Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006224.1 Hibiscus syriacus cultivar Beakdansim tig00014834_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: 77066
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:371 original size:198 final size:190
Alignment explanation
Indices: 1--400 Score: 613
Period size: 198 Copynumber: 2.1 Consensus size: 190
*
1 TGCACCCTGTTTTCCATTCATTATGGACCAAAAATATCGACAAACTAAAAAAGTCGACACATTAT
1 TGCA-CCTGTTTTCCATTCATTATGGACCAAAAATATCGACAAACTAAAAAAGTCAACACATTAT
* *
66 TTAGACATATTCTCTCATAAAACCGGTGTACTTGTACCGTTTAAATTGAAAAATTAATATTACAT
65 TTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAAATTGAAAAATTAATATTACAT
*
131 TATACTTTTGGTTTTTGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGT
130 TATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGG-T--ACACTTTAT-GT
* * *
196 TGCACCTGTTTTCCATTCATTCTGGACCAAACATATCGACACAAACTAAAAAGTGTCAACACATT
1 TGCACCTGTTTTCCATTCATTATGGACCAAAAATATCG--ACAAACTAAAAA-AGTCAACACATT
* *
261 ATTTAGATATATTCTCTCATAAAACC-GTATACTTGTACCGGTTAGATTGAAAAATTACATATTA
63 ATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAAATTGAAAAATTA-ATATTA
325 CATTTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGTACACTTTATGT
127 CA-TTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGTACACTTTATGT
390 TGCACCATGTT
1 TGCACC-TGTT
401 GGCCATATTG
Statistics
Matches: 190, Mismatches: 9, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
194 40 0.21
195 17 0.09
196 40 0.21
197 44 0.23
198 49 0.26
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (190 bp):
TGCACCTGTTTTCCATTCATTATGGACCAAAAATATCGACAAACTAAAAAAGTCAACACATTATT
TAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAAATTGAAAAATTAATATTACATT
ATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGTACACTTTATGT
Found at i:540 original size:19 final size:19
Alignment explanation
Indices: 516--561 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
506 ATATTCACAT
516 CAAAATTATAAATCGTATA
1 CAAAATTATAAATCGTATA
*
535 CAAAATTATAAATCTTATA
1 CAAAATTATAAATCGTATA
554 CAAAATTA
1 CAAAATTA
562 ACCATACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (19 bp):
CAAAATTATAAATCGTATA
Found at i:2370 original size:33 final size:33
Alignment explanation
Indices: 2333--2398 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2323 CATCTTAATA
*
2333 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * *
2366 TCACCCCTCAACATCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
2399 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:2468 original size:21 final size:20
Alignment explanation
Indices: 2432--2495 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
2422 CCCCTTATGC
* *
2432 CTCTCAAGTGTATCTTCAACT
1 CTCTCAAGTTTCTCTTC-ACT
*
2453 CTCTCAAGTTTCTCTTCGCT
1 CTCTCAAGTTTCTCTTCACT
*
2473 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTC-ACT
2494 CT
1 CT
2496 TGATTGTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.17, C:0.31, G:0.09, T:0.42
Consensus pattern (20 bp):
CTCTCAAGTTTCTCTTCACT
Found at i:2479 original size:20 final size:21
Alignment explanation
Indices: 2435--2495 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
2425 CTTATGCCTC
* * * *
2435 TCAAGTGTATCTTCAACTCTC
1 TCAAGTTTCTCTTCGACTCTA
2456 TCAAGTTTCTCTTCG-CTCTA
1 TCAAGTTTCTCTTCGACTCTA
2476 TCAAGTTTCTCTTCGACTCT
1 TCAAGTTTCTCTTCGACTCT
2496 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.18, C:0.30, G:0.10, T:0.43
Consensus pattern (21 bp):
TCAAGTTTCTCTTCGACTCTA
Found at i:4711 original size:17 final size:18
Alignment explanation
Indices: 4689--4731 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
4679 ATATATCCGG
4689 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
4706 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
4726 TATCAT
1 TATCAT
4732 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:4749 original size:20 final size:19
Alignment explanation
Indices: 4694--4740 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
4684 TCCGGTATCA
4694 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
4713 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
4734 TTTTACC
1 TTTTACC
4741 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:4898 original size:20 final size:20
Alignment explanation
Indices: 4871--4917 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
4861 TCCGGTAACG
4871 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
4890 TTCTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
4911 TTTTACC
1 TTTTACC
4918 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:5144 original size:182 final size:176
Alignment explanation
Indices: 4661--5131 Score: 649
Period size: 177 Copynumber: 2.6 Consensus size: 176
4651 CGTACTTACG
* * *
4661 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAAT-TATCCGGTAACGTTTTACCGGTTTTATCA-TTTCATACCGGTTT
* **
4726 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTAAAGTATCGACACATTATA
64 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATA-CATTTTTAAAGTATCGACACATTATA
4791 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA
128 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA
*
4840 AAAGTATCGACACTTTCAA-TATCCGGTAACGTTTTACCGGTTTTATCATTTTCTTACCGGTTTT
1 AAAGTATCGACACTTTCAATTATCCGGTAACGTTTTACCGGTTTTATCA-TTTCATACCGGTTTT
* *
4904 ATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTATA
65 ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTT-AAAGTATCGACACATTATA
* *
4969 GGAC-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATA
128 GG-CGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA
* * * * * *
5018 TTAAAGTACCGAAACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACTGGT
1 --AAAGTATCGACACTTTCAAT-TATCCGGTAACGTTTTACCGGTTTTATCATTTC-ATACCGGT
* * *
5083 TTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAA
62 TTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
5132 TTTGGATCGA
Statistics
Matches: 262, Mismatches: 22, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
177 81 0.31
178 63 0.24
179 20 0.08
180 18 0.07
181 9 0.03
182 71 0.27
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (176 bp):
AAAGTATCGACACTTTCAATTATCCGGTAACGTTTTACCGGTTTTATCATTTCATACCGGTTTTA
TCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAGTATCGACACATTATAGGC
GCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA
Found at i:7978 original size:21 final size:21
Alignment explanation
Indices: 7927--7979 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
7917 ATTATGACTA
7927 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
7948 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
7969 TCGCAATGCGA
1 TCGCAATGCGA
7980 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:8012 original size:21 final size:20
Alignment explanation
Indices: 7969--8016 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
7959 TTTTCCCAAT
*
7969 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
7989 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
8010 TCGCAAT
1 TCGCAAT
8017 ACGATACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:8034 original size:20 final size:20
Alignment explanation
Indices: 8018--8143 Score: 128
Period size: 20 Copynumber: 6.2 Consensus size: 20
8008 AATCGCAATA
*
8018 CGATACTGACTATCGCAAGG
1 CGATACTGACTATCGCAACG
* *
8038 CGATAAT-ACAAAATCGCAACG
1 CGATACTGAC--TATCGCAACG
*
8059 CGATACTGACTTTCGCAACG
1 CGATACTGACTATCGCAACG
* *
8079 CGATTCTGACTTTCGCAACG
1 CGATACTGACTATCGCAACG
* *
8099 CGATTCTGACTTTCGCAACG
1 CGATACTGACTATCGCAACG
* *
8119 AGATTCTGACTATCGCAACG
1 CGATACTGACTATCGCAACG
*
8139 AGATA
1 CGATA
8144 ATACATAATC
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 75 0.81
21 14 0.15
22 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
CGATACTGACTATCGCAACG
Found at i:8082 original size:41 final size:42
Alignment explanation
Indices: 8006--8118 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 42
7996 GCGAATTTGG
** * *
8006 AAAATCGCAATACGATACTGACTATCGCAAGGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
**
8047 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
8089 --TTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTTTCGCAACG
8119 AGATTCTGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 27 0.44
41 33 0.53
42 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:8108 original size:40 final size:40
Alignment explanation
Indices: 8050--8143 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
8040 ATAATACAAA
*
8050 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
* *
8090 TTCGCAACGCGATTCTGACTTTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
*
8130 ATCGCAACGAGATA
1 ATCGCAACGCGATA
8144 ATACATAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
ATCGCAACGCGATACTGACTTTCGCAACGAGATTCTGACT
Found at i:8714 original size:20 final size:20
Alignment explanation
Indices: 8689--8743 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
8679 CAACGGGGAA
*
8689 ATCGCAACGCGAAAATGACT
1 ATCGCAACGAGAAAATGACT
* *
8709 ATCGCAAAGAG-AAATGGCT
1 ATCGCAACGAGAAAATGACT
8728 ATCGCAACGAGAAAAT
1 ATCGCAACGAGAAAAT
8744 CTTAATGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGACT
Found at i:8806 original size:19 final size:16
Alignment explanation
Indices: 8761--8812 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
8751 CGAAATGAAA
8761 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
*
8777 TCG--TTGTGATTTTC
1 TCGCATTGCGATTTTC
8791 ATTTCGCATTGCGATTTTC
1 ---TCGCATTGCGATTTTC
8810 TCG
1 TCG
8813 TTGCGATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.34
16 6 0.21
17 3 0.10
19 10 0.34
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:10433 original size:38 final size:40
Alignment explanation
Indices: 10391--10479 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 40
10381 CCTCTTCAAC
*
10391 GATGACAGTGGCCTCTTGAACG-GG-GGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGTGGAGGGGACTCTTGAGG
*
10429 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACG--TGGAGGGGACTCTTGAGG
10471 GATGACAGG
1 GATGACAGG
10480 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 20 0.45
41 2 0.05
42 22 0.50
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (40 bp):
GATGACAGGGGCCTCTTGAACGTGGAGGGGACTCTTGAGG
Found at i:10444 original size:21 final size:21
Alignment explanation
Indices: 10415--10475 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
10405 CTTGAACGGG
*
10415 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
10436 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
10457 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
10476 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:10841 original size:20 final size:20
Alignment explanation
Indices: 10816--10854 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10806 GAAGAATAGT
10816 TTACTTTCGAAACACGAAAC
1 TTACTTTCGAAACACGAAAC
* *
10836 TTACTTTCGCAACGCGAAA
1 TTACTTTCGAAACACGAAA
10855 ATGACTATCG
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:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGAAACACGAAAC
Found at i:10865 original size:20 final size:20
Alignment explanation
Indices: 10842--10928 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
10832 AAACTTACTT
10842 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
10862 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
10882 TCAG-AACGCGGAAATGGCTA
1 TC-GCAACGCGAAAATGACTA
**
10902 TCGCAACGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
10921 TCGCAACG
1 TCGCAACG
10929 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.25
20 44 0.73
21 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:10956 original size:19 final size:18
Alignment explanation
Indices: 10901--10958 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
10891 GGAAATGGCT
*
10901 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAA-CAAA
10920 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAACAAA
10934 ATCGCAACGCGAAACACAA
1 ATCGCAACGCGAAACA-AA
10953 ATCGCA
1 ATCGCA
10959 TTGCGATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 3 0.09
19 15 0.45
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (18 bp):
ATCGCAACGCGAAACAAA
Found at i:10976 original size:19 final size:19
Alignment explanation
Indices: 10954--11050 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
10944 GAAACACAAA
10954 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
10973 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
10989 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
11006 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
11022 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
11039 TCGCATTGCGAT
1 TCGCATTGCGAT
11051 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:10995 original size:14 final size:14
Alignment explanation
Indices: 10976--11034 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
10966 TTTCATTTCG
10976 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
10990 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
11007 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
11023 CGTTGCGATTTT
1 CGTTGCGATTTT
11035 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:11001 original size:33 final size:33
Alignment explanation
Indices: 10959--11050 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
10949 ACAAATCGCA
*
10959 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
10992 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
11025 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
11051 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:11057 original size:19 final size:19
Alignment explanation
Indices: 11035--11078 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
11025 TTGCGATTTT
11035 CATTTCGCA-TTGCGATAGC
1 CATTTC-CACTTGCGATAGC
*
11054 CATTTCCACGTTGCGATAGT
1 CATTTCCAC-TTGCGATAGC
11074 CATTT
1 CATTT
11079 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (19 bp):
CATTTCCACTTGCGATAGC
Found at i:11647 original size:18 final size:18
Alignment explanation
Indices: 11624--11671 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
11614 CGGGTCGATC
11624 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
11642 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
11660 AGGTGATGGCTC
1 AGGTGATGGCTC
11672 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:13039 original size:20 final size:20
Alignment explanation
Indices: 12991--13049 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
12981 AATAGTTTCT
** *
12991 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
13011 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
13031 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
13050 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:13325 original size:22 final size:22
Alignment explanation
Indices: 13298--13341 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13288 GATGGAGATA
13298 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
13320 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
13342 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:13557 original size:20 final size:20
Alignment explanation
Indices: 13529--13601 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
13519 GATTATGTAT
*
13529 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
13549 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
13569 TATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
13589 TATCGCGTTGCGA
1 TATCGCGTTGCGA
13602 TTTTGTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:13705 original size:21 final size:22
Alignment explanation
Indices: 13656--13705 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
13646 TACTTATTCA
*
13656 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGAGAAAATCG
**
13677 CAACGCGAAATT-AGAAAATCG
1 CATTGCGAAATTGAGAAAATCG
13698 CATTGCGA
1 CATTGCGA
13706 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGAGAAAATCG
Found at i:14059 original size:6 final size:7
Alignment explanation
Indices: 14042--14066 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
14032 CAAAGTCTTT
14042 AAAAAGG
1 AAAAAGG
14049 AAAAAGG
1 AAAAAGG
14056 AAAAAGG
1 AAAAAGG
14063 AAAA
1 AAAA
14067 TCTCGTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:16857 original size:29 final size:28
Alignment explanation
Indices: 16824--16891 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 28
16814 TATCTATTTT
16824 AATCTTAAATCTTAAAATTC-AAAACTCTA
1 AATCTTAAAT-TT-AAATTCTAAAACTCTA
16853 AATCTTAAAATTTAAATTCTAAAACTCTA
1 AATCTT-AAATTTAAATTCTAAAACTCTA
16882 AATCTTAAAT
1 AATCTTAAAT
16892 ATATATAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
28 10 0.27
29 23 0.62
30 4 0.11
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (28 bp):
AATCTTAAATTTAAATTCTAAAACTCTA
Found at i:16868 original size:14 final size:15
Alignment explanation
Indices: 16844--16890 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
16834 CTTAAAATTC
16844 AAAACTCTAAATCTT
1 AAAACTCTAAATCTT
*
16859 AAAA-TTTAAAT-TCT
1 AAAACTCTAAATCT-T
16873 AAAACTCTAAATCTT
1 AAAACTCTAAATCTT
16888 AAA
1 AAA
16891 TATATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 11 0.41
15 14 0.52
16 1 0.04
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAACTCTAAATCTT
Found at i:18006 original size:21 final size:22
Alignment explanation
Indices: 17956--18006 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
17946 ATTTTCATTT
*
17956 TATGAAAAATATAAAACAAATA
1 TATGAAATATATAAAACAAATA
*
17978 TATG-AATATATAAAA-AATTA
1 TATGAAATATATAAAACAAATA
*
17998 TGTGAAATA
1 TATGAAATA
18007 AGTTATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 7 0.28
21 14 0.56
22 4 0.16
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (22 bp):
TATGAAATATATAAAACAAATA
Found at i:21588 original size:30 final size:30
Alignment explanation
Indices: 21379--21571 Score: 350
Period size: 30 Copynumber: 6.4 Consensus size: 30
21369 TCCGAAGGAC
21379 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
21409 CTATACAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
21439 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
21469 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
21499 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
21529 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
21559 CTATCCATAGGTC
1 CTATCCAGAGGTC
21572 CCAAACAACC
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 156 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:21588 original size:90 final size:90
Alignment explanation
Indices: 21379--21596 Score: 328
Period size: 90 Copynumber: 2.4 Consensus size: 90
21369 TCCGAAGGAC
* * * * *
21379 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATACAGAGGTCATAAAGATCCTCGATAACTATC
1 CTATCCAGAGGTCACAAACAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGATAACTATC
21444 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * * *
21469 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGATAACTATC
1 CTATCCAGAGGTCACAAACAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGATAACTATC
21534 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* *
21559 CTATCCATAGGTCCCAAACAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAACAACCTAGGT-AACTATCCA
21597 TATGTTCCTT
Statistics
Matches: 120, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 111 0.93
91 9 0.08
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (90 bp):
CTATCCAGAGGTCACAAACAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGATAACTATC
CAGAGGTCATAAAGATCCTCGGTAA
Found at i:21832 original size:4 final size:4
Alignment explanation
Indices: 21823--21847 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
21813 ATATAACCAT
21823 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
21848 GTCATCCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:22016 original size:2 final size:2
Alignment explanation
Indices: 22004--22036 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
21994 TACACAACTC
22004 AT AT A- 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
22037 TGTAACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25854 original size:117 final size:117
Alignment explanation
Indices: 25598--25964 Score: 472
Period size: 117 Copynumber: 3.1 Consensus size: 117
25588 ATTATGTTAC
* * * * * *
25598 TCATGTCAGTACCCAAAGTTGTGAAAGGGCGTTCCTGGGGGGGCGCCTTCTATTATTTTATCAGA
1 TCATGTCAATACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGA
*
25663 TAATAT-TTATCATTGCCCTATTATGTCACTCATGTC-CTTCGAGGGCACTAT
66 TAATATGTTATCATTGCCCTATTATGTCACTCATGTCTC-TCGGGGGCACTAT
* *
25714 TCATGT-AAGTACCCAAAGTGGTGAAAGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAG
1 TCATGTCAA-TACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAG
*
25778 ATAATATGTTATCATTGCCCTATTATATCACTCATGTCTCTCGGGGGCACTAT
65 ATAATATGTTATCATTGCCCTATTATGTCACTCATGTCTCTCGGGGGCACTAT
* * * * * *
25831 TTATGTCAATACCAAAAGTGGTGAAAGCACGTTCTCGGGGGGGGGGGGCGCCTTCGATTGTTTTG
1 TCATGTCAATACCCAAAGTGGTGAAAGCGCGTTC-C----CGGGGGGGCGCCTTCCATTATTTTG
* * *
25896 TCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCTC-CTGGGGAACTAT
61 TCAGATAATATGTTATCATTGCCCTATTATGTCACTCATGTCTCTCGGGGGCACTAT
25952 TCATGTCAATACC
1 TCATGTCAATACC
25965 TATTATTTCT
Statistics
Matches: 219, Mismatches: 23, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
115 1 0.00
116 61 0.28
117 68 0.31
118 4 0.02
121 22 0.10
122 63 0.29
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (117 bp):
TCATGTCAATACCCAAAGTGGTGAAAGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGA
TAATATGTTATCATTGCCCTATTATGTCACTCATGTCTCTCGGGGGCACTAT
Found at i:26288 original size:63 final size:63
Alignment explanation
Indices: 26208--26468 Score: 283
Period size: 63 Copynumber: 4.0 Consensus size: 63
26198 ATTATGTGAA
*
26208 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
** *
26271 GTTTGAATTTATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
* * * * *** *
26334 G--TGACATTGAAATTGTATGAAATGATCATCGACATGTTTTTACGAATAAATTTGAAGTGATAA
1 GTTTGA-A-T-AAATTGGATAAAATG-TTAT-G-GAT-AAATT--GAATAAATGTGAAGTGATAA
26397 GTTGGTT
57 GTTGGTT
* * * *
26404 GTTTAAATAAAATGGATAAAATATTATGGATAAATTGAATAAATGTGAAGTGAAAAGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
26467 GT
1 GT
26469 GACATTGAAA
Statistics
Matches: 162, Mismatches: 25, Indels: 22
0.78 0.12 0.11
Matches are distributed among these distances:
61 3 0.02
62 1 0.01
63 90 0.56
64 11 0.07
65 5 0.03
66 3 0.02
67 3 0.02
68 5 0.03
69 11 0.07
70 27 0.17
71 1 0.01
72 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (63 bp):
GTTTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:26391 original size:70 final size:70
Alignment explanation
Indices: 26307--26536 Score: 244
Period size: 70 Copynumber: 3.4 Consensus size: 70
26297 TGGATAAATT
*
26307 GAATAAATGTGAAGTGATCAGTTGGTTGTGACATTGAAATTGTATGAAATGATCATCGACATGTT
1 GAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGAAATGATCATCGACATGTT
*
26372 TTTAC
66 ATTAC
* * * * * * * * *
26377 GAATAAATTTGAAGTGATAAGTTGGTTGTTTA-AAT-AAAATGGATAAAAT-ATTAT-G-GAT-A
1 GAATAAATGTGAAGTGATAAGTTGGTTG-TGACATTGAAATTGTATGAAATGATCATCGACATGT
*
26436 AATT--
65 TATTAC
* *
26440 GAATAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCG-AATGAGCATCGACATGT
1 GAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTAT-GAAATGATCATCGACATGT
*
26504 TCTTAC
65 TATTAC
26510 GAATAAATGTGAAGTGATAAGTTGGTT
1 GAATAAATGTGAAGTGATAAGTTGGTT
26537 TTAATGTATA
Statistics
Matches: 124, Mismatches: 26, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
62 2 0.02
63 28 0.23
64 10 0.08
65 5 0.04
66 3 0.02
67 3 0.02
68 6 0.05
69 11 0.09
70 54 0.44
71 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (70 bp):
GAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGAAATGATCATCGACATGTT
ATTAC
Found at i:26400 original size:133 final size:133
Alignment explanation
Indices: 26244--26536 Score: 471
Period size: 133 Copynumber: 2.2 Consensus size: 133
26234 TGGATAAATT
* * ** * *
26244 GAATAAATGTGAAGTGATCAGTTGGTTGTTTGAATTTATTGGATAAAATGTTATGGATAAATTGA
1 GAATAAATGTGAAGTGATAAGTTGGTTGTTTAAATAAAATGGATAAAATATTATGGATAAATTGA
** * *
26309 ATAAATGTGAAGTGATCAGTTGGTTGTGACATTGAAATTGTAT-GAAATGATCATCGACATGTTT
66 ATAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCG-AATGAGCATCGACATGTTC
26373 TTAC
130 TTAC
*
26377 GAATAAATTTGAAGTGATAAGTTGGTTGTTTAAATAAAATGGATAAAATATTATGGATAAATTGA
1 GAATAAATGTGAAGTGATAAGTTGGTTGTTTAAATAAAATGGATAAAATATTATGGATAAATTGA
26442 ATAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCGAATGAGCATCGACATGTTCT
66 ATAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCGAATGAGCATCGACATGTTCT
26507 TAC
131 TAC
26510 GAATAAATGTGAAGTGATAAGTTGGTT
1 GAATAAATGTGAAGTGATAAGTTGGTT
26537 TTAATGTATA
Statistics
Matches: 147, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
133 146 0.99
134 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (133 bp):
GAATAAATGTGAAGTGATAAGTTGGTTGTTTAAATAAAATGGATAAAATATTATGGATAAATTGA
ATAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATCGAATGAGCATCGACATGTTCT
TAC
Found at i:26553 original size:14 final size:14
Alignment explanation
Indices: 26534--26560 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26524 TGATAAGTTG
26534 GTTTTAATGTATAC
1 GTTTTAATGTATAC
26548 GTTTTAATGTATA
1 GTTTTAATGTATA
26561 TGTTAAGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.52
Consensus pattern (14 bp):
GTTTTAATGTATAC
Found at i:27288 original size:21 final size:21
Alignment explanation
Indices: 27237--27288 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
27227 GGTGTCATAA
* *
27237 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
27258 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
27279 AACCCTGCGG
1 AACCCTGCGG
27289 AGATGGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:27297 original size:42 final size:42
Alignment explanation
Indices: 27251--27354 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
27241 CTACGGGCTA
* * * *
27251 GGCATGTAACCTGGCGGGCTAGGAATGTAACCC-TGCGGAGAT
1 GGCATATAAACTGGCGGGCTAGGAATAT-ACCCATGAGGAGAT
* * *
27293 GGCATATAAACTGGTGGGCTTGGCATATACCCATGAGGAGAT
1 GGCATATAAACTGGCGGGCTAGGAATATACCCATGAGGAGAT
* *
27335 GGCATATGAACTGGAGGGCT
1 GGCATATAAACTGGCGGGCT
27355 GGGCATCATC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.08
42 48 0.92
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (42 bp):
GGCATATAAACTGGCGGGCTAGGAATATACCCATGAGGAGAT
Found at i:28738 original size:26 final size:27
Alignment explanation
Indices: 28698--28757 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
28688 ACCAGTTTCC
*
28698 TAAA-TAATATGAATT-A-TAAAAATT
1 TAAATTAATATAAATTCATTAAAAATT
*
28722 TATAATTAATATAAATTCATTATAAATT
1 TA-AATTAATATAAATTCATTAAAAATT
28750 TAAATTAA
1 TAAATTAA
28758 AAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.07
25 2 0.07
26 10 0.33
27 7 0.23
28 9 0.30
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
TAAATTAATATAAATTCATTAAAAATT
Found at i:28925 original size:18 final size:19
Alignment explanation
Indices: 28874--28927 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
28864 ATAATTGTAG
28874 ACAAAAAAATATAATTAGC
1 ACAAAAAAATATAATTAGC
28893 ACAAAAAAATATAATTAGC
1 ACAAAAAAATATAATTAGC
28912 ACAAAAAAAT-TAATTA
1 ACAAAAAAATATAATTA
28928 ATAAATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.17
19 29 0.83
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.22
Consensus pattern (19 bp):
ACAAAAAAATATAATTAGC
Found at i:29313 original size:60 final size:61
Alignment explanation
Indices: 29220--29362 Score: 191
Period size: 60 Copynumber: 2.4 Consensus size: 61
29210 TAATGCAAGG
* * * *
29220 CGCGTCCCCAGGGATGCGCCTTACCCCCGTGGCATCCGACTCAGCAGAACCCCATG-AAAA
1 CGCGTCCCCAGGGATGCGCCTTACACACGTGGCATCCGACTCAGCAGAAACCCAAGTAAAA
* * * *
29280 CGCGTCCCC-GAGGATGCGCCTTACACACGTGGCATCCTAGTCAGCATAAACCCAAGTAAAG
1 CGCGTCCCCAG-GGATGCGCCTTACACACGTGGCATCCGACTCAGCAGAAACCCAAGTAAAA
29341 CGCGTCCCCAGGGATGCGCCTT
1 CGCGTCCCCAGGGATGCGCCTT
29363 TGTGCCACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 1 0.01
60 47 0.65
61 23 0.32
62 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.24, T:0.15
Consensus pattern (61 bp):
CGCGTCCCCAGGGATGCGCCTTACACACGTGGCATCCGACTCAGCAGAAACCCAAGTAAAA
Found at i:32054 original size:2 final size:2
Alignment explanation
Indices: 32047--32113 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
32037 TACCCATTCA
32047 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
32089 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
32114 CAAATTAAGA
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:32900 original size:20 final size:21
Alignment explanation
Indices: 32861--32900 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
32851 AATTTTAATT
* *
32861 TTAAAATTAATTCTATTTATC
1 TTAAAATTAATACGATTTATC
32882 TTAAAATTAA-ACGATTTAT
1 TTAAAATTAATACGATTTAT
32901 TCATTTACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAAAATTAATACGATTTATC
Found at i:37181 original size:178 final size:178
Alignment explanation
Indices: 36882--37243 Score: 724
Period size: 178 Copynumber: 2.0 Consensus size: 178
36872 TTGCAGAGTT
36882 GTCTTCATTGATAAAGCGGCCACAGGAACAAAAGTATATACGGTTTGCTTTCATTGAGAGTCGAA
1 GTCTTCATTGATAAAGCGGCCACAGGAACAAAAGTATATACGGTTTGCTTTCATTGAGAGTCGAA
36947 CTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAGCTATGAAAGCAACTTTGAGAC
66 CTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAGCTATGAAAGCAACTTTGAGAC
37012 AATTGGTGCTTAATCTTCAAGAATCTTGTATGTCTCGTCACTTGGCCA
131 AATTGGTGCTTAATCTTCAAGAATCTTGTATGTCTCGTCACTTGGCCA
37060 GTCTTCATTGATAAAGCGGCCACAGGAACAAAAGTATATACGGTTTGCTTTCATTGAGAGTCGAA
1 GTCTTCATTGATAAAGCGGCCACAGGAACAAAAGTATATACGGTTTGCTTTCATTGAGAGTCGAA
37125 CTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAGCTATGAAAGCAACTTTGAGAC
66 CTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAGCTATGAAAGCAACTTTGAGAC
37190 AATTGGTGCTTAATCTTCAAGAATCTTGTATGTCTCGTCACTTGGCCA
131 AATTGGTGCTTAATCTTCAAGAATCTTGTATGTCTCGTCACTTGGCCA
37238 GTCTTC
1 GTCTTC
37244 TGATAGCATT
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 184 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (178 bp):
GTCTTCATTGATAAAGCGGCCACAGGAACAAAAGTATATACGGTTTGCTTTCATTGAGAGTCGAA
CTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAGCTATGAAAGCAACTTTGAGAC
AATTGGTGCTTAATCTTCAAGAATCTTGTATGTCTCGTCACTTGGCCA
Found at i:38927 original size:37 final size:36
Alignment explanation
Indices: 38874--38945 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
38864 TGTTCATGTT
** *
38874 TGTTCATTTATTTTTTAAGATGCTTGTGTTTG-GTTCG
1 TGTTCATTTAAGTTTTAA-AT-ATTGTGTTTGTGTTCG
38911 TGTTCATTTAAGTTTTAAATATTGTGTTTGTGTTC
1 TGTTCATTTAAGTTTTAAATATTGTGTTTGTGTTC
38946 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 9 0.29
36 6 0.19
37 16 0.52
ACGTcount: A:0.17, C:0.07, G:0.19, T:0.57
Consensus pattern (36 bp):
TGTTCATTTAAGTTTTAAATATTGTGTTTGTGTTCG
Found at i:39022 original size:23 final size:23
Alignment explanation
Indices: 38992--39071 Score: 151
Period size: 23 Copynumber: 3.5 Consensus size: 23
38982 TTATTGTTCG
38992 CGAACATGTTCATCTAGCTTTCA
1 CGAACATGTTCATCTAGCTTTCA
39015 CGAACATGTTCATCTAGCTTTCA
1 CGAACATGTTCATCTAGCTTTCA
*
39038 CGAACATGTTCATCTAGCGTTCA
1 CGAACATGTTCATCTAGCTTTCA
39061 CGAACATGTTC
1 CGAACATGTTC
39072 GTTTTGCGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (23 bp):
CGAACATGTTCATCTAGCTTTCA
Found at i:39109 original size:22 final size:22
Alignment explanation
Indices: 39084--39175 Score: 64
Period size: 22 Copynumber: 4.2 Consensus size: 22
39074 TTTGCGTTCA
39084 TTTAATGTTCATTTAGCATTTG
1 TTTAATGTTCATTTAGCATTTG
** *
39106 TTTAACATTCATTTAGTATTCAT-
1 TTTAATGTTCATTTAGCATT--TG
*
39129 TTTGAA--TTCATTTAGCGTTTG
1 TTT-AATGTTCATTTAGCATTTG
* ** *
39150 TTTATTGTTCGGTTATCATTTG
1 TTTAATGTTCATTTAGCATTTG
39172 TTTA
1 TTTA
39176 TATATTCAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
20 2 0.04
21 3 0.06
22 43 0.80
23 3 0.06
24 3 0.06
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.55
Consensus pattern (22 bp):
TTTAATGTTCATTTAGCATTTG
Found at i:43565 original size:21 final size:20
Alignment explanation
Indices: 43469--43626 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
43459 AAATGACCAA
**
43469 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
43488 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
43508 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
*
43528 CAAAATCGCAACACGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
43549 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
43570 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
43590 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
43611 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
43627 ACACATAAAT
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:43655 original size:20 final size:20
Alignment explanation
Indices: 43594--43822 Score: 221
Period size: 20 Copynumber: 11.4 Consensus size: 20
43584 GATTTTCAAG
* ** *
43594 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
43614 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
43634 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
43654 AACCGCAACGTGTATCTGTA
1 AATCGCAACGCGTATCCGTA
*
43674 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43694 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43714 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43734 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
43754 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
43774 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
43794 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
43814 AATCACAAC
1 AATCGCAAC
43823 ACTGAAATTT
Statistics
Matches: 173, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 169 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:44554 original size:24 final size:24
Alignment explanation
Indices: 44515--44561 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44505 AAATTTGGTC
44515 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
44539 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
44562 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:44753 original size:12 final size:12
Alignment explanation
Indices: 44736--44760 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44726 ATATAATCCT
44736 GAAGAAGAAAAA
1 GAAGAAGAAAAA
44748 GAAGAAGAAAAA
1 GAAGAAGAAAAA
44760 G
1 G
44761 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:45505 original size:19 final size:18
Alignment explanation
Indices: 45457--45495 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
45447 ATATAATTTT
45457 GTTGACTCATTTTTGTTA
1 GTTGACTCATTTTTGTTA
45475 GTTGACTCATTTTTGTTA
1 GTTGACTCATTTTTGTTA
45493 GTT
1 GTT
45496 ACATGCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.18, T:0.56
Consensus pattern (18 bp):
GTTGACTCATTTTTGTTA
Found at i:47169 original size:72 final size:72
Alignment explanation
Indices: 47075--47308 Score: 286
Period size: 72 Copynumber: 3.3 Consensus size: 72
47065 GCAACGAGAG
*
47075 AATCGCAATGCAAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
47140 AAATGAA
66 AAATGAA
* * *
47147 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
47212 AAATGAA
66 AAATGAA
* * * * * *
47219 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
47279 CG--A-GAG
64 CGAAATGAA
47285 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
47309 GCAATGCGAA
Statistics
Matches: 140, Mismatches: 18, Indels: 14
0.81 0.10 0.08
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 16 0.11
72 92 0.66
73 8 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:47189 original size:105 final size:103
Alignment explanation
Indices: 47061--47330 Score: 386
Period size: 105 Copynumber: 2.6 Consensus size: 103
47051 CGGAAATTAC
*
47061 AATCGCAACGAGAGAATCGCAATGC-AAAATGAAAATCCCAA-C-AA-GAAAATCGCAATGCGGA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAAGCAAATGAAAATCGCAA--C-G-
47122 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
62 -A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
47166 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAA-GC-AAATGAAAATCGCAACGAG
*
47231 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
47271 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAA-GC-AAATGAAAATCGCA
47331 TTGCGATTCT
Statistics
Matches: 156, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 125 0.80
106 15 0.10
108 2 0.01
109 1 0.01
110 2 0.01
111 11 0.07
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (103 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAAGCAAATGAAAATCGCAACGAGAA
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:47196 original size:53 final size:52
Alignment explanation
Indices: 47061--47330 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
47051 CGGAAATTAC
* *
47061 AATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
47108 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
47166 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
47219 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
47271 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
47324 AATCGCA
1 AATCGCA
47331 TTGCGATTCT
Statistics
Matches: 206, Mismatches: 4, Indels: 20
0.90 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 66 0.32
53 114 0.55
55 2 0.01
56 1 0.00
57 2 0.01
58 11 0.05
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:47335 original size:19 final size:19
Alignment explanation
Indices: 47075--47336 Score: 303
Period size: 19 Copynumber: 14.7 Consensus size: 19
47065 GCAACGAGAG
*
47075 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
47094 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
47108 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
47128 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
47147 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
47166 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
47180 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
47200 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
47219 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
47233 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
47252 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
47271 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
47285 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
47305 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
47324 AATCGCATTGCGA
1 AATCGCAATGCGA
47337 TTCTCTCGTT
Statistics
Matches: 211, Mismatches: 9, Indels: 46
0.79 0.03 0.17
Matches are distributed among these distances:
14 40 0.19
15 5 0.02
16 5 0.02
17 9 0.04
18 1 0.00
19 111 0.53
20 40 0.19
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:47336 original size:72 final size:68
Alignment explanation
Indices: 47042--47335 Score: 267
Period size: 72 Copynumber: 4.2 Consensus size: 68
47032 GCATTTGACT
** * * * *
47042 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCCCAAC-AAG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
47106 AAA
66 AAA
*
47109 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
47174 CG-AGAGA
61 CGAAGAAA
* * * * *
47181 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
47243 CGAAATGAAA
61 CG-AA-GAAA
47253 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
47317 AAATGAAA
63 -AA-GAAA
*
47325 ATCGCATTGCG
1 ATCGCAATGCG
47336 ATTCTCTCGT
Statistics
Matches: 188, Mismatches: 20, Indels: 32
0.78 0.08 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.18
69 4 0.02
70 1 0.01
71 21 0.11
72 107 0.57
73 3 0.02
74 5 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
AAA
Found at i:47384 original size:18 final size:20
Alignment explanation
Indices: 47345--47390 Score: 78
Period size: 18 Copynumber: 2.4 Consensus size: 20
47335 GATTCTCTCG
47345 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCCGCA
47365 TTGCGATTTT-ATTT-CGCA
1 TTGCGATTTTCATTTCCGCA
47383 TTGCGATT
1 TTGCGATT
47391 CTCTCGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 12 0.46
19 4 0.15
20 10 0.38
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCA
Found at i:47518 original size:13 final size:14
Alignment explanation
Indices: 47502--47537 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
47492 CATCAATTAC
47502 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
47515 ACAAATCATCTTTT
1 ACAAATCAACTTTT
47529 ACAAATCAA
1 ACAAATCAA
47538 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:48939 original size:20 final size:20
Alignment explanation
Indices: 48908--49035 Score: 128
Period size: 21 Copynumber: 6.7 Consensus size: 20
48898 TTTTGGTTGA
48908 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
48928 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
48948 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
*
48969 AAATGAAAATCGTAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
48988 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
49003 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
49022 AATGAAAATCGCAA
1 AATGAAAATCGCAA
49036 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.09
16 4 0.04
17 2 0.02
19 30 0.32
20 17 0.18
21 32 0.34
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:48960 original size:21 final size:21
Alignment explanation
Indices: 48906--48991 Score: 129
Period size: 21 Copynumber: 4.1 Consensus size: 21
48896 TCTTTTGGTT
48906 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
48927 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
48947 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*
48968 GAAATGAAAATCGTAACGAGA
1 GAAATGAAAATCGCAACGAGA
48989 GAA
1 GAA
48992 TCGCAACGCG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.30
21 40 0.70
ACGTcount: A:0.49, C:0.14, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:49014 original size:19 final size:19
Alignment explanation
Indices: 48906--49040 Score: 109
Period size: 19 Copynumber: 7.1 Consensus size: 19
48896 TCTTTTGGTT
*
48906 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
48925 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
*
48947 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAAC--GC
*
48968 GAAATGAAAATCGTAA--C
1 GAAATGAAAATCGCAACGC
*
48985 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
49001 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
49020 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
49039 GA
1 GA
49041 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 35 0.36
20 12 0.12
21 31 0.32
22 4 0.04
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:49091 original size:21 final size:21
Alignment explanation
Indices: 49067--49136 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
49057 CGATTCTCTC
49067 GTTGCGATTTTCATTTTTCTA
1 GTTGCGATTTTCATTTTTCTA
**
49088 GTTGCAGATAGTCA-TTTTC-A
1 GTTGC-GATTTTCATTTTTCTA
* *
49108 CGTTGCGATTTTCATTTATCTC
1 -GTTGCGATTTTCATTTTTCTA
49130 GTTGCGA
1 GTTGCGA
49137 CTCTTCTGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 7 0.18
21 26 0.67
22 6 0.15
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (21 bp):
GTTGCGATTTTCATTTTTCTA
Found at i:49258 original size:33 final size:33
Alignment explanation
Indices: 49216--49286 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
49206 AATACTAACT
49216 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
49249 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
49282 TGAAA
1 TGAAA
49287 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:49691 original size:20 final size:20
Alignment explanation
Indices: 49666--49858 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
49656 CTTTAAAAAT
49666 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
49686 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
49706 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
49727 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
49747 CGCATTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
49767 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
49787 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
49807 CGCGTTACGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
49827 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
49847 CGCGTTGCGATT
1 CGCGTTGCGATT
49859 CTGGAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
20 130 0.88
21 18 0.12
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:58789 original size:30 final size:30
Alignment explanation
Indices: 58748--58812 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
58738 TTGCTACAGT
* ** *
58748 GACCACCATAGGTCTTTAGGAGCACATGGC
1 GACCTCCATAGGTCTCCAGGAGCACACGGC
58778 GACCTCCATAGGTCTCCAGGAGCACACGGC
1 GACCTCCATAGGTCTCCAGGAGCACACGGC
58808 GACCT
1 GACCT
58813 ATGTAGCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (30 bp):
GACCTCCATAGGTCTCCAGGAGCACACGGC
Found at i:58844 original size:20 final size:20
Alignment explanation
Indices: 58819--58856 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
58809 ACCTATGTAG
58819 CACTTGGCGACTTATGGACC
1 CACTTGGCGACTTATGGACC
58839 CACTTGGCGACTTATGGA
1 CACTTGGCGACTTATGGA
58857 GCTACAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (20 bp):
CACTTGGCGACTTATGGACC
Found at i:74113 original size:15 final size:15
Alignment explanation
Indices: 74093--74123 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
74083 ACACTCTGAA
74093 GCTCCTTAATCTCTC
1 GCTCCTTAATCTCTC
*
74108 GCTCCTTCATCTCTC
1 GCTCCTTAATCTCTC
74123 G
1 G
74124 TATTATGTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.42, G:0.10, T:0.39
Consensus pattern (15 bp):
GCTCCTTAATCTCTC
Done.