Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005341.1 Hibiscus syriacus cultivar Beakdansim tig00012096_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: 83879
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:1103 original size:64 final size:63
Alignment explanation
Indices: 998--1117 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 63
988 ATTGTTCAAG
* *
998 GTGTATCAATGCACATGAAGTGCATCGATGCACTAATTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCAATGCACATGAAGTGCATCGATGCACCAACTT-AAATAAAAACATCGAATGTCATTA
* * ** *
1062 GTGTATCGATGCACCA-GTAGTGCATCGATGCACCCCCTTAAATATAAACATCGAAT
1 GTGTATCAATGCA-CATGAAGTGCATCGATGCACCAACTTAAATAAAAACATCGAAT
1118 AGGATTTATG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 16 0.33
64 30 0.62
65 2 0.04
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (63 bp):
GTGTATCAATGCACATGAAGTGCATCGATGCACCAACTTAAATAAAAACATCGAATGTCATTA
Found at i:1540 original size:31 final size:30
Alignment explanation
Indices: 1502--1560 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
1492 TATATAAGCA
1502 ATGTGATAAA-GTGATGGAACATGATATGTTT
1 ATGTGATAAAGGT-ATGGAA-ATGATATGTTT
*
1533 ATGTGATAAAGGTATGGAAATTATATGT
1 ATGTGATAAAGGTATGGAAATGATATGT
1561 CTATACAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 16 0.62
32 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
ATGTGATAAAGGTATGGAAATGATATGTTT
Found at i:8347 original size:31 final size:30
Alignment explanation
Indices: 8309--8368 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
8299 TTATATAAGC
8309 TATGTGATAAA-GTGATGGAACATGATATGTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATGTT
*
8340 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
8369 ATATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:9163 original size:23 final size:23
Alignment explanation
Indices: 9103--9155 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
9093 ATATGGCACA
*
9103 CGGTGCAATTCTACGCGGTACTT
1 CGGTGCAATTCTACGCGGCACTT
*
9126 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
*
9149 TGGTGCA
1 CGGTGCA
9156 TTTATACGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTT
Found at i:11246 original size:24 final size:24
Alignment explanation
Indices: 11212--11265 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
11202 CTGAAACATA
11212 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
11236 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
11260 ATCAAA
1 ATCAAA
11266 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:12221 original size:20 final size:20
Alignment explanation
Indices: 12196--12263 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
12186 AAATAAAAGC
12196 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
12216 TGTTGCGAATTTGAAAA-TCG
1 TGTTGCGAAATT-AAAATTCG
* **
12236 AGTTGCGAAAAAAAAATTCG
1 TGTTGCGAAATTAAAATTCG
12256 TGTTGCGA
1 TGTTGCGA
12264 TTTAGAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.10
20 32 0.80
21 4 0.10
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:12243 original size:40 final size:40
Alignment explanation
Indices: 12197--12274 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
12187 AATAAAAGCT
**
12197 GTTGCGAAATTAAAATTCGTGTTGCGAATTT-GAAAATCGA
1 GTTGCGAAAAAAAAATTCGTGTTGCG-ATTTAGAAAATCGA
12237 GTTGCGAAAAAAAAATTCGTGTTGCGATTTAGAAAATC
1 GTTGCGAAAAAAAAATTCGTGTTGCGATTTAGAAAATC
12275 TTGTTGCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (40 bp):
GTTGCGAAAAAAAAATTCGTGTTGCGATTTAGAAAATCGA
Found at i:12281 original size:40 final size:39
Alignment explanation
Indices: 12196--12303 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 39
12186 AAATAAAAGC
**
12196 TGTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCG
1 TGTTGCGAAAAAAAAATTCGTGTTGCG-ATTTGAAAATCG
* *
12236 AGTTGCGAAAAAAAAATTCGTGTTGCGATTTAGAAAATCT
1 TGTTGCGAAAAAAAAATTCGTGTTGCGATTT-GAAAATCG
*
12276 TGTTGC-AAAAAGGAAACTT-GTGTTGCGA
1 TGTTGCGAAAAA--AAAATTCGTGTTGCGA
12304 AAAAGAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 9 0.15
40 45 0.76
41 5 0.08
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (39 bp):
TGTTGCGAAAAAAAAATTCGTGTTGCGATTTGAAAATCG
Found at i:12311 original size:20 final size:20
Alignment explanation
Indices: 12175--12311 Score: 72
Period size: 20 Copynumber: 7.0 Consensus size: 20
12165 CCCAAAACAT
*
12175 TTGTGTTGC-AAAAATAAAA
1 TTGTGTTGCGAAAAAGAAAA
**
12194 --GCTGTTGCG-AAATTAAAA
1 TTG-TGTTGCGAAAAAGAAAA
***
12212 TTCGTGTTGCGAATTTGAAAA
1 TT-GTGTTGCGAAAAAGAAAA
* *
12233 TCGAGTTGCGAAAAA-AAAA
1 TTGTGTTGCGAAAAAGAAAA
***
12252 TTCGTGTTGCGATTTAGAAAA
1 TT-GTGTTGCGAAAAAGAAAA
*
12273 TCT-TGTTGC-AAAAAGGAAAC
1 T-TGTGTTGCGAAAAA-GAAAA
12293 TTGTGTTGCGAAAAAGAAA
1 TTGTGTTGCGAAAAAGAAA
12312 TTCACGTTGC
Statistics
Matches: 88, Mismatches: 18, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
17 1 0.01
18 14 0.16
19 8 0.09
20 46 0.52
21 18 0.20
22 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.29
Consensus pattern (20 bp):
TTGTGTTGCGAAAAAGAAAA
Found at i:12340 original size:20 final size:20
Alignment explanation
Indices: 12317--12408 Score: 55
Period size: 20 Copynumber: 4.5 Consensus size: 20
12307 AGAAATTCAC
12317 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGA
* * *
12337 GTTGGGAATT-TGAAATTCCGT
1 GTTGCGAATTCAGAAA-T-CGA
* ** *
12358 GTTGCAAATTTGGAAAATCGC
1 GTTGCGAATTCAG-AAATCGA
12379 GTTGCG-ATTGCAGAAA-CTGA
1 GTTGCGAATT-CAGAAATC-GA
12399 GTTGCGAATT
1 GTTGCGAATT
12409 TGGAAACTGT
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
19 5 0.09
20 23 0.43
21 21 0.39
22 2 0.04
23 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATCGA
Found at i:12414 original size:20 final size:20
Alignment explanation
Indices: 12391--12432 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
12381 TGCGATTGCA
*
12391 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
12411 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
12431 GA
1 GA
12433 GTTCGCGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:12429 original size:62 final size:58
Alignment explanation
Indices: 12316--12445 Score: 138
Period size: 62 Copynumber: 2.1 Consensus size: 58
12306 AAGAAATTCA
*
12316 CGTTGCGAATTCAGAAATCGAGTTGGGAATTTGAAATTCCGTGTTGCAAATTTGGAAAATCG
1 CGTTGCG-ATTCAGAAATCGAGTTGCGAATTTGAAA-TCCGTGTTGCAAA-TTGG-AAATCG
* **
12378 CGTTGCGATTGCAGAAA-CTGAGTTGCGAATTTGGAAA-CTGTGTTGCGAAATTGGAGTTCG
1 CGTTGCGATT-CAGAAATC-GAGTTGCGAATTT-GAAATCCGTGTTGC-AAATTGGAAATCG
12438 CGTTGCGA
1 CGTTGCGA
12446 ATTTATTGGT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
60 12 0.20
61 16 0.27
62 28 0.47
63 4 0.07
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (58 bp):
CGTTGCGATTCAGAAATCGAGTTGCGAATTTGAAATCCGTGTTGCAAATTGGAAATCG
Found at i:15892 original size:22 final size:21
Alignment explanation
Indices: 15835--15898 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
15825 AGTCAAGGGT
15835 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
15856 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
* *
15878 TTCACAGGTCATTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
15899 ATTTCATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:20936 original size:16 final size:17
Alignment explanation
Indices: 20890--20941 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 17
20880 TATGTATACT
20890 TGATTATATGAATGATATG
1 TGATTATATG--TGATATG
* *
20909 TGCTTATATGTGCTATG
1 TGATTATATGTGATATG
20926 TGATT-TATGTGATATG
1 TGATTATATGTGATATG
20942 CCATATGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 10 0.34
17 10 0.34
19 9 0.31
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (17 bp):
TGATTATATGTGATATG
Found at i:21343 original size:22 final size:22
Alignment explanation
Indices: 21313--21354 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
21303 AGTCGAGGGT
*
21313 TTCATAGGTCCTTCGGGACATA
1 TTCACAGGTCCTTCGGGACATA
21335 TTCACAGGTCCTTCGGGACA
1 TTCACAGGTCCTTCGGGACA
21355 AATTTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (22 bp):
TTCACAGGTCCTTCGGGACATA
Found at i:21541 original size:28 final size:28
Alignment explanation
Indices: 21510--21568 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
21500 ATATGTTTTG
21510 ATGAT-ATAAAATGTGTTACATGAAT-TAT
1 ATGATGAT-AAATGTGTTACAT-AATGTAT
* *
21538 ATGATGATATATGTGTTCCATAATGTAT
1 ATGATGATAAATGTGTTACATAATGTAT
21566 ATG
1 ATG
21569 GAAATGTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 22 0.81
29 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (28 bp):
ATGATGATAAATGTGTTACATAATGTAT
Found at i:41039 original size:33 final size:33
Alignment explanation
Indices: 40997--41062 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
40987 CCATGTTAGT
40997 CGATGAGCTTATATTATGTCTACATAAACTAAA
1 CGATGAGCTTATATTATGTCTACATAAACTAAA
41030 CGATGAGCTTATATTATGTCTACATAAACTAAA
1 CGATGAGCTTATATTATGTCTACATAAACTAAA
41063 ACCAATACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
CGATGAGCTTATATTATGTCTACATAAACTAAA
Found at i:43100 original size:9 final size:9
Alignment explanation
Indices: 43088--43113 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
43078 TTTAAATTAA
43088 TATATTTTT
1 TATATTTTT
43097 TATATTTTT
1 TATATTTTT
43106 TATATTTT
1 TATATTTT
43114 CAATTGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TATATTTTT
Found at i:44363 original size:20 final size:20
Alignment explanation
Indices: 44341--44534 Score: 201
Period size: 20 Copynumber: 9.7 Consensus size: 20
44331 TCAGTTTCCA
** *
44341 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
44361 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
44381 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
44401 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
44421 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
44441 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* * *
44461 ATATCGCAACGCGTATCTGT
1 AAATCGCAACGCGAATCCGT
* *
44481 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
44501 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
44521 AAATCGCAACGCGA
1 AAATCGCAACGCGA
44535 TATTTAAAGC
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:44405 original size:60 final size:59
Alignment explanation
Indices: 44281--44534 Score: 190
Period size: 60 Copynumber: 4.2 Consensus size: 59
44271 ATGACCAACA
* * ** ** * *
44281 AAATCGCAACGCGAA-ATAAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC-A
1 AAATCGCAACGCGAATAT-GAAAATCGCAACGCGAACCATA-AATCGCAACGC-GTATCCGT
44341 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATATGAAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGT
* * ** * **** *
44401 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATATGAAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGT
* * * * * ** *
44461 ATATCGCAACGCGTATCTGTAAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CCATAAATCGCAACGCGT-ATCCGT
44521 AAATCGCAACGCGA
1 AAATCGCAACGCGA
44535 TATTTAAAGC
Statistics
Matches: 159, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
59 7 0.04
60 147 0.92
61 5 0.03
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (59 bp):
AAATCGCAACGCGAATATGAAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGT
Found at i:44954 original size:33 final size:33
Alignment explanation
Indices: 44915--44985 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
44905 TTCACTTAGA
* *
44915 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
44948 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
44981 TTTCA
1 TTTCA
44986 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:45122 original size:41 final size:38
Alignment explanation
Indices: 45058--45174 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
45048 TTCAATTTGC
* *
45058 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
45096 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
45137 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
45170 AGAAT
1 AGAAT
45175 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:45138 original size:21 final size:21
Alignment explanation
Indices: 45065--45140 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
45055 TGCAGAAGAG
* *
45065 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
45086 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
45106 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
45127 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
45141 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:45144 original size:14 final size:14
Alignment explanation
Indices: 45125--45181 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
45115 GAGAAATGAC
45125 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
45139 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
45158 AATCGCAACGAGAG
1 AATCGCAACGAGAG
45172 AATCGCAACG
1 AATCGCAACG
45182 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:45162 original size:33 final size:33
Alignment explanation
Indices: 45117--45197 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
45107 CGCAACGAGA
*
45117 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
45150 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
45183 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
45198 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:45215 original size:19 final size:19
Alignment explanation
Indices: 45193--45290 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
45183 GAAACCAAAA
*
45193 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45212 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
45226 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
45245 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
45259 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
45278 TCGCGTTGCGATT
1 TCGCGTTGCGATT
45291 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 4 0.07
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45234 original size:14 final size:14
Alignment explanation
Indices: 45215--45304 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
45205 TTTCATTTCG
45215 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
45229 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
45248 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
45262 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
45279 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
45295 CGTTGCGATT
1 CGTTGCGATT
45305 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 2 0.03
16 7 0.11
17 7 0.11
18 2 0.03
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:45244 original size:33 final size:33
Alignment explanation
Indices: 45198--45312 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
45188 CAAAATCGCA
*
45198 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
45231 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
45264 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
45297 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
45313 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:47162 original size:93 final size:93
Alignment explanation
Indices: 47003--47476 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
46993 TAGATTGCTT
*
47003 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47068 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47096 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47161 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47189 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47254 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
47282 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47347 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47375 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47440 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47468 AGTAAATTT
1 AGTAAATTT
47477 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:47560 original size:19 final size:19
Alignment explanation
Indices: 47520--47648 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
47510 TAGTTTACTT
* *
47520 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
47540 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
47559 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
47578 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
47592 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
47611 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
47625 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
47644 TCGCA
1 TCGCA
47649 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:47599 original size:33 final size:32
Alignment explanation
Indices: 47556--47648 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
47546 CGCGAAACCA
**
47556 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
47588 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
47621 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
47649 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:47646 original size:52 final size:52
Alignment explanation
Indices: 47520--47648 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
47510 TAGTTTACTT
**
47520 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
47572 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
47625 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
47649 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:47666 original size:19 final size:19
Alignment explanation
Indices: 47644--47778 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
47634 GAAACCAAAA
*
47644 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
47663 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
47679 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
47696 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
47712 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
47729 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
47748 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
47768 TCGTGTTGCGA
1 TCGCGTTGCGA
47779 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:47685 original size:14 final size:14
Alignment explanation
Indices: 47666--47722 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
47656 TTTCATTTCG
47666 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
47680 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
47697 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
47713 CGTTGCGATT
1 CGTTGCGATT
47723 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:47691 original size:33 final size:33
Alignment explanation
Indices: 47649--47741 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
47639 CAAAATCGCA
*
47649 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
47682 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
47715 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
47742 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:49851 original size:19 final size:19
Alignment explanation
Indices: 49827--49926 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
49817 AAAATTGACT
49827 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
49846 ATCGCAATTCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
49865 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
49879 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
49898 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
49918 ATCGCAATG
1 ATCGCAATG
49927 GGAGAATCGC
Statistics
Matches: 72, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:49956 original size:53 final size:53
Alignment explanation
Indices: 49827--49943 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
49817 AAAATTGACT
*
49827 ATCGCAATGCGAAATGAAAATCGCAATTC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
49879 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
49932 ATCGCAATGCGA
1 ATCGCAATGCGA
49944 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 28 0.46
53 33 0.54
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:49961 original size:19 final size:18
Alignment explanation
Indices: 49933--50030 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
49923 AATGGGAGAA
*
49933 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTT-ATT
*
49952 TCGCATTGCGA--TTATC
1 TCGCATTGCGATTTTATT
49968 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
49985 TCGCATTGCGA--TTCTC
1 TCGCATTGCGATTTTATT
50001 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
50018 TCGCATTGCGATT
1 TCGCATTGCGATT
50031 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 12 0.19
16 13 0.21
17 13 0.21
19 24 0.39
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:49976 original size:14 final size:14
Alignment explanation
Indices: 49957--50044 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
49947 TAATTTCGCA
49957 TTGCGATTATCTCG
1 TTGCGATTATCTCG
*
49971 TTGCGATTTTCATTTCG
1 TTGCGA--TT-ATCTCG
*
49988 CATTGCGATTCTCTCG
1 --TTGCGATTATCTCG
*
50004 TTGCGATTTTCATTTCG
1 TTGCGA--TT-ATCTCG
*
50021 CATTGCGATTCTCTCG
1 --TTGCGATTATCTCG
50037 TTGCGATT
1 TTGCGATT
50045 TTCATTTCCG
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 20 0.35
16 12 0.21
17 13 0.23
19 12 0.21
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTATCTCG
Found at i:49976 original size:33 final size:33
Alignment explanation
Indices: 49939--50062 Score: 221
Period size: 33 Copynumber: 3.7 Consensus size: 33
49929 AGAATCGCAA
* *
49939 TGCGATTTTAATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
49972 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
50005 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
50038 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
50063 AATGTAATGG
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
33 78 0.89
34 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:50145 original size:19 final size:19
Alignment explanation
Indices: 50121--50217 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
50111 AAAATTGACT
50121 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50140 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
50158 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
50172 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50191 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
50211 ATCGCAA
1 ATCGCAA
50218 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
13 1 0.01
14 9 0.13
16 4 0.06
18 10 0.14
19 29 0.42
20 16 0.23
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:50197 original size:51 final size:53
Alignment explanation
Indices: 50121--50236 Score: 218
Period size: 51 Copynumber: 2.2 Consensus size: 53
50111 AAAATTGACT
50121 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
50172 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
50225 ATCGCAATGCGA
1 ATCGCAATGCGA
50237 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 29 0.46
52 6 0.10
53 28 0.44
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:50621 original size:20 final size:20
Alignment explanation
Indices: 50428--50620 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
50418 CTTTAAATAT
50428 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
50449 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
50468 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
50488 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
50508 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
50528 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
50548 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
50568 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
50588 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
50608 CGCGTTGCGATTT
1 CGCGTTGCGATTT
50621 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:50637 original size:21 final size:21
Alignment explanation
Indices: 50607--50689 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
50597 ATTTTCATAT
*
50607 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
50628 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
50649 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
50670 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
50690 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:50680 original size:42 final size:43
Alignment explanation
Indices: 50587--50685 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
50577 ATTTATGTGT
* *
50587 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
50628 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
50670 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
50686 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:54454 original size:3 final size:3
Alignment explanation
Indices: 54446--54527 Score: 123
Period size: 3 Copynumber: 27.7 Consensus size: 3
54436 TTTTTATCCA
* *
54446 TAT TAT TAT TAT CAT TAT TAA 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
54494 TAT T-T TCAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
54528 AATATATTAA
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.06
3 66 0.92
4 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:56027 original size:11 final size:11
Alignment explanation
Indices: 56011--56035 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56001 TTATCAAAAT
56011 TATCAGTTTAA
1 TATCAGTTTAA
56022 TATCAGTTTAA
1 TATCAGTTTAA
56033 TAT
1 TAT
56036 ATATATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
TATCAGTTTAA
Found at i:56275 original size:6 final size:6
Alignment explanation
Indices: 56264--56295 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
56254 AGAAAAAAAG
56264 GAGACA GAGACA GAGACA GAGACA GAGACA GA
1 GAGACA GAGACA GAGACA GAGACA GAGACA GA
56296 ACCGGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.34, T:0.00
Consensus pattern (6 bp):
GAGACA
Found at i:68584 original size:5 final size:5
Alignment explanation
Indices: 68574--68647 Score: 61
Period size: 5 Copynumber: 15.6 Consensus size: 5
68564 GCTTGAAGAA
* *
68574 AAAAG AAAAG AAAAG AAAAG AAAA- AAGA- AAAAG -AAAG AAAA- AATAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
*
68620 AAAATG -AAA- AAAAG AGAAG AAAAAG AAA
1 AAAA-G AAAAG AAAAG AAAAG -AAAAG AAA
68648 GGGGGTCAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
4 16 0.29
5 35 0.62
6 5 0.09
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:68589 original size:10 final size:10
Alignment explanation
Indices: 68574--68647 Score: 61
Period size: 9 Copynumber: 7.8 Consensus size: 10
68564 GCTTGAAGAA
68574 AAAAGAAAAG
1 AAAAGAAAAG
68584 AAAAGAAAAG
1 AAAAGAAAAG
*
68594 AAAA-AAGA-
1 AAAAGAAAAG
68602 AAAAG-AAAG
1 AAAAGAAAAG
*
68611 AAAA-AATAG
1 AAAAGAAAAG
68620 AAAATG-AAA-
1 AAAA-GAAAAG
*
68629 AAAAGAGAAG
1 AAAAGAAAAG
68639 AAAAAGAAA
1 -AAAAGAAA
68648 GGGGGTCAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
8 7 0.14
9 20 0.40
10 16 0.32
11 7 0.14
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:68621 original size:19 final size:17
Alignment explanation
Indices: 68569--68647 Score: 88
Period size: 19 Copynumber: 4.4 Consensus size: 17
68559 ATTATGCTTG
68569 AAGAAAAAAGAAAAG-AA
1 AAGAAAAAA-AAAAGAAA
68586 AAGAAAAGAAAAAAGAAA
1 AAGAAAA-AAAAAAGAAA
68604 AAGAAAGAAAAAATAGAAA
1 AAGAAA-AAAAAA-AGAAA
*
68623 ATGAAAAAAAGAGAAGAAA
1 AAGAAAAAAA-A-AAGAAA
68642 AAGAAA
1 AAGAAA
68648 GGGGGTCAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 12 0.22
18 19 0.35
19 22 0.41
20 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:68624 original size:7 final size:6
Alignment explanation
Indices: 68573--68647 Score: 61
Period size: 6 Copynumber: 12.5 Consensus size: 6
68563 TGCTTGAAGA
68573 AAAAAG -AAAAG -AAAAG -AAAAG AAAAAAG AAAAAG AAAGAA- AAAATAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAA-AAG AAAA-AG
*
68620 AAAATG AAAAA- AAGAGAAG AAAAAG AAA
1 AAAAAG AAAAAG AA-A-AAG AAAAAG AAA
68648 GGGGGTCAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
5 18 0.31
6 25 0.42
7 14 0.24
8 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:69854 original size:50 final size:50
Alignment explanation
Indices: 69779--70021 Score: 470
Period size: 50 Copynumber: 4.9 Consensus size: 50
69769 GAAAGAGACT
69779 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
69829 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
69879 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
*
69928 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
69978 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
70022 TGGCAGAACC
Statistics
Matches: 192, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
49 49 0.26
50 143 0.74
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.40
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
Found at i:69966 original size:99 final size:100
Alignment explanation
Indices: 69779--70021 Score: 470
Period size: 99 Copynumber: 2.4 Consensus size: 100
69769 GAAAGAGACT
69779 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATAGCATCTTCTGG
69844 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
69879 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATAGCATCTTCTGG
*
69943 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
69978 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
70022 TGGCAGAACC
Statistics
Matches: 142, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
99 98 0.69
100 44 0.31
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.40
Consensus pattern (100 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
Found at i:71207 original size:118 final size:118
Alignment explanation
Indices: 70742--71504 Score: 1323
Period size: 118 Copynumber: 6.5 Consensus size: 118
70732 TAGCAAAGAT
*
70742 TTGAATCCATCACTTGATGGATCATTCTTTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TC
1 TTGAATTCATCACTTGATGGATCA-TCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
70802 ATCTGAAGAAGGAA-AAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 ATCTGAAGAAGGAAGAA-GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
70856 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATC-ATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
70921 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
70975 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATC-ATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
71040 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
71094 TTGAATTCATCACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTGAATTCATCACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
*
71159 TCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
71212 TTGAATTCATCACTTGATGGATCATC-ATTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTGAATTCATCACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
71275 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
71328 TTGAATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTGAATTCATCACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
71393 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * ** *
71446 TTGAATTCATCA-TTGATGGAACATCATCCCCAGCA-GAA-AGTTCGTAATGAGAAGAACTC
1 TTGAATTCATCACTTGATGGATCATCTTTTCCAG-AGGAAGAGTTCATAATGAGAAGAACTC
71505 ATCTGGAGAA
Statistics
Matches: 630, Mismatches: 9, Indels: 18
0.96 0.01 0.03
Matches are distributed among these distances:
114 33 0.05
115 4 0.01
116 145 0.23
117 35 0.06
118 216 0.34
119 195 0.31
120 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (118 bp):
TTGAATTCATCACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:71371 original size:234 final size:234
Alignment explanation
Indices: 70742--71504 Score: 1324
Period size: 234 Copynumber: 3.3 Consensus size: 234
70732 TAGCAAAGAT
* *
70742 TTGAATCCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCAT
1 TTGAATTCATCACTTGATGGATCA-TCTATTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCAT
70804 CTGAAGAAGGAA-AAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCA
65 CTGAAGAAGGAAGAA-GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCA
70868 CTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
129 CTTGATGGATC-ATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
70933 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
193 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
70975 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATC-ATCTATTCCAGA-GAA-AGTTCATAATGAGAAGAACTCGTC
71040 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
63 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
71105 ACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
128 ACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
*
71170 AATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
193 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
71212 TTGAATTCATCACTTGATGGATCATC-ATTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTGAATTCATCACTTGATGGATCATCTATTCCAGAGAA-AGTTCATAATGAGAAGAACTCGTCAT
71276 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAC
65 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAC
*
71341 TTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
130 TTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
71406 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
195 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
71446 TTGAATTCATCA-TTGATGGAACATC-ATCCCCAGCAGAAAGTTCGTAATGAGAAGAACTC
1 TTGAATTCATCACTTGATGGATCATCTAT-TCCAG-AGAAAGTTCATAATGAGAAGAACTC
71505 ATCTGGAGAA
Statistics
Matches: 513, Mismatches: 8, Indels: 17
0.95 0.01 0.03
Matches are distributed among these distances:
233 47 0.09
234 238 0.46
235 29 0.06
236 3 0.01
237 118 0.23
238 76 0.15
239 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (234 bp):
TTGAATTCATCACTTGATGGATCATCTATTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATC
TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACT
TGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:71666 original size:3 final size:3
Alignment explanation
Indices: 71658--71736 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
71648 TTTTTATCCA
* *
71658 TAT TAT TAT TAT CAT TAT TAA 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
*
71706 TAT TTT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
71737 AATATATTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:72210 original size:6 final size:6
Alignment explanation
Indices: 72199--72224 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
72189 AGAAAAAAAG
72199 GAGACA GAGACA GAGACA GAGACA GA
1 GAGACA GAGACA GAGACA GAGACA GA
72225 ACCGGAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00
Consensus pattern (6 bp):
GAGACA
Found at i:79891 original size:55 final size:55
Alignment explanation
Indices: 79756--80169 Score: 438
Period size: 55 Copynumber: 7.8 Consensus size: 55
79746 GAAAAATCTT
* * * **
79756 CAAACGGGTCTGCTCCCTATT-CTTTAAAGAGTATAAGACTCGAACAATCTT-GG
1 CAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
* * * *
79809 CAAATGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAA
1 CAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
* * *
79864 CAAACGTGTCTGCTCCCTATTCGTTCAG-GGGTATAAGACTCGAATAATCTTCAA
1 CAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
79918 CAAACG-GTC-GCTCCCTATTCCTTC--AGAGTATAAGACTCG----ATCTTCAA
1 CAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
* *
79965 CAAACGTGTCAGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAA
1 CAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
* ** *
80020 CAAACGGGT-TCGCTCCCTATTAGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATA
1 CAAACGTGTCT-GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCA-A
*
80076 -AAACGTGTCTGCTCTCTA-TCCTTCAGAGAGTAT-AGAACTCG----ATCTTCAA
1 CAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAA
* *
80125 AAAACGTGTTCT-CTCCCTATTCCTTTCAGAGAGTATAGGACTCGA
1 CAAACGTG-TCTGCTCCCTATTCC-TTCAGAGAGTATAAGACTCGA
80170 TCTTCATAAA
Statistics
Matches: 310, Mismatches: 30, Indels: 42
0.81 0.08 0.11
Matches are distributed among these distances:
47 14 0.05
48 3 0.01
49 16 0.05
50 20 0.06
51 33 0.11
52 31 0.10
53 23 0.07
54 75 0.24
55 93 0.30
56 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (55 bp):
CAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
Found at i:80035 original size:156 final size:158
Alignment explanation
Indices: 79756--80169 Score: 486
Period size: 156 Copynumber: 2.6 Consensus size: 158
79746 GAAAAATCTT
* * ** *
79756 CAAACGGGTCTGCTCCCTATTCTTTAAAGAGTATAAGACTCGAACAATCTT-GGCAAATGTGTCT
1 CAAAC-GGTCTGCTCCCTATTCCTT-CAGAGTATAAGACTCG----ATCTTCAACAAACGTGTC-
* * * * *
79820 GCTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTATT
59 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATT
* *
79885 CGTTCAGGG-GTATA-AGACTCGAATAATCTTCA-A
124 AGTTCAGGGAGTATAGA-ACTCGAACAATCTTCATA
79918 CAAACGGTC-GCTCCCTATTCCTTCAGAGTATAAGACTCGATCTTCAACAAACGTGTCAGCTCCC
1 CAAACGGTCTGCTCCCTATTCCTTCAGAGTATAAGACTCGATCTTCAACAAACGTGTC-GCTCCC
79982 TATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGT-TCGCTCCCTATTAGTTC
65 TATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCT-GCTCCCTATTAGTTC
80046 AGGGAGTATAGAACTCGAACAATCTTCATA
129 AGGGAGTATAGAACTCGAACAATCTTCATA
* * *
80076 -AAACGTGTCTGCTCTCTA-TCCTTCAGAG-AGTATAGAACTCGATCTTCAAAAAACGTGTTCTC
1 CAAACG-GTCTGCTCCCTATTCCTTCAGAGTA-TA-AG-ACTCGATCTTCAACAAACGTG-TCGC
80138 TCCCTATTCCTTTCAGAGAGTATAGGACTCGA
61 TCCCTATTCC-TTCAGAGAGTATAGGACTCGA
80170 TCTTCATAAA
Statistics
Matches: 224, Mismatches: 16, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
155 6 0.03
156 75 0.33
157 26 0.12
158 17 0.08
159 24 0.11
160 44 0.20
161 27 0.12
162 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (158 bp):
CAAACGGTCTGCTCCCTATTCCTTCAGAGTATAAGACTCGATCTTCAACAAACGTGTCGCTCCCT
ATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTAGTTCAG
GGAGTATAGAACTCGAACAATCTTCATA
Found at i:80295 original size:35 final size:37
Alignment explanation
Indices: 80186--80298 Score: 185
Period size: 38 Copynumber: 3.1 Consensus size: 37
80176 TAAAATAAGT
80186 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
* *
80223 TTGTTTCACTACTACTCCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACT-CTTCCGTGAAGGCTTAAGATTGAC
80261 TTGCTTCACTACTCTTCC-TGAAGGCTTAAG-TTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
80296 TTG
1 TTG
80299 TTCGAAGGCC
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 8 0.11
36 12 0.17
37 16 0.23
38 35 0.49
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
Found at i:81574 original size:19 final size:19
Alignment explanation
Indices: 81552--81703 Score: 69
Period size: 20 Copynumber: 7.4 Consensus size: 19
81542 TGAACCCCCC
81552 TTTTATTTTCTTTTTTTCA
1 TTTTATTTTCTTTTTTTCA
* * *
81571 TTTTTTTTTTTTTTCTTTCTTC
1 TTTTATTTTCTTTT-TTTC--A
* *
81593 TTTTATATTTCTTCTTTTCT
1 TTTTAT-TTTCTTTTTTTCA
81613 TTTTCATTTTTCATTTTCTTTTCA
1 TTTT-A-TTTTC--TTT-TTTTCA
* * *
81637 TTTTCTCATTT-ATTTTCTCA
1 TTTTAT--TTTCTTTTTTTCA
81657 TTTT-TTTT-TTTTTTTCA
1 TTTTATTTTCTTTTTTTCA
81674 TTTTTCATTTTCTTATTTTTC-
1 -TTTT-ATTTTCTT-TTTTTCA
81695 TTTTCATTT
1 TTTT-ATTT
81704 ATTCCATCAT
Statistics
Matches: 103, Mismatches: 14, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
17 10 0.10
18 4 0.04
19 13 0.13
20 30 0.29
21 9 0.09
22 17 0.17
23 8 0.08
24 12 0.12
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTATTTTCTTTTTTTCA
Found at i:81629 original size:55 final size:53
Alignment explanation
Indices: 81564--81703 Score: 142
Period size: 55 Copynumber: 2.6 Consensus size: 53
81554 TTATTTTCTT
* *
81564 TTTTTCATTTTTTTTTTTTTTCTTTCTTCTTTTAT-ATTTCTTCTTTTCTTTTTCA
1 TTTTTCATTTTTTTTATTTTTCTTT-TTATTTTATCATTT-TT-TTTTCTTTTTCA
* * *
81619 TTTTTCATTTTCTTTTCA-TTTTCTCATTTATTTTCTCATTTTTTTTTTTTTTTCA
1 TTTTTCATTTT-TTTT-ATTTTTCT-TTTTATTTTATCATTTTTTTTTCTTTTTCA
* *
81674 TTTTTCA-TTTTCTTATTTTTCTTTTCATTT
1 TTTTTCATTTTTTTTATTTTTCTTTTTATTT
81704 ATTCCATCAT
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
52 7 0.10
53 9 0.12
54 3 0.04
55 29 0.40
56 19 0.26
57 5 0.07
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.76
Consensus pattern (53 bp):
TTTTTCATTTTTTTTATTTTTCTTTTTATTTTATCATTTTTTTTTCTTTTTCA
Found at i:81632 original size:38 final size:39
Alignment explanation
Indices: 81580--81683 Score: 103
Period size: 37 Copynumber: 2.8 Consensus size: 39
81570 ATTTTTTTTT
* * *
81580 TTTTTCTTTCTTCTTTT-ATATTTCTTCTTTTCTTTT-TCA
1 TTTTTCATTCTTCTTTTCAT-TTTC-TCATTTATTTTCTCA
81619 TTTTTCATT-TTCTTTTCATTTTCTCATTTATTTTCTCA
1 TTTTTCATTCTTCTTTTCATTTTCTCATTTATTTTCTCA
* *
81657 TTTTT--TTTTTTTTTTCATTTT-TCATTT
1 TTTTTCATTCTTCTTTTCATTTTCTCATTT
81684 TCTTATTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
36 8 0.14
37 21 0.36
38 19 0.33
39 10 0.17
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (39 bp):
TTTTTCATTCTTCTTTTCATTTTCTCATTTATTTTCTCA
Found at i:81672 original size:31 final size:32
Alignment explanation
Indices: 81614--81703 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 32
81604 TTCTTTTCTT
* *
81614 TTTCATTTT-TCATTTTCTTTTCATTTTC-TCA
1 TTTCATTTTCTCATTTTTTTTTTATTTTCAT-A
* *
81645 TTT-ATTTTCTCATTTTTTTTTTTTTTTCATT
1 TTTCATTTTCTCATTTTTTTTTTATTTTCATA
* *
81676 TTTCATTTTCTTATTTTTCTTTTCATTT
1 TTTCATTTTCTCATTTTT-TTTTTATTT
81704 ATTCCATCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
30 5 0.10
31 22 0.46
32 14 0.29
33 7 0.15
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTCATTTTCTCATTTTTTTTTTATTTTCATA
Done.