAACACGAACTTGG
1 ATCGCAACGAATTTGGAATAAATCGCAACACGAACTTGG
* *
2311 ATCGCAA-TAATTTGGAATAAATCGCAACGCGAACTTGG
1 ATCGCAACGAATTTGGAATAAATCGCAACACGAACTTGG
* * *
2349 ACTATCGCAACGAATTTAG-A-AAATTGCAACGCGAACTT
1 ---ATCGCAACGAATTTGGAATAAATCGCAACACGAACTT
2387 CGACTATCGC
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
38 27 0.42
39 7 0.11
40 17 0.26
41 8 0.12
42 6 0.09
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (39 bp):
ATCGCAACGAATTTGGAATAAATCGCAACACGAACTTGG
Found at i:2395 original size:99 final size:99
Alignment explanation
Indices: 2211--2411 Score: 246
Period size: 99 Copynumber: 2.0 Consensus size: 99
2201 ATTTTAGACT
* * **
2211 ATCGCAACGAATTTGGAATAAATCGCAACGCGGACTTCGACTATCGCAACGAACTTGGACTATCG
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAAAATCG
*
2276 CAACGAATTTGTAATATATCGCAACACGAACTTGG
66 CAACGAATTCG-AATATATCGCAACACGAACTTGG
* * * *
2311 ATCGCAA-TAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTAGAAAATTG
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAAAATCG
* *
2375 CAACGCGAACTTCG-A-CTATCGCAACGCGAACTTGG
66 CAA--CGAA-TTCGAATATATCGCAACACGAACTTGG
2410 AT
1 AT
2412 TATCGCAATG
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
99 72 0.83
100 8 0.09
101 4 0.05
102 3 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (99 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAAAATCG
CAACGAATTCGAATATATCGCAACACGAACTTGG
Found at i:2398 original size:21 final size:21
Alignment explanation
Indices: 2207--2425 Score: 115
Period size: 21 Copynumber: 10.8 Consensus size: 21
2197 TGCGATTTTA
*
2207 GACTATCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTG
* * *
2226 GAATAAATCGCAACGCGGACTTC
1 GACT--ATCGCAACGCGAACTTG
2249 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTG
*
2268 GACTATCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTG
* * *
2287 TAATATATCGCAACACGAACTTG
1 -GA-CTATCGCAACGCGAACTTG
* *
2310 G---ATCGCAA---TAATTTG
1 GACTATCGCAACGCGAACTTG
*
2325 GAATAAATCGCAACGCGAACTTG
1 GACT--ATCGCAACGCGAACTTG
* *
2348 GACTATCGCAA--CGAATTTA
1 GACTATCGCAACGCGAACTTG
** * *
2367 GAAAATTGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTG
2388 GACTATCGCAACGCGAACTTG
1 GACTATCGCAACGCGAACTTG
* *
2409 GATTATCGCAATGCGAA
1 GACTATCGCAACGCGAA
2426 TATGTAAATC
Statistics
Matches: 152, Mismatches: 30, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
15 6 0.04
18 7 0.05
19 41 0.27
20 8 0.05
21 67 0.44
23 23 0.15
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTG
Found at i:8857 original size:22 final size:22
Alignment explanation
Indices: 8832--8874 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
8822 ATGAAATTTC
* * *
8832 TCCCGAATGACCACTGTATATG
1 TCCCGAAGGACAACTATATATG
8854 TCCCGAAGGACAACTATATAT
1 TCCCGAAGGACAACTATATAT
8875 CCCTTGACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (22 bp):
TCCCGAAGGACAACTATATATG
Found at i:11167 original size:3 final size:3
Alignment explanation
Indices: 11159--11190 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11149 TTTCGTCCCG
11159 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11191 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:15249 original size:12 final size:12
Alignment explanation
Indices: 15231--15264 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15221 TTCGAATCAA
15231 ATTTTATTATAT
1 ATTTTATTATAT
*
15243 GTTTTATTATAT
1 ATTTTATTATAT
*
15255 ATATTATTAT
1 ATTTTATTAT
15265 TTAGGAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
ATTTTATTATAT
Found at i:15778 original size:29 final size:27
Alignment explanation
Indices: 15740--15839 Score: 128
Period size: 29 Copynumber: 3.5 Consensus size: 27
15730 TACATTTTTT
*
15740 ATATTATATTCATTTAACTAGACACTATA
1 ATATTATATTC-TTTAAC-AAACACTATA
15769 ATATTATATTCCTTTAAACAAACACTATA
1 ATATTATATT-CTTT-AACAAACACTATA
15798 ATATTATATTTCTTTAACCAAACACTATA
1 ATATTATA-TTCTTTAA-CAAACACTATA
*
15827 ATCTTATATTCTT
1 ATATTATATTCTT
15840 ATTAAACAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
28 7 0.11
29 52 0.80
30 6 0.09
ACGTcount: A:0.40, C:0.16, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATTATATTCTTTAACAAACACTATA
Found at i:27037 original size:31 final size:31
Alignment explanation
Indices: 27001--27059 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
26991 AACTTAAAAG
* *
27001 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
*
27032 AGTTTTATAATAATGAAATTTAAATAAT
1 AGTTTTACAATAATGAAATTTAAATAAT
27060 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:27108 original size:22 final size:22
Alignment explanation
Indices: 27083--27166 Score: 105
Period size: 22 Copynumber: 3.8 Consensus size: 22
27073 ATAATAAATT
*
27083 TTTTAAAATAAATCAATCGATA
1 TTTTAAAATAAATCAATCCATA
27105 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* * * *
27127 TTTTAAAATAATTTATTTTCATA
1 TTTTAAAATAAATCA-ATCCATA
*
27150 TTTTAAAACAAATCAAT
1 TTTTAAAATAAATCAAT
27167 TGTAACACCC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 35 0.67
23 17 0.33
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:30493 original size:43 final size:43
Alignment explanation
Indices: 30422--30810 Score: 559
Period size: 43 Copynumber: 9.1 Consensus size: 43
30412 TTAATTACCG
* * *
30422 TTACAGTTCCCTCAGGTCCCTTTACTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
30465 TTACAGTTCCCCCAGGTTTCTTTGCTGTGTGCAAAGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
30508 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
30550 TTACAGTTCCCCCATGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
30593 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
30636 TTACAGTTTCCCCCAGGTTCATTTGCTGTGTGCAAGGGTAAGCC
1 TTACAG-TTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
30680 TTACAGTT-GCCCAGGTTCCTTTGCTGTGTCCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
30722 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * * * * *
30764 TTACAGTTTCCTCAGGCTCTTTTGATATGTGCAAGGATAAGACC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CC
30808 TTA
1 TTA
30811 TCGTTTTTGC
Statistics
Matches: 316, Mismatches: 26, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
42 118 0.37
43 152 0.48
44 46 0.15
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:30735 original size:128 final size:128
Alignment explanation
Indices: 30422--30810 Score: 584
Period size: 128 Copynumber: 3.0 Consensus size: 128
30412 TTAATTACCG
* *
30422 TTACAGTTCCCTCAGGTCCCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTTTCTT
1 TTACAGTTCCC-CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTTCCTT
* *
30487 TGCTGTGTGCAAAGGTAAGCCTTACAGTTT-CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
65 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCATTTGCTGTGTGCAAGGGTAAGCC
* *
30550 TTACAGTTCCCCCATGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
1 TTACAGTT-CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTTCCTT
30615 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCATTTGCTGTGTGCAAGGGTAAGCC
65 TGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCATTTGCTGTGTGCAAGGGTAAGCC
* * * *
30680 TTACAGTTGCCCAGGTTCCTTTGCTGTGTCCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTTT
1 TTACAGTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTTCCTTT
* * * * * *
30744 GCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTCAGGCTCTTTTGATATGTGCAAGGATAAGACC
66 GCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCATTTGCTGTGTGCAAGGGTAAG-CC
30808 TTA
1 TTA
30811 TCGTTTTTGC
Statistics
Matches: 239, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
127 26 0.11
128 132 0.55
129 41 0.17
130 40 0.17
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (128 bp):
TTACAGTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTTCCTTT
GCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCATTTGCTGTGTGCAAGGGTAAGCC
Found at i:32753 original size:22 final size:22
Alignment explanation
Indices: 32720--32850 Score: 201
Period size: 22 Copynumber: 6.0 Consensus size: 22
32710 ATCGGTTATT
32720 AATCCATATTTTAAAATAAATC
1 AATCCATATTTTAAAATAAATC
**
32742 AATAAATATTTTAAAATAAATTC
1 AATCCATATTTTAAAATAAA-TC
*
32765 -ATCCATATTTTAAAATAAATG
1 AATCCATATTTTAAAATAAATC
**
32786 TTTCCATATTTTAAAATAAATC
1 AATCCATATTTTAAAATAAATC
32808 AATCCATATTTTAAAATAAATC
1 AATCCATATTTTAAAATAAATC
32830 AATCCATATTTTAAAATAAAT
1 AATCCATATTTTAAAATAAAT
32851 TTTAAAATAG
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
21 1 0.01
22 95 0.97
23 2 0.02
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.39
Consensus pattern (22 bp):
AATCCATATTTTAAAATAAATC
Found at i:32828 original size:66 final size:66
Alignment explanation
Indices: 32722--32850 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
32712 CGGTTATTAA
32722 TCCATATTTTAAAATAAATCAATAAATATTTTAAAATAAATTC-ATCCATATTTTAAAATAAATG
1 TCCATATTTTAAAATAAATCAATAAATATTTTAAAATAAA-TCAATCCATATTTTAAAATAAATG
32786 TT
65 TT
**
32788 TCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT
1 TCCATATTTTAAAATAAATCAATAAATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT
32851 TTTAAAATAG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 2 0.03
66 58 0.97
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.40
Consensus pattern (66 bp):
TCCATATTTTAAAATAAATCAATAAATATTTTAAAATAAATCAATCCATATTTTAAAATAAATGT
T
Found at i:32867 original size:11 final size:12
Alignment explanation
Indices: 32837--32876 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
32827 ATCAATCCAT
32837 ATTTTAAAATAA
1 ATTTTAAAATAA
*
32849 ATTTTAAAATAG
1 ATTTTAAAATAA
32861 A-TTT-AAAT-A
1 ATTTTAAAATAA
32870 ATTTTAA
1 ATTTTAA
32877 TTTCTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:32870 original size:66 final size:66
Alignment explanation
Indices: 32729--32867 Score: 192
Period size: 66 Copynumber: 2.1 Consensus size: 66
32719 TAATCCATAT
**
32729 TTTAAAATAAATCAATAAATATTTTAAAATAAATTCATCCATATTTTAAAATAAATGTTTCCATA
1 TTTAAAATAAATCAATAAATATTTTAAAATAAATTCATCCATATTTTAAAATAAATGTTTAAATA
*
32794 T
66 A
**
32795 TTTAAAATAAATCAATCCATATTTTAAAATAAA-TCAATCCATATTTTAAAATAAAT-TTTAAAA
1 TTTAAAATAAATCAATAAATATTTTAAAATAAATTC-ATCCATATTTTAAAATAAATGTTT-AAA
32858 TAGA
64 TA-A
32862 TTTAAA
1 TTTAAA
32868 TAATTTTAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
65 5 0.08
66 54 0.83
67 6 0.09
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (66 bp):
TTTAAAATAAATCAATAAATATTTTAAAATAAATTCATCCATATTTTAAAATAAATGTTTAAATA
A
Found at i:37657 original size:32 final size:32
Alignment explanation
Indices: 37603--37732 Score: 167
Period size: 32 Copynumber: 4.0 Consensus size: 32
37593 CCTTTTGAAG
37603 AGAAGAT-ATTCTCAAAATTTAAATGTTTTCTT
1 AGAAGATAATTCT-AAAATTTAAATGTTTTCTT
*
37635 AGAAGATAATT-TAAAACCTTAAATGTTTTCGTT
1 AGAAGATAATTCTAAAA-TTTAAATGTTTTC-TT
* * *
37668 AGGAGATAATTCCAAAATTTAAATGTTTCCTT
1 AGAAGATAATTCTAAAATTTAAATGTTTTCTT
37700 A-AGAGATAATTCTAAAATTTAAATGTTTTCTT
1 AGA-AGATAATTCTAAAATTTAAATGTTTTCTT
37732 A
1 A
37733 TATTCTTAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
31 4 0.05
32 51 0.60
33 26 0.31
34 4 0.05
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (32 bp):
AGAAGATAATTCTAAAATTTAAATGTTTTCTT
Found at i:37710 original size:65 final size:65
Alignment explanation
Indices: 37606--37729 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 65
37596 TTTGAAGAGA
*
37606 AGATATTCTCAAAATTTAAATGTTTTCTTAGAAGATAATT-TAAAACCTTAAATGTTTTCGTTAG
1 AGATATTCTCAAAATTTAAATGTTTCCTTAGAAGATAATTCTAAAA-CTTAAATGTTTTCGTTAG
37670 G
65 G
*
37671 AGATAATTC-CAAAATTTAAATGTTTCCTTA-AGAGATAATTCTAAAATTTAAATGTTTTC
1 AGAT-ATTCTCAAAATTTAAATGTTTCCTTAGA-AGATAATTCTAAAACTTAAATGTTTTC
37730 TTATATTCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
64 1 0.02
65 44 0.81
66 9 0.17
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (65 bp):
AGATATTCTCAAAATTTAAATGTTTCCTTAGAAGATAATTCTAAAACTTAAATGTTTTCGTTAGG
Found at i:40543 original size:3 final size:3
Alignment explanation
Indices: 40535--40619 Score: 109
Period size: 3 Copynumber: 28.0 Consensus size: 3
40525 AATATGTAAT
*
40535 TAA TAA TAA TAA TAA TAAA TAA TAA -ACA AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* * *
40581 TAA CAT TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40620 AATTAAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
2 1 0.01
3 67 0.93
4 4 0.06
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:41087 original size:129 final size:131
Alignment explanation
Indices: 40791--41149 Score: 397
Period size: 129 Copynumber: 2.7 Consensus size: 131
40781 GACGACACTG
* * * * ** * * *
40791 CTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGGTGACTCGGATCCTACGTGATGAGGAGATTT
1 CTCATACATGATGAAGAGATCTGATTATCTAAGGTTGACACGGATCCTACGTGATGAGGAGATTA
* *
40856 GGTCAGGGATGACACTA-CTCATACGTGATGAAGAGTTCTTGGCCATGTTTACGAAGGTGATAAC
66 GGTCAGGGATGACAC-AGCTCATACGTGATGAAGAGTTCTTGACCA-GTCTAC-AAGGTGATAAC
40920 ACGA
128 ACGA
* * * *
40924 CTCATACATGATGAAGAGTTCTGATTATCAAAGGTTGACACGGCTCCCACGTGATGAGGAGATTA
1 CTCATACATGATGAAGAGATCTGATTATCTAAGGTTGACACGGATCCTACGTGATGAGGAGATTA
*
40989 GGTCGAGTGATGACACAGCTCATACGTGATGAAGAGTT-TTGACCA-TCTA-AAGGTGATAACAC
66 GGTC-AGGGATGACACAGCTCATACGTGATGAAGAGTTCTTGACCAGTCTACAAGGTGATAACAC
*
41051 GG
130 GA
* * * * *
41053 TTCCTACGTGATGAGGACGAT-TGGTTATCTAAGGTTGACACGGATCCTACGTGATGAGGAGA-T
1 CTCATACATGATGAAGA-GATCTGATTATCTAAGGTTGACACGGATCCTACGTGATGAGGAGATT
* *
41116 ATGGTCAGGGGATGACACAGTTCCTACGTGATGA
65 A-GGTCA-GGGATGACACAGCTCATACGTGATGA
41150 GGATGACTGG
Statistics
Matches: 194, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
128 3 0.02
129 91 0.47
130 2 0.01
131 3 0.02
133 65 0.34
134 30 0.15
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (131 bp):
CTCATACATGATGAAGAGATCTGATTATCTAAGGTTGACACGGATCCTACGTGATGAGGAGATTA
GGTCAGGGATGACACAGCTCATACGTGATGAAGAGTTCTTGACCAGTCTACAAGGTGATAACACG
A
Found at i:41283 original size:35 final size:36
Alignment explanation
Indices: 41243--41339 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
41233 GACAAAATTC
** * **
41243 GTTTCAAGGGAAATGATCTCAAAGAT-ATTTGTTTT
1 GTTTCAAGGGAAACAAACTCAAAGATGATTAATTTT
41278 GTTTCAAGGGAAACAAACTCAAAGATGATTAATTTT
1 GTTTCAAGGGAAACAAACTCAAAGATGATTAATTTT
* *
41314 GTTTCCAA-AGAAACAGACTCAAAGAT
1 GTTT-CAAGGGAAACAAACTCAAAGAT
41340 TTTTCTTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 23 0.43
36 27 0.51
37 3 0.06
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (36 bp):
GTTTCAAGGGAAACAAACTCAAAGATGATTAATTTT
Found at i:41721 original size:30 final size:31
Alignment explanation
Indices: 41666--41724 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
41656 GATTTTTTAT
** *
41666 TTTGTTTCAAGTGAAACATACTCAAAGATCA
1 TTTGTTTCAAAAGAAACAGACTCAAAGATCA
41697 TTTGTTTCAAAAGAAAC-GACTCAAAGAT
1 TTTGTTTCAAAAGAAACAGACTCAAAGAT
41725 GATGTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGATCA
Found at i:41808 original size:35 final size:35
Alignment explanation
Indices: 41762--41854 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 35
41752 ATAATTTGGA
*
41762 AAATTGTCTCAAGTGAGACAATAAAAG-TTTTAGAG
1 AAATTGTCTCAAGCGAGACAA-AAAAGTTTTTAGAG
* ** *
41797 AAATTGTCTCAAACGAGACGAAAATTGTTTTTAGAT
1 AAATTGTCTCAAGCGAGAC-AAAAAAGTTTTTAGAG
41833 AAATTGTCTCAAGCGAGACAAA
1 AAATTGTCTCAAGCGAGACAAA
41855 GTTTGTTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
35 23 0.46
36 27 0.54
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAGACAAAAAAGTTTTTAGAG
Found at i:42053 original size:21 final size:21
Alignment explanation
Indices: 41992--42053 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
41982 TGTGAAAAAA
*
41992 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAGCGAGACAAAATT
* * * *
42013 TGTTTTAA---AGA-GAAAGT
1 TGTCTCAAGCGAGACAAAATT
42030 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGCGAGACAAAATT
42051 TGT
1 TGT
42054 TTTTAAGAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 8
0.62 0.20 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGCGAGACAAAATT
Found at i:42080 original size:36 final size:38
Alignment explanation
Indices: 41994--42094 Score: 107
Period size: 38 Copynumber: 2.7 Consensus size: 38
41984 TGAAAAAATG
* * * *
41994 TCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTG
1 TCTCAAGCGAGACAAAATTTGTTTTTAAGAGAAAGCTA
42032 TCTCAAGCGAGACAAAATTTGTTTTTAAGA-AAA-CTA
1 TCTCAAGCGAGACAAAATTTGTTTTTAAGAGAAAGCTA
* * * *
42068 TCTCTAGTGAGACGACACTTTGTTTTT
1 TCTCAAGCGAGAC-AAAATTTGTTTTT
42095 TTTAAGAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 12 0.22
37 14 0.26
38 28 0.52
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (38 bp):
TCTCAAGCGAGACAAAATTTGTTTTTAAGAGAAAGCTA
Found at i:42422 original size:4 final size:4
Alignment explanation
Indices: 42413--42450 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
42403 CTTATGTAAC
*
42413 ATGT ATGT ATGT ATGT ATGT AT-T GATAT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT ATGT AT
42451 TTCTCTATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
3 1 0.03
4 29 0.94
5 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:42753 original size:24 final size:24
Alignment explanation
Indices: 42717--42781 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
42707 CTTGTATTTT
*
42717 CAAAAG-TATGAAAATATCAATTAA
1 CAAAAGTTTTGAAAATAT-AATTAA
* *
42741 -AAGAGTTTTGAAAA-ATATTTAA
1 CAAAAGTTTTGAAAATATAATTAA
42763 TCAAAAGTTTTGAAAATAT
1 -CAAAAGTTTTGAAAATAT
42782 TGCTCCTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 5 0.15
23 6 0.18
24 20 0.61
25 2 0.06
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.32
Consensus pattern (24 bp):
CAAAAGTTTTGAAAATATAATTAA
Found at i:43652 original size:11 final size:11
Alignment explanation
Indices: 43638--43685 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
43628 TGCTTTTGTC
43638 TTCTTTTTCTT
1 TTCTTTTTCTT
43649 TTCTTTTTCTT
1 TTCTTTTTCTT
43660 TTGCTATTTTTCTT
1 TT-C--TTTTTCTT
**
43674 TGATTTTTCTT
1 TTCTTTTTCTT
43685 T
1 T
43686 GTACTCTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 22 0.69
12 1 0.03
14 9 0.28
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:45760 original size:31 final size:32
Alignment explanation
Indices: 45700--45760 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
45690 TGACAAAATG
*
45700 ACACAAACAAAAGAGAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
45732 ACACAAACAAAAGAGAA-AAACAAGTTAGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGT
45761 ACATGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.13
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
Found at i:49259 original size:3 final size:3
Alignment explanation
Indices: 49251--49332 Score: 103
Period size: 3 Copynumber: 27.0 Consensus size: 3
49241 AATATGTAAT
*
49251 TAA TAA TAA TAA TAA TAAA TAA TAA -ACA AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* * *
49297 TAA CAT TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
49333 AATTAAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
2 1 0.01
3 64 0.93
4 4 0.06
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:51904 original size:34 final size:32
Alignment explanation
Indices: 51853--51973 Score: 109
Period size: 32 Copynumber: 3.7 Consensus size: 32
51843 CAAGGAAAAC
* *
51853 CTTGGGGCCTCAAAGCCTACCCAAGGAAGCACA
1 CTTGGGGCCTGAGAGCCTACCCAAGGAAGCA-A
* * * * *
51886 CATTGGGGCCTGAGAGCCTGCCAAAAGAAGTAT
1 C-TTGGGGCCTGAGAGCCTACCCAAGGAAGCAA
* * *
51919 TTTGGGGCTTGAGAGCCTACCCAAGGGAA-CAT
1 CTTGGGGCCTGAGAGCCTACCCAA-GGAAGCAA
*
51951 CTTGGGGCCTAAGAGCCTACCCA
1 CTTGGGGCCTGAGAGCCTACCCA
51974 TGGGTCACCT
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
32 42 0.60
33 4 0.06
34 24 0.34
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.17
Consensus pattern (32 bp):
CTTGGGGCCTGAGAGCCTACCCAAGGAAGCAA
Done.