Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007200.1 Hibiscus syriacus cultivar Beakdansim tig00018999_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: 414581
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1160 original size:17 final size:14
Alignment explanation
Indices: 1122--1157 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1112 CTCCGTGGCA
1122 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
1136 TTTTCTTCGGGGA-
1 TTTTCTTCGGGGAC
1149 TTCTTCTTC
1 TT-TTCTTC
1158 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1379 original size:24 final size:24
Alignment explanation
Indices: 1345--1398 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1335 CTGAAATATC
*
1345 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACAAAG
* *
1369 ATCAAAGTCTGGGTATTGACAAAG
1 ATCAAAATCTGAGTATTGACAAAG
1393 ATCAAA
1 ATCAAA
1399 TTTCGAATAC
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:0.43, C:0.15, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACAAAG
Found at i:2293 original size:20 final size:20
Alignment explanation
Indices: 2226--2292 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
2216 AAATTCAGTA
2226 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
2246 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* * *
2266 TTGCGATTGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
2286 TTGCGAT
1 TTGCGAT
2293 TTACGTATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:2302 original size:20 final size:20
Alignment explanation
Indices: 2279--2351 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
2269 CGATTGTCAG
*
2279 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2299 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
2319 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
2339 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2352 ATTAGGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2372 original size:21 final size:21
Alignment explanation
Indices: 2348--2388 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2338 TATTCGCATT
2348 GCGAA-TTAGGAAAATCGCAAC
1 GCGAATTTA-GAAAATCGCAAC
2369 GCGAATTTAGAAAATCGCAA
1 GCGAATTTAGAAAATCGCAA
2389 TACGATAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:3157 original size:19 final size:19
Alignment explanation
Indices: 3129--3170 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3119 AATTCCAAAA
*
3129 CCCC-AGGGGGTATCGATT
1 CCCCTAGGGGGAATCGATT
*
3147 CCCCTAGGGGGAATCGGTT
1 CCCCTAGGGGGAATCGATT
3166 CCCCT
1 CCCCT
3171 TCAAAGAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.14, C:0.33, G:0.31, T:0.21
Consensus pattern (19 bp):
CCCCTAGGGGGAATCGATT
Found at i:7045 original size:22 final size:21
Alignment explanation
Indices: 7005--7044 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6995 GAGTTTATTT
7005 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
7026 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
7045 ATAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:9265 original size:13 final size:13
Alignment explanation
Indices: 9247--9281 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
9237 AATATACTTA
9247 GAAAATCTTTTTG
1 GAAAATCTTTTTG
9260 GAAAATCTTTTTG
1 GAAAATCTTTTTG
9273 GAAAATCTT
1 GAAAATCTT
9282 AAAATTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (13 bp):
GAAAATCTTTTTG
Found at i:11060 original size:17 final size:17
Alignment explanation
Indices: 11038--11071 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11028 CCAAAACTTT
11038 TCAAAAAGTCAATTCAC
1 TCAAAAAGTCAATTCAC
11055 TCAAAAAGTCAATTCAC
1 TCAAAAAGTCAATTCAC
11072 CCCCTCTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (17 bp):
TCAAAAAGTCAATTCAC
Found at i:11918 original size:16 final size:15
Alignment explanation
Indices: 11890--11927 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
11880 AGGATTACTT
11890 ATCTATCACCTCTCC
1 ATCTATCACCTCTCC
11905 ATCTATCTACCTCTCC
1 ATCTATC-ACCTCTCC
11921 ATCTATC
1 ATCTATC
11928 CTTAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (15 bp):
ATCTATCACCTCTCC
Found at i:12361 original size:2 final size:2
Alignment explanation
Indices: 12354--12392 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
12344 TCTATTTTAT
12354 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
12393 ATTTTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12508 original size:39 final size:37
Alignment explanation
Indices: 12468--12809 Score: 384
Period size: 36 Copynumber: 9.7 Consensus size: 37
12458 AAAATCAATT
* * *
12468 TTTTTTAAAATCTATATATTATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
12505 TTTTGGAAATATATATATAATATATAGTTTTTGAAAGCA
1 TTTTTGAAA-ATATATATAATATATAG-TTTTGAAAACA
12544 -TTTTGAAAATATATATAATATATAAGTTTTGAAAAC-
1 TTTTTGAAAATATATATAATATAT-AGTTTTGAAAACA
12580 ----------T-TATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
12606 TTTTTGAAAACATATATAATATATAGTTTT-AAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
12642 TTTTTGAAAACATATATAATATATAGTTTT-AAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
12678 TTTTTGAAAACATGTATAATATATAGTTTT-AAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
12714 TTTTTGAAAA-CTATATAATATATATTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
12750 TTTTT-AAAA-A-ATATAATATATAGTTTT-AAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
12783 TTTTTGAAAATATTATATATATATATA
1 TTTTTGAAAATA-TATATA-ATATATA
12810 TATTGGAAAT
Statistics
Matches: 269, Mismatches: 15, Indels: 41
0.83 0.05 0.13
Matches are distributed among these distances:
25 12 0.04
26 12 0.04
27 1 0.00
33 10 0.04
34 20 0.07
35 21 0.08
36 98 0.36
37 54 0.20
38 31 0.12
39 10 0.04
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:12602 original size:25 final size:27
Alignment explanation
Indices: 12544--12604 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 27
12534 TTTGAAAGCA
12544 TTTTGAAAA-TATATATAATATATAAG
1 TTTTGAAAACTATATATAATATATAAG
12570 TTTTGAAAACT-TATATAATATAT-AG
1 TTTTGAAAACTATATATAATATATAAG
12595 TTTTGAAAAC
1 TTTTGAAAAC
12605 ATTTTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 12 0.35
26 21 0.62
27 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (27 bp):
TTTTGAAAACTATATATAATATATAAG
Found at i:12845 original size:3 final size:3
Alignment explanation
Indices: 12837--12879 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
12827 ATATATAATA
* *
12837 TAT TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
12880 ATGTTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:13317 original size:22 final size:24
Alignment explanation
Indices: 13287--13333 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
13277 CAACGGAACC
*
13287 ACCACCAAC-AGAGA-ACACAAAA
1 ACCAACAACAAGAGATACACAAAA
13309 ACCAACAACAAGAGATACACAAAA
1 ACCAACAACAAGAGATACACAAAA
13333 A
1 A
13334 ATCGAAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.62, C:0.28, G:0.09, T:0.02
Consensus pattern (24 bp):
ACCAACAACAAGAGATACACAAAA
Found at i:14000 original size:22 final size:21
Alignment explanation
Indices: 13964--14004 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
13954 TTTTCTAGAT
*
13964 TTTTATATTTCTTTCCTTTTTA
1 TTTTATATTTATTT-CTTTTTA
*
13986 TTTTATTTTTATTTCTTTT
1 TTTTATATTTATTTCTTTT
14005 AGAAATTAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTATATTTATTTCTTTTTA
Found at i:14470 original size:4 final size:4
Alignment explanation
Indices: 14459--14489 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
14449 TTATTTTATT
14459 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
14490 ACATAGTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:16065 original size:23 final size:22
Alignment explanation
Indices: 16035--16092 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 22
16025 CATGCATGTT
16035 AAACATACATATATTAATAAAAA
1 AAACATACATATA-TAATAAAAA
16058 AAACATACATATATAATAAAAA
1 AAACATACATATATAATAAAAA
16080 ACATACATACATA
1 A-A-ACATACATA
16093 ACATTGAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 10 0.30
23 14 0.42
24 9 0.27
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACATACATATATAATAAAAA
Found at i:16080 original size:20 final size:21
Alignment explanation
Indices: 16035--16093 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
16025 CATGCATGTT
16035 AAACATACATATATTAATAAAAA
1 AAACATACATATA-TAAT-AAAA
16058 AAACATACATATATAAT-AAA
1 AAACATACATATATAATAAAA
*
16078 AAACATACATACATAA
1 AAACATACATATATAA
16094 CATTGAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 18 0.51
22 4 0.11
23 13 0.37
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (21 bp):
AAACATACATATATAATAAAA
Found at i:23171 original size:23 final size:24
Alignment explanation
Indices: 23145--23189 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
23135 CAAATTCACT
*
23145 TTTAATTT-CATCTAAATTTAGTC
1 TTTAATTTACATCGAAATTTAGTC
*
23168 TTTAATTTAGATCGAAATTTAG
1 TTTAATTTACATCGAAATTTAG
23190 GTTTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (24 bp):
TTTAATTTACATCGAAATTTAGTC
Found at i:23260 original size:24 final size:23
Alignment explanation
Indices: 23193--23263 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
23183 AATTTAGGTT
* *
23193 TATAAATATTA-AGGGGTGCAAAA
1 TATAAA-ATTATAGGGGTGCGAGA
23216 TATAAAATTATAGGGGTGCGAGA
1 TATAAAATTATAGGGGTGCGAGA
*
23239 TATAAAATTCTAGGGGGTGCGAGA
1 TATAAAATTATA-GGGGTGCGAGA
23263 T
1 T
23264 TAGATTATCA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 4 0.09
23 27 0.63
24 12 0.28
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.27
Consensus pattern (23 bp):
TATAAAATTATAGGGGTGCGAGA
Found at i:26211 original size:16 final size:16
Alignment explanation
Indices: 26190--26221 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
26180 CTTAAAAGTA
26190 AATAAAATTTATAATT
1 AATAAAATTTATAATT
26206 AATAAAATTTATAATT
1 AATAAAATTTATAATT
26222 TATATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAAATTTATAATT
Found at i:26287 original size:26 final size:24
Alignment explanation
Indices: 26258--26321 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 24
26248 TATTATAAAA
* *
26258 ATATATTTTATATAA-TTATATTTT
1 ATATATTTTATATAATTTA-AATTC
*
26282 TTATATTTTTATTATAATTTAAATTC
1 ATATA-TTTTA-TATAATTTAAATTC
26308 ATATATTTTATATA
1 ATATATTTTATATA
26322 TAATAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 8 0.24
25 10 0.30
26 12 0.36
27 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
ATATATTTTATATAATTTAAATTC
Found at i:26322 original size:9 final size:9
Alignment explanation
Indices: 26258--26322 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
26248 TATTATAAAA
26258 ATATATTTT
1 ATATATTTT
*
26267 ATATA-ATT
1 ATATATTTT
*
26275 ATATTTTTT
1 ATATATTTT
26284 ATAT-TTTT
1 ATATATTTT
*
26292 ATTATAATTT
1 A-TATATTTT
*
26302 A-A-A-TTC
1 ATATATTTT
26308 ATATATTTT
1 ATATATTTT
26317 ATATAT
1 ATATAT
26323 AATAATAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.07
7 2 0.05
8 13 0.30
9 22 0.50
10 4 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (9 bp):
ATATATTTT
Found at i:28094 original size:19 final size:19
Alignment explanation
Indices: 28043--28087 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
28033 TCCCATTCAA
28043 GAAACCCTAGTTTGTGGGG
1 GAAACCCTAGTTTGTGGGG
28062 GAAACCCTAGTTTGTGGGG
1 GAAACCCTAGTTTGTGGGG
28081 GAAACCC
1 GAAACCC
28088 AAATTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (19 bp):
GAAACCCTAGTTTGTGGGG
Found at i:28399 original size:10 final size:10
Alignment explanation
Indices: 28386--28410 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28376 GAAAAATTCG
28386 AAAAATTAAA
1 AAAAATTAAA
28396 AAAAATTAAA
1 AAAAATTAAA
28406 AAAAA
1 AAAAA
28411 CACAAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:30069 original size:5 final size:5
Alignment explanation
Indices: 30059--30111 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
30049 AATGGTCAAC
* *
30059 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
30108 GGTC
1 GGTC
30112 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:30074 original size:17 final size:17
Alignment explanation
Indices: 30052--30112 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
30042 AACGGTCAAT
30052 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
30069 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
30091 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
30108 GGTCA
1 GGTCA
30113 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:30079 original size:7 final size:7
Alignment explanation
Indices: 29990--30062 Score: 128
Period size: 7 Copynumber: 10.4 Consensus size: 7
29980 GTCAAAGAAA
29990 GTCAACG
1 GTCAACG
29997 GTCAACG
1 GTCAACG
30004 GTCAACG
1 GTCAACG
30011 GTCAACG
1 GTCAACG
30018 GTCAACG
1 GTCAACG
30025 GTCAACG
1 GTCAACG
*
30032 GTCAGCG
1 GTCAACG
30039 GTCAACG
1 GTCAACG
*
30046 GTCAATG
1 GTCAACG
30053 GTCAACG
1 GTCAACG
30060 GTC
1 GTC
30063 GGGTCGGGTC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.26, C:0.27, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:30087 original size:22 final size:22
Alignment explanation
Indices: 30059--30111 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
30049 AATGGTCAAC
30059 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
30081 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
30103 GGTCGGGTC
1 GGTCGGGTC
30112 AGACCGGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:30132 original size:19 final size:19
Alignment explanation
Indices: 30110--30264 Score: 206
Period size: 19 Copynumber: 8.1 Consensus size: 19
30100 TCGGGTCGGG
30110 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
30129 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
30148 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
30167 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
30186 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
30205 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
* *
30224 TCAAATCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
30244 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
30264 T
1 T
30265 TCCAGCAGCT
Statistics
Matches: 123, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
18 3 0.02
19 95 0.77
20 17 0.14
21 8 0.07
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:30225 original size:29 final size:27
Alignment explanation
Indices: 30108--30264 Score: 113
Period size: 29 Copynumber: 5.5 Consensus size: 27
30098 GGTCGGGTCG
* *
30108 GGTCAGACCGG-TCAAACCGGTTCAGACC
1 GGTCAAACCGGTTC-AACCGG-TCAAACC
30136 GGTCAAACCGGTTCAGACCGGTCAAACC
1 GGTCAAACCGGTTCA-ACCGGTCAAACC
* *
30164 GGTTCAGACCGG-TCAAACCGGTTCAGACC
1 GG-TCAAACCGGTTC-AACCGG-TCAAACC
*
30193 GGTCAAACCGGTTCGAACCGGTTGAAACC
1 GGTCAAACCGGTTC-AACCGG-TCAAACC
* *
30222 GGTCAAATCGG-TCAGAACCGGTTGAAAACC
1 GGTCAAACCGGTTC--AACCGG-T-CAAACC
*
30252 GGTTAAACCGGTT
1 GGTCAAACCGGTT
30265 TCCAGCAGCT
Statistics
Matches: 108, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
28 36 0.33
29 57 0.53
30 14 0.13
31 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.17
Consensus pattern (27 bp):
GGTCAAACCGGTTCAACCGGTCAAACC
Found at i:30253 original size:11 final size:9
Alignment explanation
Indices: 30114--30264 Score: 104
Period size: 9 Copynumber: 15.8 Consensus size: 9
30104 GTCGGGTCAG
*
30114 ACCGGTCAA
1 ACCGGTTAA
*
30123 ACCGGTTCAG
1 ACCGGTT-AA
*
30133 ACCGGTCAA
1 ACCGGTTAA
*
30142 ACCGGTTCAG
1 ACCGGTT-AA
*
30152 ACCGGTCAA
1 ACCGGTTAA
*
30161 ACCGGTTCAG
1 ACCGGTT-AA
*
30171 ACCGGTCAA
1 ACCGGTTAA
*
30180 ACCGGTTCAG
1 ACCGGTT-AA
*
30190 ACCGGTCAA
1 ACCGGTTAA
*
30199 ACCGGTTCGA
1 ACCGGTT-AA
30209 ACCGGTTGAA
1 ACCGGTT-AA
*
30219 ACCGGTCAA
1 ACCGGTTAA
* *
30228 ATCGGTCAGA
1 ACCGGTTA-A
30238 ACCGGTTGAAA
1 ACCGGTT--AA
30249 ACCGGTTAA
1 ACCGGTTAA
30258 ACCGGTT
1 ACCGGTT
30265 TCCAGCAGCT
Statistics
Matches: 110, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
9 52 0.47
10 49 0.45
11 8 0.07
12 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:36775 original size:5 final size:5
Alignment explanation
Indices: 36765--36817 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
36755 AACGGTCAAC
*
36765 GGTCG GGTCG GGTCG ACGGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTCG --GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
36814 GGTC
1 GGTC
36818 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 33 0.79
7 9 0.21
ACGTcount: A:0.06, C:0.23, G:0.53, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:36783 original size:17 final size:17
Alignment explanation
Indices: 36758--36796 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
36748 AGCGGTCAAC
*
36758 GGTCAACGGTCGGGTCG
1 GGTCGACGGTCGGGTCG
36775 GGTCGACGGTCGGGTCG
1 GGTCGACGGTCGGGTCG
36792 GGTCG
1 GGTCG
36797 GGTCAACGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.18
Consensus pattern (17 bp):
GGTCGACGGTCGGGTCG
Found at i:36786 original size:7 final size:7
Alignment explanation
Indices: 36724--36768 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
36714 GTCAAAGAAA
36724 GTCAACG
1 GTCAACG
36731 GTCAACG
1 GTCAACG
36738 GTCAACG
1 GTCAACG
*
36745 GTCAGCG
1 GTCAACG
36752 GTCAACG
1 GTCAACG
36759 GTCAACG
1 GTCAACG
36766 GTC
1 GTC
36769 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:36793 original size:22 final size:22
Alignment explanation
Indices: 36765--36817 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
36755 AACGGTCAAC
*
36765 GGTCGGGTCGGGTCGACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
36787 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
36809 GGTCGGGTC
1 GGTCGGGTC
36818 AGACCGGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.06, C:0.23, G:0.53, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:36807 original size:17 final size:17
Alignment explanation
Indices: 36758--36818 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
36748 AGCGGTCAAC
36758 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
36775 GGTCGACGGTCGGGTCGGGTCG
1 GGTC-A---AC-GGTCGGGTCG
36797 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
36814 GGTCA
1 GGTCA
36819 GACCGGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 19 0.51
18 2 0.05
21 2 0.05
22 14 0.38
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:36832 original size:9 final size:9
Alignment explanation
Indices: 36814--36883 Score: 68
Period size: 9 Copynumber: 7.3 Consensus size: 9
36804 GGTCGGGTCG
*
36814 GGTCAGACC
1 GGTCAAACC
36823 GGTCAAACC
1 GGTCAAACC
*
36832 GGTTCAGACC
1 GG-TCAAACC
36842 GGTCAAACC
1 GGTCAAACC
36851 GGTCAGAACC
1 GGTCA-AACC
*
36861 GGTTGAAAACC
1 GG-T-CAAACC
*
36872 GGTTAAACC
1 GGTCAAACC
36881 GGT
1 GGT
36884 TTCCAGCAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
9 29 0.56
10 15 0.29
11 7 0.13
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:36838 original size:19 final size:18
Alignment explanation
Indices: 36814--36863 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
36804 GGTCGGGTCG
36814 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
36832 GGTTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
36851 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
36864 TGAAAACCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:36882 original size:20 final size:21
Alignment explanation
Indices: 36846--36884 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36836 CAGACCGGTC
36846 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
36867 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
36885 TCCAGCAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:38346 original size:2 final size:2
Alignment explanation
Indices: 38339--38376 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
38329 ATTAATAACG
38339 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
38377 TAAATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40455 original size:19 final size:21
Alignment explanation
Indices: 40412--40456 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
40402 ACTTAAACTT
*
40412 TTAAATATTTAAAATTTAATG
1 TTAAATATTTAAAATTTAATA
*
40433 TTAAAT-TTT-AAATTTATTA
1 TTAAATATTTAAAATTTAATA
40452 TTAAA
1 TTAAA
40457 ATAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 3 0.14
21 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAAATATTTAAAATTTAATA
Found at i:41285 original size:2 final size:2
Alignment explanation
Indices: 41280--41327 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
41270 ACTATATACA
* * * *
41280 AT AT AT AT AT AT AT AT AT TT AT AT TT TT CT A- 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
41321 AT AT AT A
1 AT AT AT A
41328 GTCGAGAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:44164 original size:20 final size:20
Alignment explanation
Indices: 44141--44189 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
44131 CTCAAAATCA
*
44141 TTTTTCAAAAATTCATTTTG
1 TTTTTCAAAAATTAATTTTG
* *
44161 TTTTTGAAAATTTAATTTTG
1 TTTTTCAAAAATTAATTTTG
*
44181 -CTTTCAAAA
1 TTTTTCAAAA
44190 TCAAATCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAAATTAATTTTG
Found at i:48623 original size:20 final size:20
Alignment explanation
Indices: 48574--48623 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
48564 ATAAGTCCGT
**
48574 AGTATTGATAACTAGAGGTT
1 AGTATTGATAACTAGAGGCC
* * *
48594 ATTATCGATACCTAGAGGCC
1 AGTATTGATAACTAGAGGCC
48614 AGTATTGATA
1 AGTATTGATA
48624 TTAAGTAGCA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (20 bp):
AGTATTGATAACTAGAGGCC
Found at i:50242 original size:127 final size:127
Alignment explanation
Indices: 50016--50267 Score: 319
Period size: 127 Copynumber: 2.0 Consensus size: 127
50006 AAAGTAGCAG
* *
50016 ACTAGTAGCTTAGAGAGACCCTCCACACTCTCTGACAGTTGTACCTTATGTTAGAAGGTAAGATT
1 ACTAGTAGCTTAGAGAGACCCTCCACACTCTCTGACAGTTGCACCTTATGCTAGAAGGTAAGATT
* * *
50081 GAGTACACCACTGCTCTACTAAAAGGTGACACCATAGATTGGTGGAAGACGATCGAGATGAA
66 GAGTACACCACCGCTCTACTAAAAGATAACACCATAGATTGGTGGAAGACGATCGAGATGAA
* * * * * *
50143 ACTAGTGGCTTAGGGAGACCCTCCACACTCTTTGATAGTTGCACCTTACT-CTAGAGGGTAAGCT
1 ACTAGTAGCTTAGAGAGACCCTCCACACTCTCTGACAGTTGCACCTTA-TGCTAGAAGGTAAGAT
*** * * *
50207 TGAGTATGTCACCG-TCTTACTCAAATATAACACCATAGATTGGTGGGAGACGATCGAGATG
65 TGAGTACACCACCGCTC-TACTAAAAGATAACACCATAGATTGGTGGAAGACGATCGAGATG
50268 GTAATAGAGC
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
126 2 0.02
127 103 0.97
128 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (127 bp):
ACTAGTAGCTTAGAGAGACCCTCCACACTCTCTGACAGTTGCACCTTATGCTAGAAGGTAAGATT
GAGTACACCACCGCTCTACTAAAAGATAACACCATAGATTGGTGGAAGACGATCGAGATGAA
Found at i:53182 original size:23 final size:23
Alignment explanation
Indices: 53117--53227 Score: 138
Period size: 23 Copynumber: 4.9 Consensus size: 23
53107 CACCTTGTAA
* *
53117 TTTGCAACGAAGTGCCACATAAT
1 TTTGCACCGAAGTGCCACATAGT
* *
53140 TGT-C-CCGAA-TGACCACATAGG
1 TTTGCACCGAAGTG-CCACATAGT
*
53161 TTTGCACCGAAGTGCCATATAGT
1 TTTGCACCGAAGTGCCACATAGT
53184 TTTGCACCGAAGTGCCACATAGT
1 TTTGCACCGAAGTGCCACATAGT
*
53207 TTTGCACCAAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
53228 TTTGTCCCGA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
20 2 0.03
21 13 0.17
22 2 0.03
23 56 0.75
24 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGT
Found at i:53211 original size:46 final size:44
Alignment explanation
Indices: 53117--53248 Score: 158
Period size: 46 Copynumber: 3.0 Consensus size: 44
53107 CACCTTGTAA
*
53117 TTTGCAACGAAGTGCCACATAATTGTCCCGAATGACCACATAGG
1 TTTGCACCGAAGTGCCACATAATTGTCCCGAATGACCACATAGG
* * * *
53161 TTTGCACCGAAGTGCCATATAGTTTTGCACCGAAGTG-CCACATAGT
1 TTTGCACCGAAGTGCCACATAATTGT-C-CCGAA-TGACCACATAGG
* * *
53207 TTTGCACCAAAGTGCCACATATTTGTCCCGAAAGACCACATA
1 TTTGCACCGAAGTGCCACATAATTGTCCCGAATGACCACATA
53249 ATTGTCCTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.01
44 34 0.46
45 2 0.03
46 35 0.47
47 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATAATTGTCCCGAATGACCACATAGG
Found at i:53245 original size:21 final size:21
Alignment explanation
Indices: 53221--53270 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
53211 CACCAAAGTG
*
53221 CCACATATTTGTCCCGAA-AGA
1 CCACATAATTGTCCCGAATA-A
*
53242 CCACATAATTGTCCTGAATAA
1 CCACATAATTGTCCCGAATAA
53263 CCACATAA
1 CCACATAA
53271 AATCCTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (21 bp):
CCACATAATTGTCCCGAATAA
Found at i:53357 original size:13 final size:15
Alignment explanation
Indices: 53328--53360 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
53318 ATACTTTGTG
53328 TTATTAATCACATCA
1 TTATTAATCACATCA
53343 TTATT-ATCA-ATCA
1 TTATTAATCACATCA
53356 TTATT
1 TTATT
53361 CGAAGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 4 0.22
15 5 0.28
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATTAATCACATCA
Found at i:53903 original size:54 final size:54
Alignment explanation
Indices: 53830--53951 Score: 165
Period size: 54 Copynumber: 2.3 Consensus size: 54
53820 ACTTCCCTTC
* * * * *
53830 AAGGGTATCGATACCTCCT-CATTGTACCGATATCGATATAACATTCGATGTTTT
1 AAGGGTATCGATACATCCTCCA-AGTACCAATACCAATATAACATTCGATGTTTT
**
53884 AAGGGTATCGATACATCCTCCAAGTACCAATACCAATATGGCATTCGATGTTTT
1 AAGGGTATCGATACATCCTCCAAGTACCAATACCAATATAACATTCGATGTTTT
53938 AAGGGTATCGATAC
1 AAGGGTATCGATAC
53952 CGTCCTTCAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 58 0.97
55 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (54 bp):
AAGGGTATCGATACATCCTCCAAGTACCAATACCAATATAACATTCGATGTTTT
Found at i:85354 original size:19 final size:19
Alignment explanation
Indices: 85330--85400 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
85320 ACCAACAAAA
85330 TCGCAATGCGATCTTTAAT
1 TCGCAATGCGATCTTTAAT
85349 TCGCAATGCGATCTTTAAT
1 TCGCAATGCGATCTTTAAT
*
85368 TCGAAATGCGATCTTTAAT
1 TCGCAATGCGATCTTTAAT
*
85387 TCGCATTGCGATCT
1 TCGCAATGCGATCT
85401 CCACTATCGC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (19 bp):
TCGCAATGCGATCTTTAAT
Found at i:85476 original size:20 final size:20
Alignment explanation
Indices: 85448--85499 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
85438 TAGTTGAAAA
* *
85448 TCGCATTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCCATT
85468 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
85488 TCGCGTTGCGAT
1 TCGCGTTGCGAT
85500 AGTCTACAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:85634 original size:6 final size:6
Alignment explanation
Indices: 85623--85690 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
85613 GACACGTATT
85623 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
85670 ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACC
85691 CGAGACGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.08
6 56 0.92
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:85670 original size:29 final size:29
Alignment explanation
Indices: 85623--85693 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
85613 GACACGTATT
85623 ACCACGACCACGACCACGACCACGACCACG
1 ACCACGACC-CGACCACGACCACGACCACG
85653 ACCACGACCCGACCACGACCACGACCACG
1 ACCACGACCCGACCACGACCACGACCACG
85682 ACCACGACCCGA
1 ACCACGACCCGA
85694 GACGAGACGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 32 0.78
30 9 0.22
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (29 bp):
ACCACGACCCGACCACGACCACGACCACG
Found at i:85701 original size:5 final size:5
Alignment explanation
Indices: 85691--85726 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
85681 GACCACGACC
85691 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
85727 GCGGCGGCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.36, C:0.22, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:86226 original size:6 final size:6
Alignment explanation
Indices: 86215--86262 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
86205 TCTCGTCTCG
86215 GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT
1 GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT GGTAAT
86263 ACGTGTCTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
GGTAAT
Found at i:86533 original size:22 final size:22
Alignment explanation
Indices: 86442--86535 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 22
86432 AATTTGCAAA
86442 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
86464 ATCCCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
86486 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
86505 ATCGCAACGACAACTGTAGGCT
1 ATCGCAACGACAACTGTAGACT
86527 ATCGCAACG
1 ATCGCAACG
86536 CGAAATGAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 13 0.23
20 2 0.04
21 2 0.04
22 39 0.70
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:86546 original size:41 final size:42
Alignment explanation
Indices: 86468--86555 Score: 110
Period size: 41 Copynumber: 2.1 Consensus size: 42
86458 TAGACTATCC
* *
86468 CAACAACAACTGTAGACTATCGCAACGAATTTGG-AAAATCG
1 CAACGACAACTGTAGACTATCGCAACGAATATGGAAAAATCG
*
86509 CAACGACAACTGTAGGCTATCGCAACGCGAA-AT-GAAAAATCG
1 CAACGACAACTGTAGACTATCGCAA--CGAATATGGAAAAATCG
86551 CAACG
1 CAACG
86556 TGAAATGGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 24 0.59
42 13 0.32
43 4 0.10
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (42 bp):
CAACGACAACTGTAGACTATCGCAACGAATATGGAAAAATCG
Found at i:86552 original size:20 final size:20
Alignment explanation
Indices: 86527--86578 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
86517 ACTGTAGGCT
86527 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* *
86547 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
86567 ATCGCAACGCGA
1 ATCGCAACGCGA
86579 TTTTTAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:86921 original size:2 final size:2
Alignment explanation
Indices: 86914--86939 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86904 ATGAAAAATA
86914 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
86940 TTTAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90060 original size:2 final size:2
Alignment explanation
Indices: 90053--90119 Score: 91
Period size: 2 Copynumber: 33.5 Consensus size: 2
90043 TAAGTCTAAA
* *
90053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT GT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
90095 CT 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
90120 ATAGTCGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
1 1 0.02
2 56 0.97
3 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:96463 original size:39 final size:40
Alignment explanation
Indices: 96402--96482 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 40
96392 ACCATTATAT
* * *
96402 TTTATTACAATGAATATTTTTTA-TAAATTATATTAATTA
1 TTTATTACAATAAAAATGTTTTATTAAATTATATTAATTA
* *
96441 TTTATTATAATAAAAATGTTTTATTGTTAATTATATTAATTA
1 TTTATTACAATAAAAATGTTTTA-T-TAAATTATATTAATTA
96483 CCTGTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 19 0.56
42 15 0.44
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (40 bp):
TTTATTACAATAAAAATGTTTTATTAAATTATATTAATTA
Found at i:96584 original size:30 final size:30
Alignment explanation
Indices: 96548--96605 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
96538 TTGAAAACTG
96548 TTAATAA-A-TATATTGTAAATATTTAATATT
1 TTAATAATATTATATTGTAAA-A-TTAATATT
*
96578 TTAATAATATTATTTTGTAAAATTAATA
1 TTAATAATATTATATTGTAAAATTAATA
96606 AATAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 13 0.52
31 2 0.08
32 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (30 bp):
TTAATAATATTATATTGTAAAATTAATATT
Found at i:96655 original size:26 final size:24
Alignment explanation
Indices: 96638--96730 Score: 107
Period size: 23 Copynumber: 3.8 Consensus size: 24
96628 ATTTATTATC
*
96638 TATTATTAAAATTATAATATAGTA
1 TATTATTAAAATTATAATATATTA
* * *
96662 TATTATTATAA-TATAATTTAATA
1 TATTATTAAAATTATAATATATTA
*
96685 TATTATTATAATATTAAAATATATTA
1 TATTATTA-AA-ATTATAATATATTA
96711 TATTATTAAAATTATTAATA
1 TATTATTAAAATTA-TAATA
96731 AATATGTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
23 18 0.32
24 15 0.26
25 7 0.12
26 17 0.30
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
TATTATTAAAATTATAATATATTA
Found at i:96671 original size:18 final size:18
Alignment explanation
Indices: 96648--96727 Score: 73
Period size: 18 Copynumber: 4.8 Consensus size: 18
96638 TATTATTAAA
*
96648 ATTATAATATAGTATATT
1 ATTATAATATATTATATT
96666 ATTATAATATA--AT-TT
1 ATTATAATATATTATATT
* *
96681 AATAT-AT-TATTATAAT
1 ATTATAATATATTATATT
*
96697 ATTAAAATATATTATATT
1 ATTATAATATATTATATT
*
96715 ATTAAAAT-TATTA
1 ATTATAATATATTA
96728 ATAAATATGT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 8 0.15
16 6 0.12
17 7 0.13
18 27 0.52
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (18 bp):
ATTATAATATATTATATT
Found at i:96686 original size:23 final size:23
Alignment explanation
Indices: 96638--96783 Score: 92
Period size: 23 Copynumber: 6.3 Consensus size: 23
96628 ATTTATTATC
* *
96638 TATTATTAAAATTATAATATAGTA
1 TATTATTATAA-TATAATATAATA
*
96662 TATTATTATAATATAATTTAATA
1 TATTATTATAATATAATATAATA
*
96685 TATTATTATAATATTAAAATATATTA
1 TATTATTATAATA-T--AATATAATA
*
96711 TATTATTAAAATTATTAATA-AATA
1 TATTATTATAA-TA-TAATATAATA
*
96735 TGTT-TTAATAAT-TAATAT--T-
1 TATTATT-ATAATATAATATAATA
* *
96754 T-TTATTAAAATATAATAAAATA
1 TATTATTATAATATAATATAATA
96776 GTA-TATTA
1 -TATTATTA
96784 ATACTAAATA
Statistics
Matches: 98, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
18 6 0.06
19 8 0.08
20 1 0.01
21 6 0.06
23 32 0.33
24 20 0.20
25 4 0.04
26 17 0.17
27 4 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTATTATAATATAATATAATA
Found at i:96794 original size:42 final size:42
Alignment explanation
Indices: 96713--96794 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
96703 ATATATTATA
*
96713 TTATTAAAATTATTAATAAATATGTTTTAATAATTAATATTT
1 TTATTAAAATTATTAATAAATATGTTTTAATAATAAATATTT
*
96755 TTATTAAAA-TA-TAATAAA-ATAGTATATTAATACTAAATAT
1 TTATTAAAATTATTAATAAATAT-GT-T-TTAATAATAAATAT
96795 ATAAAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 2 0.06
40 9 0.26
41 3 0.09
42 21 0.60
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (42 bp):
TTATTAAAATTATTAATAAATATGTTTTAATAATAAATATTT
Found at i:97336 original size:23 final size:23
Alignment explanation
Indices: 97310--97368 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
97300 TCAAAAACTT
97310 AAATATAATTATACCAAAAA-TAA
1 AAATATAATTAT-CCAAAAATTAA
* *
97333 AAAT-TAAATTATTCAAAAATTTA
1 AAATAT-AATTATCCAAAAATTAA
97356 AAATATATATTAT
1 AAATATA-ATTAT
97369 TACTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 7 0.23
23 17 0.57
24 6 0.20
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATAATTATCCAAAAATTAA
Found at i:98163 original size:21 final size:21
Alignment explanation
Indices: 98136--98193 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
98126 CGTCACTAGT
**
98136 CACTGTGGATTGTCATGTCAG
1 CACTGTGGATTGTCACATCAG
*
98157 CATTGTGGATTGTCACATCAG
1 CACTGTGGATTGTCACATCAG
*
98178 CACTGTGGAGTGTCAC
1 CACTGTGGATTGTCAC
98194 GTTAATATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (21 bp):
CACTGTGGATTGTCACATCAG
Found at i:98832 original size:75 final size:74
Alignment explanation
Indices: 98751--98900 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 74
98741 CAGTACAATT
*
98751 TAAAATTTAATTGTTTATATTGTTATTAAAAAGTAAATTTGAAAAGATAAAATGTCCATTATAAA
1 TAAAATTTAATTGTTTAAATTGTTATTAAAAAGTAAATTTGAAAAGAT-AAATGTCCATTATAAA
98816 CATTATATTG
65 CATTATATTG
* *
98826 TAAAATTTAATTGTTTAAATTGTTGTTAAAAAGTAAATTTGAAAAGATAAATGTTCATTATAAAC
1 TAAAATTTAATTGTTTAAATTGTTATTAAAAAGTAAATTTGAAAAGATAAATGTCCATTATAAAC
98891 ATTATATTG
66 ATTATATTG
98900 T
1 T
98901 CATTTGCTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 26 0.36
75 46 0.64
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (74 bp):
TAAAATTTAATTGTTTAAATTGTTATTAAAAAGTAAATTTGAAAAGATAAATGTCCATTATAAAC
ATTATATTG
Found at i:103784 original size:12 final size:12
Alignment explanation
Indices: 103767--103791 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
103757 CCTAACGTCT
103767 TTACATTATTAC
1 TTACATTATTAC
103779 TTACATTATTAC
1 TTACATTATTAC
103791 T
1 T
103792 GTTGAATTTA
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTACATTATTAC
Found at i:109856 original size:20 final size:18
Alignment explanation
Indices: 109822--109858 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
109812 GAAATTTAAA
109822 TTTTAAATTAATTAATTT
1 TTTTAAATTAATTAATTT
109840 TTTTAAAATTAAATTAATT
1 TTTT-AAATT-AATTAATT
109859 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAATTAATTAATTT
Found at i:121919 original size:23 final size:23
Alignment explanation
Indices: 121889--121935 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
121879 TTGCTTCACT
121889 TGTTAAAAGTTTTGTTTATAGTC
1 TGTTAAAAGTTTTGTTTATAGTC
121912 TGTTAAAAGTTTTGTTTATAGTC
1 TGTTAAAAGTTTTGTTTATAGTC
121935 T
1 T
121936 ATCTCTAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (23 bp):
TGTTAAAAGTTTTGTTTATAGTC
Found at i:122181 original size:21 final size:21
Alignment explanation
Indices: 122136--122187 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
122126 ACCAACAACT
**
122136 ATAACAAACTAATAACAATTA
1 ATAACAAACTAATAACAAACA
* *
122157 ATAACAAGCTAATAACAAACC
1 ATAACAAACTAATAACAAACA
122178 ATAACAAACT
1 ATAACAAACT
122188 CTAACATTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (21 bp):
ATAACAAACTAATAACAAACA
Found at i:123913 original size:11 final size:10
Alignment explanation
Indices: 123874--123919 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
123864 CCAAGTAACC
123874 AACAACT-AT
1 AACAACTAAT
*
123883 AATAAACTAAT
1 AA-CAACTAAT
123894 AACAACTAAT
1 AACAACTAAT
123904 AACAAGCTAAT
1 AACAA-CTAAT
123915 AACAA
1 AACAA
123920 ACCATAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 2 0.06
10 16 0.50
11 14 0.44
ACGTcount: A:0.61, C:0.17, G:0.02, T:0.20
Consensus pattern (10 bp):
AACAACTAAT
Found at i:123913 original size:21 final size:20
Alignment explanation
Indices: 123874--123932 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
123864 CCAAGTAACC
*
123874 AACAACTATAATAAACTAAT
1 AACAACTATAACAAACTAAT
*
123894 AACAACTAATAACAAGCTAAT
1 AACAACT-ATAACAAACTAAT
*
123915 AACAAACCATAACAAACT
1 AAC-AACTATAACAAACT
123933 CTAACAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 23 0.70
22 3 0.09
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.19
Consensus pattern (20 bp):
AACAACTATAACAAACTAAT
Found at i:124254 original size:2 final size:2
Alignment explanation
Indices: 124247--124273 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
124237 CCTAAAAGTT
124247 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
124274 TACGGACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:129754 original size:20 final size:20
Alignment explanation
Indices: 129725--129762 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
129715 CACTCATCTA
* *
129725 TTAGTTAATTTATTTTTTGG
1 TTAGTCAATTAATTTTTTGG
129745 TTAGTCAATTAATTTTTT
1 TTAGTCAATTAATTTTTT
129763 TAAATCATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.63
Consensus pattern (20 bp):
TTAGTCAATTAATTTTTTGG
Found at i:129833 original size:2 final size:2
Alignment explanation
Indices: 129828--129858 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
129818 ATTTTTTTAT
*
129828 TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
129859 TTACTTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:130009 original size:35 final size:36
Alignment explanation
Indices: 129888--130221 Score: 233
Period size: 37 Copynumber: 9.2 Consensus size: 36
129878 TGAAAATACT
* *
129888 TATA-ATATACATAATTTTTGAAAACATTTT-GAAAA
1 TATATATATATATAGTTTTT-AAAACATTTTAGAAAA
* * * *
129923 TGTATATAATATATAGTTTTAAAAATATTTTTTGAAAA
1 TATATAT-ATATATAGTTTTTAAAACA-TTTTAGAAAA
*
129961 CTATATA-GTATATAGTTTTTAAAACATTTTAGAAAA
1 -TATATATATATATAGTTTTTAAAACATTTTAGAAAA
* *
129997 TATATATAATATATAATTTTTAAAATCATTTTTGAAAA
1 TATATAT-ATATATAGTTTTTAAAA-CATTTTAGAAAA
* ****
130035 CT-TATATATATATAGTTTTGAATGTTTTTTA-AAACA
1 -TATATATATATATAGTTTTTAAAACATTTTAGAAA-A
* * * *
130071 TTTAAATAT-TATAATTTTTGAAAATATTTTA-AAAA
1 TATATATATATATAGTTTTT-AAAACATTTTAGAAAA
* *
130106 TATATA-ATATATAATTTTTAAAACGTTTCT-GAAAA
1 TATATATATATATAGTTTTTAAAACATTT-TAGAAAA
* *
130141 TATATAT-TATAAAGTTTTTAAAACGTTTTTA-AAAA
1 TATATATATATATAGTTTTTAAAAC-ATTTTAGAAAA
* * *
130176 CATGTATAATATATAGTTTTTAAAAGCATTTT-GGAAA
1 TATATAT-ATATATAGTTTTTAAAA-CATTTTAGAAAA
*
130213 TTTATATAT
1 TATATATAT
130222 TACATATTTT
Statistics
Matches: 236, Mismatches: 41, Indels: 43
0.74 0.13 0.13
Matches are distributed among these distances:
34 9 0.04
35 72 0.31
36 43 0.18
37 84 0.36
38 22 0.09
39 6 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (36 bp):
TATATATATATATAGTTTTTAAAACATTTTAGAAAA
Found at i:130099 original size:26 final size:28
Alignment explanation
Indices: 130059--130113 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
130049 GTTTTGAATG
* *
130059 TTTTTTAAAACA-TTTAAATAT-TATAA
1 TTTTTGAAAACATTTTAAAAATATATAA
*
130085 TTTTTGAAAATATTTTAAAAATATATAA
1 TTTTTGAAAACATTTTAAAAATATATAA
130113 T
1 T
130114 ATATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.42
27 8 0.33
28 6 0.25
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TTTTTGAAAACATTTTAAAAATATATAA
Found at i:130199 original size:72 final size:70
Alignment explanation
Indices: 129888--130238 Score: 264
Period size: 74 Copynumber: 4.8 Consensus size: 70
129878 TGAAAATACT
* * * * *
129888 TATAATATACATAATTTTTGAAAACATTTTGAAAATGTATATAATATATAGTTTTAAAAATATTT
1 TATAATAT--ATAGTTTTT-AAAACATTTTGAAAAT-TATATATTATA-AATTTTTAAAAT-CTT
129953 TTTGAAAACTA
60 TTTGAAAACTA
* *
129964 TATAGTATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAATTTTTAAAATCATTTT
1 TATAATATATAGTTTTTAAAACATTTT-GAAAAT-TATATATTATA-AATTTTTAAAATC-TTTT
130029 TGAAAACT-
62 TGAAAACTA
* **** * * *
130037 TATATATATATAGTTTTGAATGTTTTTTAAAACATTTAAATATTAT-AATTTTTGAAAAT-ATTT
1 TATA-ATATATAGTTTTTAAAACATTTTGAAA-A-TTATATATTATAAATTTTT-AAAATCTTTT
*
130100 T-AAAAATA
62 TGAAAACTA
* *
130108 TATAATATATAATTTTTAAAACGTTTCTGAAAA-TATATATTATAAAGTTTTTAAAA-CGTTTTT
1 TATAATATATAGTTTTTAAAACATTT-TGAAAATTATATATTATAAA-TTTTTAAAATC-TTTTT
* *
130171 AAAAACATG
63 GAAAAC-TA
* * *
130180 TATAATATATAGTTTTTAAAAGCATTTTGGAAATTTATATATTACATATTTTTGAAAAT
1 TATAATATATAGTTTTTAAAA-CATTTT-GAAAATTATATATTATAAATTTTT-AAAAT
130239 ATTTATATAT
Statistics
Matches: 223, Mismatches: 33, Indels: 39
0.76 0.11 0.13
Matches are distributed among these distances:
68 9 0.04
69 6 0.03
70 31 0.14
71 16 0.07
72 29 0.13
73 35 0.16
74 89 0.40
75 1 0.00
76 7 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (70 bp):
TATAATATATAGTTTTTAAAACATTTTGAAAATTATATATTATAAATTTTTAAAATCTTTTTGAA
AACTA
Found at i:130265 original size:3 final size:3
Alignment explanation
Indices: 130257--130303 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
130247 ATATATATAG
* *
130257 TAT TAT TAT TAT TAT TATT TAT TTT TAT T-T TATT TCT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT TAT
130303 T
1 T
130304 TATGCTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:130819 original size:17 final size:17
Alignment explanation
Indices: 130799--130832 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
130789 AACGCAAAAT
* *
130799 AAACCAAAACAACAGCA
1 AAACAAAAACAAAAGCA
130816 AAACAAAAACAAAAGCA
1 AAACAAAAACAAAAGCA
130833 GACAGCCCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.24, G:0.06, T:0.00
Consensus pattern (17 bp):
AAACAAAAACAAAAGCA
Found at i:135258 original size:75 final size:74
Alignment explanation
Indices: 135142--135503 Score: 297
Period size: 75 Copynumber: 4.8 Consensus size: 74
135132 TGAAAATACT
* *
135142 TATAATATACATAATTTTTGAAAACATTTTGAAAATGTATATAATATATAGTTTTAAAAATATTT
1 TATAATAT--ATAGTTTTT-AAAACATTTTGAAAATATATATAATATATAGTTTTAAAAATA-TT
*
135207 TTTTGAAAAC-TA
62 TTTTAAAAACATA
* *
135219 TATAGTATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCA-TTT
1 TATAATATATAGTTTTTAAAACATTTT-GAAAATATATATAATATATAGTTTTAAAAAT-ATTTT
* *
135283 TTGAAAACTTA
64 TTAAAAACATA
* **** * * * * * *
135294 TATAATATATAGTTTTGAATGTTTTTTAAAACATTTAAATATTATATAATTTTTGAAAAACA--T
1 TATAATATATAGTTTTTAAAACATTTTGAAA-ATATATATAATATAT-AGTTTT-AAAAATATTT
*
135357 TTTAAAAATATA
63 TTTAAAAACATA
* * * * *
135369 TATAATATATAATTTTTAAAACGTTTCTGAAAATATATAT--TATAAAGTTTTTAAAAT-GTTTT
1 TATAATATATAGTTTTTAAAACATTT-TGAAAATATATATAATATATAGTTTTAAAAATATTTTT
*
135431 TAAAAACATG
65 TAAAAACATA
* * * * * *
135441 TATAATATATAGTTTTTAAAAGCATTTTGGAAATTTATATATTACATATTTTTGAAAATATTT
1 TATAATATATAGTTTTTAAAA-CATTTTGAAAATATATATAATATATAGTTTTAAAAATATTT
135504 ATATATATAT
Statistics
Matches: 228, Mismatches: 44, Indels: 28
0.76 0.15 0.09
Matches are distributed among these distances:
71 4 0.02
72 47 0.21
73 8 0.04
74 37 0.16
75 110 0.48
76 11 0.05
77 11 0.05
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (74 bp):
TATAATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTTT
AAAAACATA
Found at i:135267 original size:37 final size:37
Alignment explanation
Indices: 135133--135503 Score: 262
Period size: 37 Copynumber: 9.9 Consensus size: 37
135123 AACGGTCTTT
*
135133 GAAAATACT-TATAATATACATAATTTTTGAAAACATTTT-
1 GAAAATA-TATATAATAT--ATAGTTTTT-AAAACATTTTA
* * * *
135172 GAAAATGTATATAATATATAGTTTTAAAAATATTTTTTT
1 GAAAATATATATAATATATAGTTTTTAAAACA--TTTTA
* *
135211 GAAAA-CTATATAGTATATAGTTTTTAAAACATTTTA
1 GAAAATATATATAATATATAGTTTTTAAAACATTTTA
*
135247 GAAAATATATATAATATATAGTTTTTAAAATCATTTTT
1 GAAAATATATATAATATATAGTTTTTAAAA-CATTTTA
* ****
135285 GAAAACT-TATATAATATATAGTTTTGAATGTTTTTTA
1 GAAAA-TATATATAATATATAGTTTTTAAAACATTTTA
* * * *
135322 -AAACATTTAAATATTATATAATTTTTGAAAAACATTTTA
1 GAAA-ATATATATAATATATAGTTTTT--AAAACATTTTA
* *
135361 -AAAATATATATAATATATAATTTTTAAAACGTTTCT-
1 GAAAATATATATAATATATAGTTTTTAAAACATTT-TA
* **
135397 GAAAATATATAT--TATAAAGTTTTTAAAATGTTTTTA
1 GAAAATATATATAATATATAGTTTTTAAAA-CATTTTA
* *
135433 -AAAACATGTATAATATATAGTTTTTAAAAGCATTTT-
1 GAAAATATATATAATATATAGTTTTTAAAA-CATTTTA
* * * * *
135469 GGAAATTTATATATTACATA-TTTTTGAAAATATTT
1 GAAAATATATATAATATATAGTTTTT-AAAACATTT
135504 ATATATATAT
Statistics
Matches: 266, Mismatches: 47, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
35 24 0.09
36 38 0.14
37 97 0.36
38 77 0.29
39 30 0.11
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
GAAAATATATATAATATATAGTTTTTAAAACATTTTA
Found at i:135524 original size:3 final size:3
Alignment explanation
Indices: 135516--135568 Score: 81
Period size: 3 Copynumber: 17.3 Consensus size: 3
135506 ATATATATAG
135516 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT T-T TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT
135562 TAT TAT T
1 TAT TAT T
135569 TATGCTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:135569 original size:25 final size:25
Alignment explanation
Indices: 135518--135571 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
135508 ATATATAGTA
135518 TTATTATTATTATTATTATTATTAT
1 TTATTATTATTATTATTATTATTAT
135543 TTATTATT-TTATTTATTATTATTAT
1 TTATTATTATTA-TTATTATTATTAT
135568 TTAT
1 TTAT
135572 GCTTTTTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 3 0.11
25 25 0.89
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTATTATTATTATTATTATTATTAT
Found at i:135577 original size:25 final size:25
Alignment explanation
Indices: 135530--135577 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
135520 ATTATTATTA
*
135530 TTATTATTATTATTTATTATTTTAT
1 TTATTATTATTATTTATGATTTTAT
*
135555 TTATTATTATTATTTATGCTTTT
1 TTATTATTATTATTTATGATTTT
135578 TGCAGGGTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (25 bp):
TTATTATTATTATTTATGATTTTAT
Found at i:139469 original size:16 final size:17
Alignment explanation
Indices: 139448--139486 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
139438 GTGTAAAACT
*
139448 GTTGACATTTGACCG-C
1 GTTGACAGTTGACCGAC
*
139464 GTTGACCGTTGACCGAC
1 GTTGACAGTTGACCGAC
139481 GTTGAC
1 GTTGAC
139487 CACCGTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (17 bp):
GTTGACAGTTGACCGAC
Found at i:139485 original size:17 final size:16
Alignment explanation
Indices: 139456--139487 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
139446 CTGTTGACAT
139456 TTGACCGCGTTGACCG
1 TTGACCGCGTTGACCG
139472 TTGACCGACGTTGACC
1 TTGACCG-CGTTGACC
139488 ACCGTTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25
Consensus pattern (16 bp):
TTGACCGCGTTGACCG
Found at i:141314 original size:31 final size:31
Alignment explanation
Indices: 141276--141355 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
141266 AGGGTCGAGG
141276 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGAGACATATGGACT
*
141307 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGAGACATATGGACT
* * *
141338 GATTACCTAGGTTTTTCG
1 GTTTACCTATGTTCTTCG
141356 GAATCTATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGAGACATATGGACT
Found at i:141356 original size:31 final size:31
Alignment explanation
Indices: 141278--141369 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
141268 GGTCGAGGGT
* *
141278 TTACCTATGTTCTTCGAGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
141309 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* * *
141340 TTACCTAGGTTTTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
141370 GTCCTTCGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:144386 original size:24 final size:24
Alignment explanation
Indices: 144294--144388 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
144284 ATTTTTTACT
* *
144294 TGAATTCTGTTCTGA-TACATGACC
1 TGAATTCTGTTCTGATTTC-TGATC
* *
144318 TGAATTTTGTTATGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
* *
144342 T-AGATTATGTTCTGATATCTGATC
1 TGA-ATTCTGTTCTGATTTCTGATC
*
144366 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
144389 ATCTCTGTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.02
24 54 0.93
25 3 0.05
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:145397 original size:95 final size:92
Alignment explanation
Indices: 145235--145436 Score: 251
Period size: 95 Copynumber: 2.2 Consensus size: 92
145225 CTAAAGGAAT
* * * * * * *
145235 AGTATCGGTACCATTACTCAGAGTATCGATATCATATATGGTATTGGTACCATTATAGCATTTTG
1 AGTATCGGTACTACTACTCAGAGTATCGATAGCATATATGATATCGGTACCATTATAACATTCTG
*
145300 TTTTGACAGTATCAGTACTGCCTCAAC
66 TTTTGACAGTATCAGTACTGCATCAAC
* *
145327 AGTATCGGTACTACTACTCTAAGTAGTGTCGATAGCATATATGATATCGGTACCATTTTAACATT
1 AGTATCGGTACTACTACTC--AG-AGTATCGATAGCATATATGATATCGGTACCATTATAACATT
* *
145392 CTGTTTTGACAGTATCTGTACTGCATCAAT
63 CTGTTTTGACAGTATCAGTACTGCATCAAC
* *
145422 AGTATTGGTATTACT
1 AGTATCGGTACTACT
145437 TCATTATTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
92 17 0.18
94 2 0.02
95 74 0.80
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (92 bp):
AGTATCGGTACTACTACTCAGAGTATCGATAGCATATATGATATCGGTACCATTATAACATTCTG
TTTTGACAGTATCAGTACTGCATCAAC
Found at i:146025 original size:13 final size:13
Alignment explanation
Indices: 146007--146036 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
145997 TAATGTGTTT
146007 AAAAAATTTAAGA
1 AAAAAATTTAAGA
*
146020 AAAAAATTTATGA
1 AAAAAATTTAAGA
146033 AAAA
1 AAAA
146037 CAAAAGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
AAAAAATTTAAGA
Found at i:148074 original size:87 final size:87
Alignment explanation
Indices: 147956--148128 Score: 274
Period size: 87 Copynumber: 2.0 Consensus size: 87
147946 CTCGTGACAC
* * *
147956 CGGCATGACGAGTTCCATTGAAATTTTAAAAAAAATCAACCGTTGAACAACGTTCAATCCAATGG
1 CGGCATGACGAGTTCCATTGAAATTTAAAAAAAAATCAACCGTTGAACAACATTCAATCCAACGG
*
148021 TCAAAAAAGTCAATATTATAGT
66 TCAAAAAAGTCAAAATTATAGT
* * * *
148043 CGGCGTGACGAGTTCCATTGAAATTTAAAAAAAATTCGACCGTTTAACAACATTCAATCCAACGG
1 CGGCATGACGAGTTCCATTGAAATTTAAAAAAAAATCAACCGTTGAACAACATTCAATCCAACGG
148108 TCAAAAAAGTCAAAATTATAG
66 TCAAAAAAGTCAAAATTATAG
148129 CCGTTGGAAC
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (87 bp):
CGGCATGACGAGTTCCATTGAAATTTAAAAAAAAATCAACCGTTGAACAACATTCAATCCAACGG
TCAAAAAAGTCAAAATTATAGT
Found at i:150910 original size:21 final size:21
Alignment explanation
Indices: 150884--150978 Score: 131
Period size: 21 Copynumber: 4.6 Consensus size: 21
150874 AGTTTCCAGA
150884 TTCGCGTTGCGATAATCGAAG
1 TTCGCGTTGCGATAATCGAAG
150905 TTCGCGTTGCGATAATCGAAG
1 TTCGCGTTGCGATAATCGAAG
** * *
150926 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAATCGAAG
*
150947 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAATCGAAG
150966 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
150979 TTATTCCAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.23
21 49 0.77
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAATCGAAG
Found at i:150964 original size:40 final size:42
Alignment explanation
Indices: 150909--151003 Score: 167
Period size: 40 Copynumber: 2.3 Consensus size: 42
150899 TCGAAGTTCG
*
150909 CGTTGCGATAATCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
150949 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
150991 CGTTGCGATAGTC
1 CGTTGCGATAGTC
151004 AAAATTTTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
40 28 0.54
41 2 0.04
42 22 0.42
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:150994 original size:21 final size:20
Alignment explanation
Indices: 150930--150999 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
150920 TCGAAGTTCG
150930 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * *
150949 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
150968 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
150991 CGTTGCGAT
1 CGTTGCGAT
151000 AGTCAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
18 1 0.03
19 14 0.35
20 1 0.03
21 16 0.40
23 8 0.20
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:151009 original size:61 final size:60
Alignment explanation
Indices: 150888--151009 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 60
150878 TCCAGATTCG
* * ** *
150888 CGTTGCGATAATCGAAGTTCGCGTTGCGATAATCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAATCGAAGTTCGCGTTGCGATAATCCAAATTC-CGTTGCGATAGTCAAAATT
* *
150949 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGCGATAGTCAAAATT
1 CGTTGCGATAATCGAAGTTCGCGTTGCGA--TAATCCAAATTCCGTTGCGATAGTCAAAATT
151010 TTTGTTTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 44 0.85
63 8 0.15
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (60 bp):
CGTTGCGATAATCGAAGTTCGCGTTGCGATAATCCAAATTCCGTTGCGATAGTCAAAATT
Found at i:151696 original size:40 final size:40
Alignment explanation
Indices: 151641--151722 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
151631 ATACTATCGT
*
151641 AACGAATTTGAAAAATCGCAACGCGAACTTCGACTACCGC
1 AACGAATTTGAAAAATCACAACGCGAACTTCGACTACCGC
* * *
151681 AACGAATTTGGAAAATCACAACGCGAACTTGGACTATCGC
1 AACGAATTTGAAAAATCACAACGCGAACTTCGACTACCGC
151721 AA
1 AA
151723 TGTGAATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (40 bp):
AACGAATTTGAAAAATCACAACGCGAACTTCGACTACCGC
Found at i:151768 original size:21 final size:21
Alignment explanation
Indices: 151737--151789 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
151727 AATATGTAAA
* *
151737 TCGCATTGCGATAGTCTAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
151758 TCGTGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
151779 TTGCGTTGCGA
1 TCGCGTTGCGA
151790 ATCTGGAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:154993 original size:31 final size:31
Alignment explanation
Indices: 154928--155091 Score: 116
Period size: 31 Copynumber: 5.3 Consensus size: 31
154918 TGAAAAATAA
* * * *
154928 AAAATATTAAATAAATTTTTAAAATTTCATAT
1 AAAATATTAAATTAATTCTT-AAATTTTAGAT
*
154960 AAAATATTAAATTGATTCTTAAATTTTAGAT
1 AAAATATTAAATTAATTCTTAAATTTTAGAT
* ** *
154991 -AAATGTTACTTTAATTCTTAAATTTTACAT
1 AAAATATTAAATTAATTCTTAAATTTTAGAT
* * * * *
155021 GAAATATTAAATT-AGTCTTTAAACTCTAGTT
1 AAAATATTAAATTAATTC-TTAAATTTTAGAT
* * * * *
155052 AAAATATCAATTTGACTCTTAAATTTTTAAAT
1 AAAATATTAAATTAATTCTTAAA-TTTTAGAT
155084 AAAATATT
1 AAAATATT
155092 GATTCAACCC
Statistics
Matches: 101, Mismatches: 27, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
30 28 0.28
31 42 0.42
32 31 0.31
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (31 bp):
AAAATATTAAATTAATTCTTAAATTTTAGAT
Found at i:156450 original size:17 final size:17
Alignment explanation
Indices: 156428--156465 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
156418 AACGGTCAAC
156428 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
156445 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
156462 GGTC
1 GGTC
156466 CGGTCAACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:156455 original size:7 final size:7
Alignment explanation
Indices: 156394--156438 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
156384 GTCAAAGAAA
156394 GTCAACG
1 GTCAACG
156401 GTCAACG
1 GTCAACG
156408 GTCAACG
1 GTCAACG
156415 GTCAACG
1 GTCAACG
156422 GTCAACG
1 GTCAACG
156429 GTCAACG
1 GTCAACG
156436 GTC
1 GTC
156439 GGGTCGGGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:156463 original size:22 final size:22
Alignment explanation
Indices: 156435--156487 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
156425 AACGGTCAAC
*
156435 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCCGGTCAACGGTCG
*
156457 GGTCGGGTCCGGTCAACAGTCG
1 GGTCGGGTCCGGTCAACGGTCG
*
156479 GGTTGGGTC
1 GGTCGGGTC
156488 AGACCGGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.09, C:0.23, G:0.47, T:0.21
Consensus pattern (22 bp):
GGTCGGGTCCGGTCAACGGTCG
Found at i:156502 original size:9 final size:9
Alignment explanation
Indices: 156484--156543 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
156474 AGTCGGGTTG
*
156484 GGTCAGACC
1 GGTCAAACC
156493 GGTCAAACC
1 GGTCAAACC
*
156502 GGTCCAGACC
1 GGT-CAAACC
156512 GGTCAAACC
1 GGTCAAACC
*
156521 GGTTCAAAACT
1 GG-TC-AAACC
156532 GGTCAAACC
1 GGTCAAACC
156541 GGT
1 GGT
156544 TTTCCAGCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.58
10 12 0.28
11 6 0.14
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:156511 original size:19 final size:19
Alignment explanation
Indices: 156487--156543 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
156477 CGGGTTGGGT
156487 CAGACCGGTCAAACCGGTC
1 CAGACCGGTCAAACCGGTC
156506 CAGACCGGTCAAACCGGTTC
1 CAGACCGGTCAAACCGG-TC
* * *
156526 AAAACTGGTCAAACCGGT
1 CAGACCGGTCAAACCGGT
156544 TTTCCAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.14
Consensus pattern (19 bp):
CAGACCGGTCAAACCGGTC
Found at i:156537 original size:20 final size:20
Alignment explanation
Indices: 156490--156544 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
156480 GTTGGGTCAG
* *
156490 ACCGGTCAAACCGG-TCCAG
1 ACCGGTCAAACCGGTTCAAA
156509 ACCGGTCAAACCGGTTCAAA
1 ACCGGTCAAACCGGTTCAAA
*
156529 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
156545 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTCAAA
Found at i:163740 original size:17 final size:17
Alignment explanation
Indices: 163720--163757 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
163710 GAAAGTCAAC
163720 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
163737 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
163754 GGTC
1 GGTC
163758 GGGTCAGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:163755 original size:22 final size:24
Alignment explanation
Indices: 163727--163776 Score: 86
Period size: 22 Copynumber: 2.2 Consensus size: 24
163717 AACGGTCAAC
163727 GGTCGGGTCGGGTCA-AC-GGTCG
1 GGTCGGGTCGGGTCAGACGGGTCG
163749 GGTCGGGTCGGGTCAGACGGGTCG
1 GGTCGGGTCGGGTCAGACGGGTCG
163773 GGTC
1 GGTC
163777 AGACCGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 15 0.58
23 2 0.08
24 9 0.35
ACGTcount: A:0.08, C:0.22, G:0.52, T:0.18
Consensus pattern (24 bp):
GGTCGGGTCGGGTCAGACGGGTCG
Found at i:163785 original size:9 final size:9
Alignment explanation
Indices: 163773--163832 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
163763 AGACGGGTCG
*
163773 GGTCAGACC
1 GGTCAAACC
163782 GGTCAAACC
1 GGTCAAACC
*
163791 GGTCCAGACC
1 GGT-CAAACC
163801 GGTCAAACC
1 GGTCAAACC
*
163810 GGTTCAAAACT
1 GG-TC-AAACC
163821 GGTCAAACC
1 GGTCAAACC
163830 GGT
1 GGT
163833 TTTCCAGCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.58
10 12 0.28
11 6 0.14
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:163785 original size:14 final size:13
Alignment explanation
Indices: 163732--163785 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
163722 TCAACGGTCG
163732 GGTCGGGTCA-AC
1 GGTCGGGTCAGAC
163744 GGTCGGGTC-G--
1 GGTCGGGTCAGAC
163754 GGTCGGGTCAGAC
1 GGTCGGGTCAGAC
163767 GGGTCGGGTCAGACC
1 -GGTCGGGTCAGA-C
163782 GGTC
1 GGTC
163786 AAACCGGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
12 9 0.25
14 16 0.44
15 1 0.03
ACGTcount: A:0.11, C:0.24, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAGAC
Found at i:163800 original size:19 final size:19
Alignment explanation
Indices: 163776--163832 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
163766 CGGGTCGGGT
163776 CAGACCGGTCAAACCGGTC
1 CAGACCGGTCAAACCGGTC
163795 CAGACCGGTCAAACCGGTTC
1 CAGACCGGTCAAACCGG-TC
* * *
163815 AAAACTGGTCAAACCGGT
1 CAGACCGGTCAAACCGGT
163833 TTTCCAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.14
Consensus pattern (19 bp):
CAGACCGGTCAAACCGGTC
Found at i:163826 original size:20 final size:20
Alignment explanation
Indices: 163779--163833 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
163769 GTCGGGTCAG
* *
163779 ACCGGTCAAACCGG-TCCAG
1 ACCGGTCAAACCGGTTCAAA
163798 ACCGGTCAAACCGGTTCAAA
1 ACCGGTCAAACCGGTTCAAA
*
163818 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
163834 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTCAAA
Found at i:164918 original size:18 final size:18
Alignment explanation
Indices: 164897--164931 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
164887 TCTAAAACGT
*
164897 CCGTTTTGATCACAAAAC
1 CCGTTTTAATCACAAAAC
*
164915 CCGTTTTAATCGCAAAA
1 CCGTTTTAATCACAAAA
164932 TCAATGCCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (18 bp):
CCGTTTTAATCACAAAAC
Found at i:166336 original size:38 final size:36
Alignment explanation
Indices: 166261--166337 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 36
166251 TACTATAATT
*
166261 AATTTATATATTTTCTTTAAAAAAATTAAAATCATA
1 AATTTATATATTTTCTTTAAAAAAATTAAAAACATA
* * * *
166297 AATTTATATAATTTTTTTTTTACAAAATTAAAAAGATA
1 AATTTATAT-A-TTTTCTTTAAAAAAATTAAAAACATA
166335 AAT
1 AAT
166338 AGGTTTATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 9 0.26
37 1 0.03
38 24 0.71
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
AATTTATATATTTTCTTTAAAAAAATTAAAAACATA
Done.