Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005367.1 Hibiscus syriacus cultivar Beakdansim tig00012200_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: 65217
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:805 original size:50 final size:51
Alignment explanation
Indices: 739--1667 Score: 933
Period size: 53 Copynumber: 18.0 Consensus size: 51
729 CGAACAATCT
* * *
739 TCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCTAACA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* *
790 T-TTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
*
840 TATTCTGCGAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG-A-A
1 TCTTCT---AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* * * * *
892 -C-TCAAACGGGTTCGCTTCCTCTTTCTTCAGGAAGTATAGAACTCGAACA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* * *
941 TCTTCTTACGGG-TCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* * *
991 TCTTCAAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACTCGAAAA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
1042 TCTTCTGCGAAC-GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
1 TCTTCT---AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* * * *
1095 TCTTCAAACGGGTTCGCTCCCTCTTT-TTTAGGAAGTATAGAACTCGAAAATCT
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG--AA-CA
* * *
1148 TCTTCTTACGGGTTCGCTCCCTCTTTCTCTA-GGAGTATGGAACTCGAAAATA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG--AACA
* * * *
1200 TTCTTCTTAC-GGTTC-CTCCTTCTTTCTTTAAGGAGTATGGAACTCGGACATCT
1 -TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTC-GA-A-CA
* * *
1253 TCTTCTTAC-GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* * * *
1303 TCTTCTTCTTACGGGTTC-CTCCTTCTTTCTTTAAGGAGTATGGAACTCGGACATCT
1 ---TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTC-GA-A-CA
* * * *
1359 TCTTCTTAA-GGATTCGCTCCTTCTTTCTTTAAGGAGTATGAAACTCGAACA
1 TCTTC-TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* * *
1410 TCTTCAAAC-GGTTCGCCCCCTCTTTCTTTA-GGAGTATGGAACTCGAAAA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* *
1459 TCTTCTGCGAACGGATTCGCT-CATCTTTCTTTAGGGAGTATGGAACTCGAACA
1 TCTTCT---AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
* * * *
1512 TCTT-TAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCT
1 TCTTCT-AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG--AA-CA
* * * *
1566 TCTTCTTACGGTTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATA
1 TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG--AACA
* * * *
1619 TTCTTCTTA-TGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAA
1 -TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAA
1668 TAATCTTTTC
Statistics
Matches: 753, Mismatches: 81, Indels: 88
0.82 0.09 0.10
Matches are distributed among these distances:
47 37 0.05
48 1 0.00
49 23 0.03
50 143 0.19
51 113 0.15
52 55 0.07
53 241 0.32
54 137 0.18
55 2 0.00
56 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (51 bp):
TCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA
Found at i:870 original size:104 final size:105
Alignment explanation
Indices: 729--1678 Score: 1116
Period size: 104 Copynumber: 9.1 Consensus size: 105
719 GAGAGAGACA
* * *
729 CGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCTAACAT-TT
1 CGAA-AATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
793 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
65 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * *
834 CGAAAATATTCTGCGAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG-A-A-C-TC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
* * * *
895 AAACGGGTTCGCTTCCTCTTTCTTCAGGAAGTATAGAACT
66 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * *
935 CGAACATCTTC-T-T-ACGGG-TCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
*
996 AAACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATGGAACT
66 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* *
1036 CGAAAATCTTCTGCGAAC-GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
* *
1100 AAACGGGTTCGCTCCCTCTTT-TTTAGGAAGTATAGAACT
66 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * *
1139 CGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTA-GGAGTATGGAACTCGAAAATATTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG--AACA-TC
** * *
1203 TTCTTAC-GGTTC-CTCCTTCTTTCTTTAAGGAGTATGGAACT
63 TTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * *
1244 CGGACATCTTCTTCTTAC-GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACA---TC
** * *
1308 TTCTTACGGGTTC-CTCCTTCTTTCTTTAAGGAGTATGGAACT
63 TTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * * *
1350 CGGACATCTTCTTCTTAA-GGATTCGCTCCTTCTTTCTTTAAGGAGTATGAAACTCGAACATCTT
1 CGAAAATCTTCTTC-TAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
*
1414 CAAAC-GGTTCGCCCCCTCTTTCTTTA-GGAGTATGGAACT
65 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * * *
1453 CGAAAATCTTCTGCGAACGGATTCGCT-CATCTTTCTTTAGGGAGTATGGAACTCGAACATCTTT
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
* * *
1517 AAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
66 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
* * * *
1557 CGAAAATCTTCTTCTTACGGTTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATATTC
1 CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCG--AACA-TC
** * * *
1622 TTCTTA-TGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACT
63 TTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
1664 CGAATAATCTT-TTCT
1 CGAA-AATCTTCTTCT
1679 GCTTCACTAT
Statistics
Matches: 736, Mismatches: 80, Indels: 56
0.84 0.09 0.06
Matches are distributed among these distances:
97 32 0.04
98 6 0.01
99 1 0.00
100 1 0.00
101 94 0.13
102 40 0.05
103 109 0.15
104 211 0.29
105 94 0.13
106 55 0.07
107 82 0.11
108 11 0.01
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (105 bp):
CGAAAATCTTCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTC
AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACT
Found at i:2156 original size:36 final size:36
Alignment explanation
Indices: 2045--2239 Score: 176
Period size: 36 Copynumber: 5.4 Consensus size: 36
2035 ACTCTTCCTA
* * * * **
2045 GAAGGCTTAAAATGGATTTCCTTCACGACTCTTTTAT
1 GAAGGCTTAAGATGG-TTTGCTTCACTATTCTTTGGT
* ** *
2082 GAAGACACAAGATGGTTTACTTCACTATTCTTTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* * *
2118 GAAGGCTTAAGATGGTTTGCTTCCCTACTCTTTAGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* **
2154 GAAGGCTTAAGATTG-TTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* * * **
2189 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
*
2225 GAAGGCTTCAGATGG
1 GAAGGCTTAAGATGG
2240 ACTTTGCCCC
Statistics
Matches: 133, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
35 29 0.22
36 93 0.70
37 11 0.08
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
Found at i:2227 original size:71 final size:71
Alignment explanation
Indices: 2101--2237 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 71
2091 AGATGGTTTA
** * * **
2101 CTTCACTATTCTTTGGTGAAGGCTTAAGATGGTTTGCTTCCCTACTCTTTAGTGAAGGCTTAAGA
1 CTTCACTATTCTCCGGTGAAGGCTTAAGATGGATTGCTTCACTACTCTCCAGTGAAGGCTTAAGA
2166 TTGTTG
66 TTGTTG
* * * * *
2172 CTTCACTATTCTCCGGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGTGAAGGCTTCAGA
1 CTTCACTATTCTCCGGTGAAGGCTTAAGATGGATTGCTTCACTACTCTCCAGTGAAGGCTTAAGA
2237 T
66 T
2238 GGACTTTGCC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (71 bp):
CTTCACTATTCTCCGGTGAAGGCTTAAGATGGATTGCTTCACTACTCTCCAGTGAAGGCTTAAGA
TTGTTG
Found at i:3770 original size:125 final size:124
Alignment explanation
Indices: 3544--3798 Score: 357
Period size: 125 Copynumber: 2.0 Consensus size: 124
3534 ACTAGTGCTG
*** * * * *
3544 CAACATTATCTTATACTGGTATGGGCCTTCAAAATGCCTCAACACCTCAATTTGTAAGGCTCATT
1 CAACATTATCTTATACTGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAAGCCCATT
* * *
3609 CTCAACGCCTTCTTGGTCTGAATCTCATCATTTCAACATGATGTTGGTTCAGTCGTGCCC
66 CTCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATG-GGGTTCAGTCGTGCCC
* *
3669 CAACATTATCTTATACTGGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAAGCCCGTT
1 CAACATTATCTTATACTGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAAGCCCATT
* * **
3734 CTTAATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGGGGTTCAGTCGTGCCC
66 CTCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATGGGGTTCAGTCGTGCCC
3793 CAACAT
1 CAACAT
3799 ATCACAACTT
Statistics
Matches: 114, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
124 21 0.18
125 93 0.82
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (124 bp):
CAACATTATCTTATACTGGTACAAGCCTTCAAAATGCCCCAACACCTCAAATTGTAAAGCCCATT
CTCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATGGGGTTCAGTCGTGCCC
Found at i:11871 original size:10 final size:10
Alignment explanation
Indices: 11856--11899 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
11846 GTATTTGTGT
11856 TGTTCGTTTA
1 TGTTCGTTTA
11866 TGTTCGTTTA
1 TGTTCGTTTA
11876 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
11889 TGTTCATTTA
1 TGTTCGTTTA
11899 T
1 T
11900 TATGTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 20 0.67
13 10 0.33
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:11886 original size:23 final size:23
Alignment explanation
Indices: 11856--11936 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
11846 GTATTTGTGT
11856 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCGTTTATTG
* *
11879 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCGTTTATTG
**
11902 TGTTATTTTATGTTCGTTCGT-TTG
1 TGTTCGTTTATGTTCGTT--TATTG
*
11926 CGTTCGTTTAT
1 TGTTCGTTTAT
11937 CATTTAATTG
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 36 0.77
24 10 0.21
25 1 0.02
ACGTcount: A:0.11, C:0.10, G:0.19, T:0.60
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTTATTG
Found at i:20436 original size:3 final size:3
Alignment explanation
Indices: 20417--20528 Score: 147
Period size: 3 Copynumber: 37.7 Consensus size: 3
20407 TCTACAAAAA
*
20417 TAT TA- TAT TAT T-G 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
* * * *
20463 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAC TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
20511 TAT TAAT TAT TAA TAT TA
1 TAT T-AT TAT TAT TAT TA
20529 ATACATATTA
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
2 3 0.03
3 94 0.94
4 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:21195 original size:2 final size:2
Alignment explanation
Indices: 21188--21254 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
21178 TTTTTAAAAC
21188 AT AT 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 AT AT
21230 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 A
21255 ACCCCATCCG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21443 original size:24 final size:24
Alignment explanation
Indices: 21416--21524 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
21406 AAACGGAGAT
*
21416 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
21440 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
21464 ATCAAAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
21488 GTAATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
*
21511 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
21525 TAAAAAATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.01
24 67 0.99
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:21445 original size:12 final size:12
Alignment explanation
Indices: 21418--21487 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
21408 ACGGAGATAT
* *
21418 CAGAAATCAAAA
1 CAGAATTCAGAA
*
21430 CAGAATTCAGAT
1 CAGAATTCAGAA
21442 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
21454 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
21466 CAAAAATCAGAA
1 CAGAATTCAGAA
21478 CAGAATTCAG
1 CAGAATTCAG
21488 GTAATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:21521 original size:48 final size:48
Alignment explanation
Indices: 21416--21524 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
21406 AAACGGAGAT
* * *
21416 ATCAGAAATCAAAACAGAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
* *
21464 ATCAAAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAA-TCAAG
*
21513 -TCGGAAATCAGA
1 ATCAGAAATCAGA
21525 TAAAAAATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 47 0.90
49 5 0.10
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
Found at i:22672 original size:18 final size:18
Alignment explanation
Indices: 22651--22686 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22641 CTGTCATCCG
*
22651 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
22669 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
22687 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:24022 original size:15 final size:15
Alignment explanation
Indices: 24002--24035 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
23992 GGTCAACGCC
24002 GGTCAACAGTCAACG
1 GGTCAACAGTCAACG
*
24017 GGTCAACGGTCAACG
1 GGTCAACAGTCAACG
24032 GGTC
1 GGTC
24036 GGGTCGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (15 bp):
GGTCAACAGTCAACG
Found at i:26207 original size:30 final size:30
Alignment explanation
Indices: 26171--26551 Score: 400
Period size: 30 Copynumber: 12.7 Consensus size: 30
26161 CTGTAATTAC
* *
26171 TATTTTAATCCTTTAAGTTTTTATTTTTGT
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
**
26201 TATTTTAGTCCTTTAAGTTTCCGTTTTTGT
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
* * * *
26231 TAATTTAGTCCTTTAAGTTTCTGTTTATGC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
* *
26261 TA-TTTAGCCCTTTAAGTTTCTATTTTTAT
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
** * * *
26290 TATTTTAGTAGTTTAAATTTTTATTTTTGC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
*
26320 TATTTTAGTCCCTTAA-TTTCTATTTTT-T
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
* *
26348 CCTATTTTAGTCCTTTAAGTTTATGTTTTT-T
1 --TATTTTAGTCCTTTAAGTTTCTATTTTTGT
*
26379 CTATTTTAGTCCTTTAAG-TT-TATGTTTTGC
1 -TATTTTAGTCCTTTAAGTTTCTAT-TTTTGT
*
26409 TATTTTAGTCCTTTAAGTTTCTATTTTTTT
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
*
26439 ATATTTTAGTCCTTTAAGTTTCTATTTTTTTTT
1 -TATTTTAGTCCTTTAAGTTTCTA--TTTTTGT
* *
26472 TATTTTAGTCCTTTAAGTTTTTATTTTTTT
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
* **
26502 TATTTTAATCCTTTAAGTTTCT-TTTTTAC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTGT
*
26531 TATTTTAGTCC-TCAAGTTTCT
1 TATTTTAGTCCTTTAAGTTTCT
26552 GTTAATCTTA
Statistics
Matches: 301, Mismatches: 39, Indels: 24
0.83 0.11 0.07
Matches are distributed among these distances:
28 11 0.04
29 72 0.24
30 153 0.51
31 36 0.12
32 22 0.07
33 7 0.02
ACGTcount: A:0.18, C:0.11, G:0.08, T:0.62
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAGTTTCTATTTTTGT
Found at i:26246 original size:60 final size:60
Alignment explanation
Indices: 26171--26542 Score: 407
Period size: 59 Copynumber: 6.2 Consensus size: 60
26161 CTGTAATTAC
* **
26171 TATTTTAATCCTTTAAGTTTTTATTTTTGTTATTTTAGTCCTTTAAGTTTCCGTTTTTGT
1 TATTTTAGTCCTTTAAGTTTTTATTTTTGTTATTTTAGTCCTTTAAGTTTCTATTTTTGT
* * * * * * *
26231 TAATTTAGTCCTTTAAGTTTCTGTTTATGCTA-TTTAGCCCTTTAAGTTTCTATTTTTAT
1 TATTTTAGTCCTTTAAGTTTTTATTTTTGTTATTTTAGTCCTTTAAGTTTCTATTTTTGT
** * * *
26290 TATTTTAGTAGTTTAAATTTTTATTTTTGCTATTTTAGTCCCTTAA-TTTCTATTTTT-T
1 TATTTTAGTCCTTTAAGTTTTTATTTTTGTTATTTTAGTCCTTTAAGTTTCTATTTTTGT
* * *
26348 CCTATTTTAGTCCTTTAAGTTTATGTTTTT-TCTATTTTAGTCCTTTAAG-TT-TATGTTTTGC
1 --TATTTTAGTCCTTTAAGTTTTTATTTTTGT-TATTTTAGTCCTTTAAGTTTCTAT-TTTTGT
* * *
26409 TATTTTAGTCCTTTAAGTTTCTATTTTTTTATATTTTAGTCCTTTAAGTTTCTATTTTTTTTT
1 TATTTTAGTCCTTTAAGTTTTTATTTTTGT-TATTTTAGTCCTTTAAGTTTCTA--TTTTTGT
* * **
26472 TATTTTAGTCCTTTAAGTTTTTATTTTTTTTATTTTAATCCTTTAAGTTTCT-TTTTTAC
1 TATTTTAGTCCTTTAAGTTTTTATTTTTGTTATTTTAGTCCTTTAAGTTTCTATTTTTGT
26531 TATTTTAGTCCT
1 TATTTTAGTCCT
26543 CAAGTTTCTG
Statistics
Matches: 264, Mismatches: 36, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
58 1 0.00
59 105 0.40
60 99 0.38
61 2 0.01
62 23 0.09
63 33 0.12
64 1 0.00
ACGTcount: A:0.18, C:0.11, G:0.08, T:0.62
Consensus pattern (60 bp):
TATTTTAGTCCTTTAAGTTTTTATTTTTGTTATTTTAGTCCTTTAAGTTTCTATTTTTGT
Found at i:28361 original size:37 final size:32
Alignment explanation
Indices: 28280--28357 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
28270 GTACTAACGA
28280 ATTTCTTTTCTTTTGTTTGTGTACACTAATTT
1 ATTTCTTTTCTTTTGTTTGTGTACACTAATTT
28312 ATTTCTTTTCTTTTGTTTGTGTACACTAATTT
1 ATTTCTTTTCTTTTGTTTGTGTACACTAATTT
28344 ATTTCTTTTCTTTT
1 ATTTCTTTTCTTTT
28358 CTTTATATCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.14, C:0.13, G:0.08, T:0.65
Consensus pattern (32 bp):
ATTTCTTTTCTTTTGTTTGTGTACACTAATTT
Found at i:28482 original size:126 final size:126
Alignment explanation
Indices: 28324--28577 Score: 481
Period size: 126 Copynumber: 2.0 Consensus size: 126
28314 TTCTTTTCTT
28324 TTGTTTGTGTACACTAATTTATTTCTTTTCTTTTCTTTATATCATTTATCATCATTTTTGCATTG
1 TTGTTTGTGTACACTAATTTATTTCTTTTCTTTTCTTTATATCATTTATCATCATTTTTGCATTG
*
28389 CATTGCATCATCATGACATAATGAGAAAGTGTTGATCCGTAAGGGGATATTCAAGAGAAAA
66 CATTGCATCATCATGACATAATGAGAAAGTGTTGATCCGCAAGGGGATATTCAAGAGAAAA
28450 TTGTTTGTGTACACTAATTTATTTCTTTTCTTTTCTTTATATCATTTATCATCATTTTTGCATTG
1 TTGTTTGTGTACACTAATTTATTTCTTTTCTTTTCTTTATATCATTTATCATCATTTTTGCATTG
* *
28515 TATTGCATCATCATGACATAATGTGAAAGTGTTGATCCGCAAGGGGATATTCAAGAGAAAA
66 CATTGCATCATCATGACATAATGAGAAAGTGTTGATCCGCAAGGGGATATTCAAGAGAAAA
28576 TT
1 TT
28578 TTCACAAGAA
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (126 bp):
TTGTTTGTGTACACTAATTTATTTCTTTTCTTTTCTTTATATCATTTATCATCATTTTTGCATTG
CATTGCATCATCATGACATAATGAGAAAGTGTTGATCCGCAAGGGGATATTCAAGAGAAAA
Found at i:30353 original size:12 final size:12
Alignment explanation
Indices: 30336--30384 Score: 73
Period size: 12 Copynumber: 4.1 Consensus size: 12
30326 AAAAACAAAG
30336 AGCAAAGAGAAA
1 AGCAAAGAGAAA
30348 AGCAAAGAGAAA
1 AGCAAAGAGAAA
*
30360 AG-AAAAAGAAA
1 AGCAAAGAGAAA
30371 AGCAAAGAGCAAA
1 AGCAAAGAG-AAA
30384 A
1 A
30385 AGAAAATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 10 0.30
12 19 0.58
13 4 0.12
ACGTcount: A:0.69, C:0.08, G:0.22, T:0.00
Consensus pattern (12 bp):
AGCAAAGAGAAA
Found at i:30386 original size:19 final size:19
Alignment explanation
Indices: 30323--30390 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
30313 AAAAAGAAGC
30323 AAAA-AAAA-CAAAGAGCA
1 AAAAGAAAAGCAAAGAGCA
* *
30340 AAGAGAAAAGCAAAGAGAAAAGA
1 AAAAGAAAAGCAAAGAG----CA
30363 AAAAGAAAAGCAAAGAGCA
1 AAAAGAAAAGCAAAGAGCA
30382 AAAAGAAAA
1 AAAAGAAAA
30391 TAAGAAGCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 3 0.07
18 4 0.10
19 17 0.41
23 17 0.41
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGCAAAGAGCA
Found at i:31644 original size:37 final size:37
Alignment explanation
Indices: 31601--31691 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
31591 AAACAAAGGG
*
31601 TCGTCTCGCTTGAGACAAGTTTT-CTTAAAAATAAATT
1 TCGTCTCGCTTGAGACAAGTTTTAC-TAAAAACAAATT
* * *
31638 TTGTCTCACTCGAGAC-AGTTTTAGCTAAAAACAAATT
1 TCGTCTCGCTTGAGACAAGTTTTA-CTAAAAACAAATT
*
31675 TCATCTCGCTTGAGACA
1 TCGTCTCGCTTGAGACA
31692 TTTTTCCTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
36 6 0.14
37 36 0.84
38 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (37 bp):
TCGTCTCGCTTGAGACAAGTTTTACTAAAAACAAATT
Found at i:31965 original size:64 final size:64
Alignment explanation
Indices: 31806--32015 Score: 239
Period size: 62 Copynumber: 3.3 Consensus size: 64
31796 ACTTTGAAAT
* * * *
31806 TGTTTCTCTTAAAACAAAGTTTTGTCTTTCTTGAGACAGTTTCTT-TTG---AAGATATTTGAGT
1 TGTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTT-TTCTTGAAAAAAATCTTTGAGT
31867 A
64 A
* *
31868 TGTTTTTCTTGAAACAATGTTTTGTCTCTCTTGAGATAGTTTTTCTTGAAAAAAATCTTTGAGTA
1 TGTTTCTCTTGAAACAA-GTTTTGTCTCTCTTGAGACAGTTTTTCTTGAAAAAAATCTTTGAGTA
* * **
31933 TGTTTCTCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACCTATCTTTGAGT
1 TGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGAAA-A-AAATCTTTGAGT
*
31998 C
64 A
*
31999 TGTTTCCCTTGAAACAA
1 TGTTTCTCTTGAAACAA
32016 AACAAACAAC
Statistics
Matches: 127, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
61 4 0.03
62 38 0.30
64 30 0.24
65 29 0.23
66 26 0.20
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (64 bp):
TGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGAAAAAAATCTTTGAGTA
Found at i:32394 original size:20 final size:19
Alignment explanation
Indices: 32244--32386 Score: 106
Period size: 20 Copynumber: 7.6 Consensus size: 19
32234 GGGTTATAAA
*
32244 TATTATATGA-AA-ATTAT
1 TATTATATTATAATATTAT
32261 TATTATTATTAT--TATTAT
1 TATTA-TATTATAATATTAT
*
32279 TATTATTATTAT--TATTAAAC
1 TATTA-TATTATAATATT--AT
* *
32299 AATTATATTATAATTATCAT
1 TATTATATTATAA-TATTAT
32319 TA-TATATTAT-A-ATTAT
1 TATTATATTATAATATTAT
32335 TATTATATTATAATTATTAT
1 TATTATATTATAA-TATTAT
32355 TATTATATTATAATAATTAT
1 TATTATATTATAAT-ATTAT
*
32375 TAGTAATATTAT
1 TA-TTATATTAT
32387 TAATTTATGT
Statistics
Matches: 104, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
16 6 0.06
17 13 0.12
18 27 0.26
19 15 0.14
20 32 0.31
21 8 0.08
22 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (19 bp):
TATTATATTATAATATTAT
Found at i:32405 original size:3 final size:3
Alignment explanation
Indices: 32256--32388 Score: 130
Period size: 3 Copynumber: 45.3 Consensus size: 3
32246 TTATATGAAA
* **
32256 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-A ACA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
32303 A-T ATT ATA ATT ATC ATT ATAT ATT ATA ATT ATT ATT A-T ATT ATA
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
32347 ATT ATT ATT ATT A-T ATT ATA ATA ATT ATT AGT AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
32389 ATTTATGTTT
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
2 7 0.06
3 99 0.91
4 3 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:35559 original size:135 final size:131
Alignment explanation
Indices: 35306--35579 Score: 334
Period size: 135 Copynumber: 2.1 Consensus size: 131
35296 CGTTTCGACA
* * *
35306 ATAACCAGTCGTCCACATCACGTAAGAACCGTGTTATCACCCCCTAAAGATGGCATGTCATCTCA
1 ATAACCAGCCGTCCACATCACGTAAGAACCGTGTTATCACCCCCTAAAGATGGCAAGACATCTCA
* * * *
35371 TCACGTAGGTACCATGTCATCCACCGACCAAACCTCCTCATCATGTAGAAGCCGTGTCTCCCCTA
66 TCACGTAGGAACAATGTCATCCACCGACCAAACCTCCTCATCACGTAGAAGCCGTGTCACCCCTA
35436 G
131 G
* ** *
35437 ATAACCAGCCGTCCTCATCGTGTAAGAATCGTGTTATCACCCTCCCTAAAGATGGCCAAGACATC
1 ATAACCAGCCGTCCACATCACGTAAGAACCGTGTTATCA-CC-CCCTAAAGATGG-CAAGACAT-
* * * * *
35502 CTTATCACGTAGGAACAATGTCATTCC-CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAC
62 CTCATCACGTAGGAACAATGTCA-TCCACCGACCAAACCTCCTCATCACGTAGAAGCCGTGTCAC
*
35566 CCTTAG
126 CCCTAG
*
35572 ATGACCAG
1 ATAACCAG
35580 ACCTTTTAGG
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
131 34 0.28
132 2 0.02
133 12 0.10
134 6 0.05
135 63 0.52
136 3 0.03
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.23
Consensus pattern (131 bp):
ATAACCAGCCGTCCACATCACGTAAGAACCGTGTTATCACCCCCTAAAGATGGCAAGACATCTCA
TCACGTAGGAACAATGTCATCCACCGACCAAACCTCCTCATCACGTAGAAGCCGTGTCACCCCTA
G
Found at i:35783 original size:3 final size:3
Alignment explanation
Indices: 35777--35818 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
35767 TATATTATTG
*
35777 TAT TAT TAT TAT TAC TAT TAT TAT TAAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA
35819 CATATTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:35825 original size:16 final size:15
Alignment explanation
Indices: 35777--35818 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
35767 TATATTATTG
35777 TATTATTATTATTAC
1 TATTATTATTATTAC
*
35792 TATTATTATTAATTAT
1 TATTATTATT-ATTAC
35808 TATTATTATTA
1 TATTATTATTA
35819 CATATTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:37299 original size:30 final size:30
Alignment explanation
Indices: 37264--37509 Score: 291
Period size: 30 Copynumber: 8.2 Consensus size: 30
37254 TTTGTAATTA
* * *
37264 CTATTTTAATCTTTTAAGTTTATGTTTTTG
1 CTATTTTAATCCTTTAAGTTTCTATTTTTG
* *
37294 CTATTTTAGTCCTTTAAGTTTCTGTTTTTG
1 CTATTTTAATCCTTTAAGTTTCTATTTTTG
* * *
37324 -T-TGTTT-AGCCTTTAATTTTCTATTTTTT
1 CTAT-TTTAATCCTTTAAGTTTCTATTTTTG
37352 CTATTTTAATCCTTTAAGTTTCTATTTTTG
1 CTATTTTAATCCTTTAAGTTTCTATTTTTG
* *
37382 CTATTTTAGTCCTTTAAGTTTCTATTTGTG
1 CTATTTTAATCCTTTAAGTTTCTATTTTTG
* * *
37412 CTATTTTAGTCTTTTAAGTTTCTATTTTTTT
1 CTATTTTAATCCTTTAAGTTTCTA-TTTTTG
* * * *
37443 CTATTTTAGTCTTTTAAGTTTTTGTTTTTG
1 CTATTTTAATCCTTTAAGTTTCTATTTTTG
*
37473 CTATTTTAACCCTTTAAGTTTCTATTTTTG
1 CTATTTTAATCCTTTAAGTTTCTATTTTTG
37503 CTATTTT
1 CTATTTT
37510 GGTCCTCAAA
Statistics
Matches: 187, Mismatches: 24, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
28 18 0.10
29 8 0.04
30 135 0.72
31 26 0.14
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (30 bp):
CTATTTTAATCCTTTAAGTTTCTATTTTTG
Found at i:46978 original size:21 final size:21
Alignment explanation
Indices: 46953--46997 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
46943 ATTCTTAAAA
*
46953 GATATGCTGAAAAATTGCTTT
1 GATATGCTCAAAAATTGCTTT
*
46974 GATATGCTCAAGAATTGCTTT
1 GATATGCTCAAAAATTGCTTT
46995 GAT
1 GAT
46998 TTTTTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (21 bp):
GATATGCTCAAAAATTGCTTT
Found at i:52657 original size:21 final size:21
Alignment explanation
Indices: 52631--52677 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
52621 GTTTCCAGAT
52631 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
52652 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
52673 TCGCA
1 TCGCA
52678 TTACGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:52718 original size:21 final size:20
Alignment explanation
Indices: 52698--53044 Score: 414
Period size: 21 Copynumber: 16.8 Consensus size: 20
52688 CATATTCGCA
52698 TTGCGATAG-TCCAAGTTCG
1 TTGCGATAGCTCCAAGTTCG
** *
52717 CATTGCGAT-TTTCCAAATTCG
1 --TTGCGATAGCTCCAAGTTCG
52738 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
* *
52759 TTGTGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
* *
52780 TTGCGATAATCTCCAAATTCG
1 TTGCGAT-AGCTCCAAGTTCG
52801 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
52822 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
52843 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
52864 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
52885 TTGTGATAGTCTCCAA-TTCG
1 TTGCGATAG-CTCCAAGTTCG
52905 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
52926 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
*
52947 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
52968 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
52989 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
53010 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
53031 TTGCGATAG-TCCAA
1 TTGCGATAGCTCCAA
53045 AATCGCAACG
Statistics
Matches: 302, Mismatches: 18, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
19 12 0.04
20 20 0.07
21 269 0.89
22 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (20 bp):
TTGCGATAGCTCCAAGTTCG
Found at i:52754 original size:42 final size:41
Alignment explanation
Indices: 52698--53041 Score: 489
Period size: 42 Copynumber: 8.3 Consensus size: 41
52688 CATATTCGCA
*
52698 TTGCGATAG--TCCAAGTTCGCATTGCGAT-TTTCCAAATTCG
1 TTGCGATAGTCTCCAAGTTCG--TTGCGATATCTCCAAATTCG
*
52738 TTGCGATAGTCTCCAAGTTCGTTGTGATAGTCTCCAAATTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAATTCG
* * *
52780 TTGCGATAATCTCCAAATTCGTTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAATTCG
* *
52822 TTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAATTCG
*
52864 TTGCGATAGTCTCCAAGTTCGTTGTGATAGTCTCC-AATTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAATTCG
52905 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAATTCG
* *
52947 TTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAATTCG
52989 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATA-TCTCCAAATTCG
53031 TTGCGATAGTC
1 TTGCGATAGTC
53042 CAAAATCGCA
Statistics
Matches: 284, Mismatches: 15, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
40 15 0.05
41 39 0.14
42 230 0.81
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (41 bp):
TTGCGATAGTCTCCAAGTTCGTTGCGATATCTCCAAATTCG
Found at i:52799 original size:63 final size:63
Alignment explanation
Indices: 52728--53041 Score: 567
Period size: 63 Copynumber: 5.0 Consensus size: 63
52718 ATTGCGATTT
* * *
52728 TCCAAATTCGTTGCGATAGTCTCCAAGTTCGTTGTGATAGTCTCCAAATTCGTTGCGATAATC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
*
52791 TCCAAATTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
*
52854 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGTGATAGTCTCC-AATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
*
52916 TCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
52979 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
53042 CAAAATCGCA
Statistics
Matches: 243, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
62 60 0.25
63 183 0.75
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (63 bp):
TCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTC
Found at i:53670 original size:6 final size:6
Alignment explanation
Indices: 53644--53709 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
53634 TCTCGTCTCG
53644 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
53689 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
53710 AATACGTGTC
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.25
6 45 0.75
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:54036 original size:21 final size:21
Alignment explanation
Indices: 53997--54039 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
53987 CACTGAGTTT
53997 TTTTCTCTATATTTTTTGGTCA
1 TTTTCTCTATA-TTTTTGGTCA
54019 TTTTCTCTCATA-TTTTGGTCA
1 TTTTCTCT-ATATTTTTGGTCA
54040 CTCTTTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 8 0.40
23 3 0.15
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTTCTCTATATTTTTGGTCA
Found at i:54475 original size:23 final size:23
Alignment explanation
Indices: 54432--54477 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
54422 ACATATTAGG
**
54432 TAGCGCTTACATAATGTAATAGA
1 TAGCGCTTACATAATAAAATAGA
*
54455 TAGCGCTTATATAATAAAATAGA
1 TAGCGCTTACATAATAAAATAGA
54478 CATTTAACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (23 bp):
TAGCGCTTACATAATAAAATAGA
Found at i:54537 original size:87 final size:93
Alignment explanation
Indices: 54388--54630 Score: 345
Period size: 87 Copynumber: 2.6 Consensus size: 93
54378 GGTTATGTTA
*
54388 TATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTACATAATGTAATA
1 TATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATA
54453 GATAGCGCTTATATAAT-AAA-A-TA-G
66 GATAGCGCTTATATAATAAAATATTATG
*
54477 -A-CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGTGCTTATATAATGTAATA
1 TATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATA
* *
54540 GGTAGCTCTTATATAATAAAATATGTTATG
66 GATAGCGCTTATATAATAAAATA--TTATG
* *
54570 TTATATCATTTAACCGGAAATATTATCAAGTACAATAACATATTATGTAGCGTTTATATAA
1 ---TATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAA
54631 AAATAGATTA
Statistics
Matches: 136, Mismatches: 7, Indels: 13
0.87 0.04 0.08
Matches are distributed among these distances:
87 75 0.55
88 4 0.03
89 1 0.01
92 2 0.01
93 1 0.01
97 1 0.01
98 52 0.38
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (93 bp):
TATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATA
GATAGCGCTTATATAATAAAATATTATG
Found at i:54562 original size:23 final size:23
Alignment explanation
Indices: 54515--54562 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
54505 AATAACATAT
**
54515 TAGGTAGTGCTTATATAATGTAA
1 TAGGTAGTGCTTATATAATAAAA
54538 TAGGTAGCT-CTTATATAATAAAA
1 TAGGTAG-TGCTTATATAATAAAA
54561 TA
1 TA
54563 TGTTATGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (23 bp):
TAGGTAGTGCTTATATAATAAAA
Found at i:55198 original size:199 final size:197
Alignment explanation
Indices: 54785--55928 Score: 1496
Period size: 199 Copynumber: 5.7 Consensus size: 197
54775 GTGCATTATC
* * * * ** * * *
54785 AAAACGTGTTGATACATTATGTTGACATATTTTCTAATT-GACTAATATATTTCTACTGGATACA
1 AAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAAC-GGTATATTTATACCGGTTACA
* * * * * *
54849 TTGTAAATTTACCTATTATACTATAATTATTGGTTTCGATATTTTTGGGGTCGATAC-TTTTAAT
65 TTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGGTCGATACAATTT--T
* * * *
54913 AAATGTATCGACACTTTATGTGTGCACCTCATTTGGCATTCATTCTGGACACAAAGTATCGACAC
128 AAATGTATCGACACTTTATGCGTGCACCTC-GTTGGCATTCATTCTGGAAAAAAAGTATCGACAC
54978 -AATTT
192 AAATTT
* * * * * *
54983 AAATAGTGTTGATACATTATATTGACCTATTTTCTAACTAAATCGGTATATTTATATCGATTACA
1 AAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAA-CGGTATATTTATACCGGTTACA
* *
55048 TTGCAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGTTCGATACAATTTTAA
65 TTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGGTCGATACAATTTTAA
* *
55113 ATGTATCGACACTTTATGCGTGCACCTCGTTGGTTATTCATTCTGGAAAAAAAATATCGACACAA
130 ATGTATCGACACTTTATGCGTGCACCTCGTTGG-CATTCATTCTGGAAAAAAAGTATCGACACAA
*
55178 ACTT
194 ATTT
* *
55182 AAAAAGTGTCGATACATTATATTGACCTATTTTCTAACTAAACTGGTATATTTATACCGGTTACA
1 AAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAAC-GGTATATTTATACCGGTTACA
*
55247 TTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTTTAA
65 TTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGGTCGATACAATTTTAA
* *
55312 ATGTATCGACATTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAACGTATCGACACAA
130 ATGTATCGACACTTTATGCGTGCACCTCGTT-GGCATTCATTCTGGAAAAAAAGTATCGACACAA
55377 ATTT
194 ATTT
*
55381 AAAAAGTGTCGATACAATATGTTGACCTATTTTCTAATTAAACTGGTATATTTATACCGGTTACA
1 AAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAAC-GGTATATTTATACCGGTTACA
* * *
55446 TTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACAATTTTAA
65 TTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGGTCGATACAATTTTAA
* * *
55511 ATGTATCGACACTTTATGCGTGCACCTCATTAGGCATTCGTTCTAG-AAAAAAGTATCGACACAA
130 ATGTATCGACACTTTATGCGTGCACCTCGTT-GGCATTCATTCTGGAAAAAAAGTATCGACACAA
55575 ATTT
194 ATTT
* *
55579 AAAAAGTGTCGATACATTGTGTTGACCTATTTTCTAATTAAACCGGTATATTTCTACCGGTTACA
1 AAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAA-CGGTATATTTATACCGGTTACA
* * * * *
55644 TTGTAAATTTACATATTACATTATAGTTATCGGTTTCGATGTTTTTGGGGTC-A-ATAGTTTTGA
65 TTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGGTCGATACAATTTT--
* *
55707 AAAATGTATCGACATTTTATGTGTGCACCTCGTTTGGGCATTCATTCT-GAACAAAAAGTATCGA
128 -AAATGTATCGACACTTTATGCGTGCACCTCG-TT-GGCATTCATTCTGGAA-AAAAAGTATCGA
*
55771 CACAAATTC
189 CACAAATTT
* * * * * *
55780 CACAAGTGTCGATACATTATGTTGACATGTTTTCTAATTAAACCGGTATGTTTCTACCGGTTACA
1 AAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAA-CGGTATATTTATACCGGTTACA
* *
55845 TTGTAAATTTACCTATTACATTATAATTATCGGTTTTGATGTTTTTGGGGTCGATAC--TTTTGA
65 TTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGGTCGATACAATTTT--
55908 AAAATGTATCGACACTTTATG
128 -AAATGTATCGACACTTTATG
55929 TTTACATATT
Statistics
Matches: 852, Mismatches: 78, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
196 6 0.01
197 5 0.01
198 217 0.25
199 448 0.53
200 20 0.02
201 154 0.18
202 1 0.00
203 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (197 bp):
AAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACGGTATATTTATACCGGTTACAT
TGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGGTCGATACAATTTTAAA
TGTATCGACACTTTATGCGTGCACCTCGTTGGCATTCATTCTGGAAAAAAAGTATCGACACAAAT
TT
Found at i:59542 original size:2 final size:2
Alignment explanation
Indices: 59535--59566 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59525 GTCTCCGGAG
59535 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
59567 CATTCCCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60691 original size:209 final size:200
Alignment explanation
Indices: 60195--60941 Score: 829
Period size: 201 Copynumber: 3.8 Consensus size: 200
60185 GTAATTTAAT
* * * *
60195 AAAGTATCGACACAAATTTAAAAAGTGTCGATATATTATTTTGACCTATTTTCTAATTAAACTGG
1 AAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTATAATTAAACTGA
* ** * *
60260 TATATTTATACTGGTTACATTGTAAATTTATATATTACATTATAATTATCGGTTTTGATGTTTTT
66 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTT
* * * *
60325 GGGGTCGATACTTTTTACAAATGTATCGACACTTTATGCGTGCAGCTCGTTTGGGCGTTGATTCT
131 GGGGTCGATAC-TTATAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCGTTCATTCT
60390 GGACAA
195 GGACAA
* * * **
60396 AAAGTATCGACACAAATTTAAAAAGTGTTGATACATTATGTTCATCGCTTTTATAATTAAACTGA
1 AAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTATAATTAAACTGA
60461 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTT
66 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTT
60526 GGGGTCGATACTTATAGAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGGCTTTGGGCA
131 GGGGTCGATACTTATA-AAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GGGC-----G--
60591 TTCATTCTGGACAA
187 TTCATTCTGGACAA
**
60605 AAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTATAATTAAACCAA
1 AAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTATAATTAAACTGA
* * * ** * *
60670 TATTTTTATACCCGTTACATTGT-CATGAAACCTATTACATTATAATCA-TCGTGTTCGATGTTT
66 TATATTTATACCGGTTACATTGTAAAT-TTACCTATTACATTATAATTATTGGT-TTCGATGTTT
* * *
60733 TT--GG-C-AT-C----------G-AT----ACTTTATGCGTGCACCTTGTTTGAGCATTCATTC
129 TTGGGGTCGATACTTATAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCGTTCATTC
60778 TGGACAAA
194 TGGAC-AA
* * * * * *
60786 AAAGTGTCGACACAAATTTAAAAAGTATTGATACATTATGTTGACCTATTTTCTAATT-AACCGG
1 AAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTATAATTAAACTGA
* * * *
60850 TATATTTATACCCGGTTACATTGTTAATTTACCTATTACATTATAATGATTGGTTTCAATGGTTT
66 TATATTTATA-CCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTT
*
60915 TGGGGTCGATACTTTTAGAAAATGTAT
130 TGGGGTCGATACTTATA-AAAATGTAT
60942 AAACACATTT
Statistics
Matches: 464, Mismatches: 50, Indels: 67
0.80 0.09 0.12
Matches are distributed among these distances:
180 25 0.05
181 96 0.21
182 5 0.01
183 2 0.00
184 1 0.00
185 2 0.00
186 1 0.00
187 3 0.01
188 21 0.05
192 2 0.00
193 1 0.00
197 1 0.00
198 2 0.00
200 4 0.01
201 160 0.34
202 4 0.01
204 1 0.00
205 2 0.00
206 1 0.00
207 3 0.01
208 5 0.01
209 122 0.26
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (200 bp):
AAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTATAATTAAACTGA
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTT
GGGGTCGATACTTATAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCGTTCATTCTG
GACAA
Found at i:60926 original size:181 final size:180
Alignment explanation
Indices: 60583--60929 Score: 484
Period size: 181 Copynumber: 1.9 Consensus size: 180
60573 CGTTTGGGGC
* *
60583 TTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTG
1 TTTGAGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTTG
* *
60648 ACCTATTTTATAATTAAACCAATATTTTTATACCCGTTACATTGTCATGAAACCTATTACATTAT
66 ACCTATTTTATAATTAAACCAATATATTTATACCCGTTACATTGTAATGAAACCTATTACATTAT
* *
60713 AATCATCGTGTTCGATGTTTTTGGCATCGATACTTTATGCGTGCACCTTG
131 AATCATCGTGTTCAATGGTTTTGGCATCGATACTTTATGCGTGCACCTTG
* *
60763 TTTGAGCATTCATTCTGGACAAAAAAGTGTCGACACAAATTTAAAAAGTATTGATACATTATGTT
1 TTTGAGCATTCATTCTGGAC-AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTT
* ** **
60828 GACCTATTTTCTAATT-AACCGGTATATTTATACCCGGTTACATTGTTAAT-TTACCTATTACAT
65 GACCTATTTTATAATTAAACCAATATATTTATACCC-GTTACATTG-TAATGAAACCTATTACAT
* * **
60891 TATAATGATTG-GTTTCAATGGTTTTGGGGTCGATACTTT
128 TATAATCATCGTG-TTCAATGGTTTTGGCATCGATACTTT
60930 TAGAAAATGT
Statistics
Matches: 146, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
180 36 0.25
181 107 0.73
182 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (180 bp):
TTTGAGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTTG
ACCTATTTTATAATTAAACCAATATATTTATACCCGTTACATTGTAATGAAACCTATTACATTAT
AATCATCGTGTTCAATGGTTTTGGCATCGATACTTTATGCGTGCACCTTG
Done.