Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004477.1 Hibiscus syriacus cultivar Beakdansim tig00009869_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: 60090
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:978 original size:16 final size:15
Alignment explanation
Indices: 957--991 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
947 GAAATCATTG
957 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
*
973 AAAAATTATGTAAAA
1 AAAAATTATATAAAA
988 AAAA
1 AAAA
992 TTAGAGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:1156 original size:18 final size:18
Alignment explanation
Indices: 1133--1171 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1123 AAAACATTTG
1133 TGTTGCGAAAATAAAAGT
1 TGTTGCGAAAATAAAAGT
* *
1151 TGTTGCGAAATTAAAATT
1 TGTTGCGAAAATAAAAGT
1169 TGT
1 TGT
1172 GTTGCGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (18 bp):
TGTTGCGAAAATAAAAGT
Found at i:1176 original size:20 final size:20
Alignment explanation
Indices: 1128--1239 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
1118 TACCCAAAAC
1128 ATTTGTGTTGCGAAAATAAA
1 ATTTGTGTTGCGAAAATAAA
* *
1148 A-GT-TGTTGCGAAATTAAA
1 ATTTGTGTTGCGAAAATAAA
*** *
1166 ATTTGTGTTGCGGTTTAGAAA
1 ATTTGTGTTGC-GAAAATAAA
* **
1187 ATCT-TGTTGCGAAAAGGAA
1 ATTTGTGTTGCGAAAATAAA
*
1206 ACTTGTGTTGCGAAAA-AGAA
1 ATTTGTGTTGCGAAAATA-AA
1226 ATTT-TCGTTGCGAA
1 ATTTGT-GTTGCGAA
1240 TTCAGAAATC
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
18 15 0.22
19 10 0.14
20 37 0.54
21 7 0.10
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (20 bp):
ATTTGTGTTGCGAAAATAAA
Found at i:1226 original size:40 final size:39
Alignment explanation
Indices: 1130--1239 Score: 89
Period size: 40 Copynumber: 2.8 Consensus size: 39
1120 CCCAAAACAT
* * ** *
1130 TTGTGTTGCGAAAATAAAA-GTTGTTGCGAAATTAAAAT
1 TTGTGTTGCGAAAAGAAAATCTTGTTGCGAAAAGAAAAC
*** *
1168 TTGTGTTGCGGTTTAGAAAATCTTGTTGCGAAAAGGAAAC
1 TTGTGTTGC-GAAAAGAAAATCTTGTTGCGAAAAGAAAAC
*
1208 TTGTGTTGCGAAAA-AGAAATTTTCGTTGCGAA
1 TTGTGTTGCGAAAAGA-AAATCTT-GTTGCGAA
1240 TTCAGAAATC
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
38 10 0.18
39 14 0.25
40 31 0.56
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (39 bp):
TTGTGTTGCGAAAAGAAAATCTTGTTGCGAAAAGAAAAC
Found at i:1255 original size:20 final size:20
Alignment explanation
Indices: 1232--1341 Score: 70
Period size: 20 Copynumber: 5.5 Consensus size: 20
1222 AGAAATTTTC
1232 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGA
*
1252 GTTGCGAATT-A-AAATTCCGT
1 GTTGCGAATTCAGAAA-T-CGA
** *
1272 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTCAGAAATCGA
* *
1292 GTTGCGAGA--AAGAAATTCGC
1 GTTGCGA-ATTCAGAAA-TCGA
1312 GTTGCG-ATTGCAGAAA-CTGA
1 GTTGCGAATT-CAGAAATC-GA
1332 GTTGCGAATT
1 GTTGCGAATT
1342 TGGGAAATTC
Statistics
Matches: 72, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
18 4 0.06
19 7 0.10
20 48 0.67
21 10 0.14
22 3 0.04
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATCGA
Found at i:1256 original size:40 final size:40
Alignment explanation
Indices: 1212--1339 Score: 113
Period size: 40 Copynumber: 3.2 Consensus size: 40
1202 GGAAACTTGT
*
1212 GTTGCGAAAAAGAAATTTTCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAAAAGAAATTTCCGTTGCGAATTCAGAAATCGA
** ** *
1252 GTTGCGAATTA-AAA-TTCCGTGTTGCGAATTTGGAAATCGC
1 GTTGCGAAAAAGAAATTTCC--GTTGCGAATTCAGAAATCGA
*
1292 GTTGCGAGAAAGAAA-TTCGCGTTGCG-ATTGCAGAAA-CTGA
1 GTTGCGAAAAAGAAATTTC-CGTTGCGAATT-CAGAAATC-GA
1332 GTTGCGAA
1 GTTGCGAA
1340 TTTGGGAAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
38 3 0.04
39 7 0.10
40 52 0.75
41 6 0.09
42 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (40 bp):
GTTGCGAAAAAGAAATTTCCGTTGCGAATTCAGAAATCGA
Found at i:1275 original size:80 final size:80
Alignment explanation
Indices: 1191--1341 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 80
1181 TAGAAAATCT
* * **
1191 TGTTGCGAA-AAGGAAACTTGTGTTGCGAAAAAGAAATTTTCGTTGCGAATT-CAGAAA-TCGAG
1 TGTTGCGAATAAGGAAA-TCGCGTTGCGAAAAAGAAATTCGCGTTGCG-ATTGCAGAAACT-GAG
1253 TTGCGAATTAAAATTCCG
63 TTGCGAATTAAAATTCCG
** *
1271 TGTTGCGAATTTGGAAATCGCGTTGCGAGAAAGAAATTCGCGTTGCGATTGCAGAAACTGAGTTG
1 TGTTGCGAATAAGGAAATCGCGTTGCGAAAAAGAAATTCGCGTTGCGATTGCAGAAACTGAGTTG
1336 CGAATT
66 CGAATT
1342 TGGGAAATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
79 3 0.05
80 52 0.85
81 6 0.10
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (80 bp):
TGTTGCGAATAAGGAAATCGCGTTGCGAAAAAGAAATTCGCGTTGCGATTGCAGAAACTGAGTTG
CGAATTAAAATTCCG
Found at i:1379 original size:20 final size:21
Alignment explanation
Indices: 1324--1381 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1314 TGCGATTGCA
1324 GAAACTGAGTTGCGAATTTGG
1 GAAACTGAGTTGCGAATTTGG
* *
1345 GAAATTCACGTTGCGAATTT-G
1 GAAACTGA-GTTGCGAATTTGG
*
1366 GAAACTGTGTTGCGAA
1 GAAACTGAGTTGCGAA
1382 ATTAGAGTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 8 0.26
21 12 0.39
22 11 0.35
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (21 bp):
GAAACTGAGTTGCGAATTTGG
Found at i:1701 original size:22 final size:20
Alignment explanation
Indices: 1676--1719 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1666 CCGAGTATGA
1676 TATATACAAAAGTATGAGTGTT
1 TATATA-AAAAG-ATGAGTGTT
*
1698 TATATAAAATGATGAGTGTT
1 TATATAAAAAGATGAGTGTT
1718 TA
1 TA
1720 AAATAATACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (20 bp):
TATATAAAAAGATGAGTGTT
Found at i:3096 original size:22 final size:21
Alignment explanation
Indices: 3063--3110 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
3053 AGTTTTGGTT
*
3063 GGGTTTAGAATTTTATAATTTA
1 GGGTTTAGAATTTGA-AATTTA
*
3085 GGGTTT-GAAATTTGAAGTTTA
1 GGGTTTAG-AATTTGAAATTTA
3106 GGGTT
1 GGGTT
3111 AAAGTCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
GGGTTTAGAATTTGAAATTTA
Found at i:6864 original size:22 final size:24
Alignment explanation
Indices: 6836--6888 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
6826 TCTACCAATT
6836 TATATAT-AATTTTA-TAAAAAAA
1 TATATATAAATTTTATTAAAAAAA
**
6858 TATATATAAATTTTATTAAAAGTA
1 TATATATAAATTTTATTAAAAAAA
6882 TATATAT
1 TATATAT
6889 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 7 0.26
24 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TATATATAAATTTTATTAAAAAAA
Found at i:7201 original size:17 final size:17
Alignment explanation
Indices: 7179--7212 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
7169 TTTTAGGTTT
7179 TAAAAATCAAATAAATA
1 TAAAAATCAAATAAATA
7196 TAAAAATCAAATAAATA
1 TAAAAATCAAATAAATA
7213 GAATTATATA
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:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAATCAAATAAATA
Found at i:7887 original size:39 final size:39
Alignment explanation
Indices: 7840--7980 Score: 273
Period size: 39 Copynumber: 3.6 Consensus size: 39
7830 TTTTTGAAAA
7840 TATATAATATATAGTTTTTGAAAACATTTTGAAAACATG
1 TATATAATATATAGTTTTTGAAAACATTTTGAAAACATG
7879 TATATAATATATAGTTTTTGAAAACATTTTGAAAACATG
1 TATATAATATATAGTTTTTGAAAACATTTTGAAAACATG
*
7918 TATATAATATATAGTTTTTGAAAACCTTTTGAAAACATG
1 TATATAATATATAGTTTTTGAAAACATTTTGAAAACATG
7957 TATATAATATATAGTTTTTGAAAA
1 TATATAATATATAGTTTTTGAAAA
7981 TATATATAAT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 101 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (39 bp):
TATATAATATATAGTTTTTGAAAACATTTTGAAAACATG
Found at i:7889 original size:37 final size:38
Alignment explanation
Indices: 7831--8176 Score: 396
Period size: 37 Copynumber: 9.6 Consensus size: 38
7821 TTATATAATT
7831 TTTTG-AAA-ATATATA-ATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAACA
* *
7866 TTTTGAAAACATGTATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAT-ATATATAGTTTTTGAAAACA
* * *
7905 TTTTGAAAACATGTATATAATATATAGTTTTTGAAAACC
1 TTTTGAAAATATATATAT-ATATATAGTTTTTGAAAACA
* *
7944 TTTTGAAAACATGTATATAATATATAG----T-------
1 TTTTGAAAATATATATAT-ATATATAGTTTTTGAAAACA
7972 TTTTGAAAATATATATA-ATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAACA
8009 TTTTGAAAATATATATA-ATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAACA
* *
8046 TTTTGGAAATATATATA-ATATATAATTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAACA
8083 TTTTGAAAATATATATA-ATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTGAAAACA
8120 TTTTGAAAACT-TATATATAATATATAG-TTTT--AAACA
1 TTTTGAAAA-TATATATAT-ATATATAGTTTTTGAAAACA
8156 CTTTTGAAAATATATAT-TATA
1 -TTTTGAAAATATATATATATA
8177 GTTTCTTGAA
Statistics
Matches: 283, Mismatches: 8, Indels: 40
0.85 0.02 0.12
Matches are distributed among these distances:
26 8 0.03
28 15 0.05
30 1 0.00
35 9 0.03
36 10 0.04
37 142 0.50
38 5 0.02
39 93 0.33
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (38 bp):
TTTTGAAAATATATATATATATATAGTTTTTGAAAACA
Found at i:8022 original size:28 final size:27
Alignment explanation
Indices: 7944--8010 Score: 109
Period size: 26 Copynumber: 2.5 Consensus size: 27
7934 TTTGAAAACC
7944 TTTTGAAAACATGTATATAATATATAGT
1 TTTTGAAAACAT-TATATAATATATAGT
*
7972 TTTTGAAAATA-TATATAATATATAGT
1 TTTTGAAAACATTATATAATATATAGT
7998 TTTTGAAAACATT
1 TTTTGAAAACATT
8011 TTGAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 25 0.69
27 1 0.03
28 10 0.28
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (27 bp):
TTTTGAAAACATTATATAATATATAGT
Found at i:8258 original size:11 final size:11
Alignment explanation
Indices: 8240--8300 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
8230 ATTATATTGG
8240 TTTA-TTATTA
1 TTTATTTATTA
8250 TTTATTTATTA
1 TTTATTTATTA
8261 -TTATTTTATTA
1 TTTA-TTTATTA
*
8272 TTTA-TTATCTT
1 TTTATTTAT-TA
*
8283 TTTATTTTTTA
1 TTTATTTATTA
*
8294 TATATTT
1 TTTATTT
8301 TCTATTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
10 11 0.26
11 25 0.60
12 6 0.14
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:8259 original size:22 final size:23
Alignment explanation
Indices: 8192--8279 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 23
8182 TTGAAAATAT
* *
8192 TTATATTATATATTATAGTATAGTA
1 TTATATTAT-TATT-TATTATATTA
* *
8217 TTATATTA-TATATATTATATTGG
1 TTATATTATTATTTATTATATT-A
8240 TT-TATTATTATTTATT-TATTA
1 TTATATTATTATTTATTATATTA
*
8261 TTATTTTATTATTTATTAT
1 TTATATTATTATTTATTAT
8280 CTTTTTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
21 2 0.04
22 29 0.56
23 13 0.25
25 8 0.15
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (23 bp):
TTATATTATTATTTATTATATTA
Found at i:8262 original size:25 final size:25
Alignment explanation
Indices: 8198--8273 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
8188 ATATTTATAT
8198 TATATATTATAGTATAGTATTA-TATTA
1 TATATATTATA-T-TAGT-TTATTATTA
*
8225 TATATATTATATTGGTTTATTATTA
1 TATATATTATATTAGTTTATTATTA
* *
8250 TTTAT-TTATTATTATTTTATTATT
1 TATATATTA-TATTAGTTTATTATT
8274 TATTATCTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.14
25 25 0.58
26 1 0.02
27 11 0.26
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TATATATTATATTAGTTTATTATTA
Found at i:8306 original size:18 final size:17
Alignment explanation
Indices: 8247--8309 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
8237 TGGTTTATTA
8247 TTATTTATTTATTATTATT
1 TTATTT-TTTATTATT-TT
*
8266 TTATTATTTATTATCTTT
1 TTATTTTTTATTAT-TTT
8284 TTATTTTTTATATATTTT
1 TTATTTTTTAT-TATTTT
*
8302 CTATTTTT
1 TTATTTTT
8310 GTGTAATTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 30 0.77
19 9 0.23
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTATTTTTTATTATTTT
Found at i:20275 original size:11 final size:11
Alignment explanation
Indices: 20259--20283 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20249 CCTTAAATTG
20259 AAAAAAGAAAA
1 AAAAAAGAAAA
20270 AAAAAAGAAAA
1 AAAAAAGAAAA
20281 AAA
1 AAA
20284 TGTGGGTACA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:21868 original size:24 final size:25
Alignment explanation
Indices: 21825--21874 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
21815 TATAATATAT
*
21825 ATATATATATATATAATTTTTTAAA
1 ATATATATATATATAATTTTTGAAA
*
21850 ATATATA-ATATATAGTTTTTGAAA
1 ATATATATATATATAATTTTTGAAA
21874 A
1 A
21875 CATTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
ATATATATATATATAATTTTTGAAA
Found at i:21901 original size:39 final size:37
Alignment explanation
Indices: 21850--22191 Score: 453
Period size: 37 Copynumber: 9.4 Consensus size: 37
21840 ATTTTTTAAA
21850 ATATATAATATATAGTTTTTGAAAACATTTTGAAAACAT
1 ATATATAATATATAGTTTTTGAAAACATTTTG-AAA-AT
*
21889 GTATATAATATATAGTTTTTGAAAACA---TG-----
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAT
21918 -TATATAATATATAGTTTTTGAAAACATTTTGAAAAT
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAT
21954 ATATATAATATATAGTTTTTGAAAACATTTTTGAAAAT
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAT
*
21992 ATATATAATATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAT
22029 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAT
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAT
*
22066 ATATATAATATATAGTTTTTGAAAACTTTTTGAAAACCT
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAA--T
22105 ATATATAATATATAGTTTTTGAAAACACTTTT-AAAA-
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAT
* *
22141 ATATAT-AT-TATAGTTTCTTGAAAATA-TTT-AAATT
1 ATATATAATATATAGTTT-TTGAAAACATTTTGAAAAT
*
22175 ATATATTATAGTATAGT
1 ATATATAATA-TATAGT
22192 ATTATATTAT
Statistics
Matches: 278, Mismatches: 7, Indels: 38
0.86 0.02 0.12
Matches are distributed among these distances:
28 26 0.09
31 2 0.01
33 6 0.02
34 14 0.05
35 12 0.04
36 8 0.03
37 113 0.41
38 36 0.13
39 57 0.21
40 4 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAAAT
Found at i:21958 original size:28 final size:28
Alignment explanation
Indices: 21877--21944 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
21867 TTTGAAAACA
21877 TTTTGAAAACATGTATATAATATATAGT
1 TTTTGAAAACATGTATATAATATATAGT
21905 TTTTGAAAACATGTATATAATATATAGT
1 TTTTGAAAACATGTATATAATATATAGT
21933 TTTTGAAAACAT
1 TTTTGAAAACAT
21945 TTTGAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (28 bp):
TTTTGAAAACATGTATATAATATATAGT
Found at i:22002 original size:75 final size:75
Alignment explanation
Indices: 21904--22191 Score: 410
Period size: 75 Copynumber: 3.9 Consensus size: 75
21894 TAATATATAG
*
21904 TTTTTGAAAACATGTATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAG
1 TTTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAG
21969 TTTTTGAAAACA
64 TTTTTGAAAACA
*
21981 TTTTTGAAAATATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTT
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTT
22046 TTTGAAAACA
66 TTTGAAAACA
*
22056 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACTTTTTGAAAACCTATATATAATATATAG
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAA--TATATATAATATATAG
22120 TTTTTGAAAACA
64 TTTTTGAAAACA
* * * *
22132 CTTTT-AAAA-ATATAT-AT-TATAGTTTCTTGAAAATA-TTT-AAATTATATATTATAGTATAG
1 TTTTTGAAAATATATATAATATATAGTTT-TTGAAAACATTTTGAAAATATATATAATA-TATAG
22191 T
64 T
22192 ATTATATTAT
Statistics
Matches: 198, Mismatches: 8, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
70 10 0.05
71 6 0.03
72 3 0.02
73 11 0.06
74 53 0.27
75 70 0.35
76 35 0.18
77 10 0.05
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (75 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTT
TTTGAAAACA
Found at i:22022 original size:11 final size:11
Alignment explanation
Indices: 22008--22067 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
21998 AATATATAGT
22008 TTTTGAAAATA
1 TTTTGAAAATA
22019 TTTTGAAAATA
1 TTTTGAAAATA
*
22030 TATAT-AATATATA
1 T-TTTGAA-A-ATA
*
22043 GTTTTTGAAAACA
1 --TTTTGAAAATA
22056 TTTTGAAAATA
1 TTTTGAAAATA
22067 T
1 T
22068 ATATAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 25 0.64
12 3 0.08
13 5 0.13
14 3 0.08
15 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:22050 original size:112 final size:111
Alignment explanation
Indices: 21918--22191 Score: 416
Period size: 112 Copynumber: 2.5 Consensus size: 111
21908 TGAAAACATG
21918 TATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACATT
1 TATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAAC-TT
*
21983 TTTGAAAA-TATATATAATATATAGTTTTTGAAAATA-TTTTGAAAATA
65 TTTGAAAACTATATATAATATATAGTTTTTGAAAACACTTTT-AAAA-A
22030 TATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACTTT
1 TATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACTTT
22095 TTGAAAACCTATATATAATATATAGTTTTTGAAAACACTTTTAAAAA
66 TTGAAAA-CTATATATAATATATAGTTTTTGAAAACACTTTTAAAAA
* * *
22142 TATAT-AT-TATAGTTTCTTGAAAATA-TTT-AAATTATATATTATAGTATAGT
1 TATATAATATATAGTTT-TTGAAAACATTTTGAAAATATATATAATA-TATAGT
22192 ATTATATTAT
Statistics
Matches: 153, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
109 13 0.08
110 17 0.11
111 20 0.13
112 68 0.44
113 31 0.20
114 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (111 bp):
TATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACTTT
TTGAAAACTATATATAATATATAGTTTTTGAAAACACTTTTAAAAA
Found at i:22204 original size:10 final size:10
Alignment explanation
Indices: 22176--22268 Score: 59
Period size: 10 Copynumber: 8.8 Consensus size: 10
22166 ATTTAAATTA
22176 TATATTATAGT
1 TATATTATA-T
22187 ATAGTATTATAT
1 -TA-TATTATAT
22199 TATATTATA-
1 TATATTATAT
22208 TATATTATAT
1 TATATTATAT
*
22218 TGGT-TTACTAT
1 T-ATATTA-TAT
22229 T-TATTATTAT
1 TATATTA-TAT
22239 TATTTATTATTAT
1 TA--TATTA-TAT
*
22252 TATATTTTAT
1 TATATTATAT
22262 T-TATTAT
1 TATATTAT
22269 CTTTTTATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
9 15 0.22
10 22 0.32
11 11 0.16
12 3 0.04
13 18 0.26
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (10 bp):
TATATTATAT
Found at i:22244 original size:13 final size:13
Alignment explanation
Indices: 22226--22268 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
22216 ATTGGTTTAC
22226 TATTTATTATTAT
1 TATTTATTATTAT
22239 TATTTATTATTAT
1 TATTTATTATTAT
22252 TATATT-TTATTTAT
1 TAT-TTATTA-TTAT
22266 TAT
1 TAT
22269 CTTTTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTTATTATTAT
Found at i:22248 original size:16 final size:17
Alignment explanation
Indices: 22226--22268 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
22216 ATTGGTTTAC
22226 TATTTATTATTAT-TATT
1 TATTTATTATTATAT-TT
22243 TA-TTATTATTATATTT
1 TATTTATTATTATATTT
22259 TATTTATTAT
1 TATTTATTAT
22269 CTTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATTATTATATTT
Found at i:22261 original size:20 final size:20
Alignment explanation
Indices: 22191--22299 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 20
22181 TATAGTATAG
*
22191 TATTATATTATA-TTA-TAT
1 TATTATATTTTATTTATTAT
** *
22209 ATATTATA-TTGGTTTACTATT
1 -TATTATATTTTATTTATTA-T
*
22230 TATTAT-TATTATTTATTAT
1 TATTATATTTTATTTATTAT
22249 TATTATATTTTATTTATTAT
1 TATTATATTTTATTTATTAT
* *
22269 CT-TTTTATTTT-TTTAATTTT
1 -TATTATATTTTATTT-ATTAT
*
22289 TATTTTATTTT
1 TATTATATTTT
22300 TTGTGTAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
18 1 0.01
19 21 0.29
20 48 0.67
21 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTATATTTTATTTATTAT
Found at i:22268 original size:30 final size:30
Alignment explanation
Indices: 22228--22293 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
22218 TGGTTTACTA
22228 TTTA-TTATTAT-TATTTATTATTATT-ATAT
1 TTTATTTATTATCTATTTATT-TTATTAAT-T
* *
22257 TTTATTTATTATCTTTTTATTTTTTTAATT
1 TTTATTTATTATCTATTTATTTTATTAATT
22287 TTTATTT
1 TTTATTT
22294 TATTTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 4 0.12
30 19 0.59
31 9 0.28
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTATTTATTATCTATTTATTTTATTAATT
Found at i:26241 original size:41 final size:41
Alignment explanation
Indices: 26177--26263 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
26167 TAAGAATCCC
* **
26177 AAATTAGAGACAAGTGTCATGAGAAACTATCCACGAACGTA
1 AAATCAGAGACAAACGTCATGAGAAACTATCCACGAACGTA
*
26218 AAATCAGAGACAAACGTCGTGAGAAACTATCCACGAACGTA
1 AAATCAGAGACAAACGTCATGAGAAACTATCCACGAACGTA
26259 AAATC
1 AAATC
26264 GTGTATCCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (41 bp):
AAATCAGAGACAAACGTCATGAGAAACTATCCACGAACGTA
Found at i:27027 original size:26 final size:26
Alignment explanation
Indices: 26996--27082 Score: 174
Period size: 26 Copynumber: 3.3 Consensus size: 26
26986 CTATTGAAAA
26996 TGGAGTTTAAGCTTTCAAACCAAGAC
1 TGGAGTTTAAGCTTTCAAACCAAGAC
27022 TGGAGTTTAAGCTTTCAAACCAAGAC
1 TGGAGTTTAAGCTTTCAAACCAAGAC
27048 TGGAGTTTAAGCTTTCAAACCAAGAC
1 TGGAGTTTAAGCTTTCAAACCAAGAC
27074 TGGAGTTTA
1 TGGAGTTTA
27083 TCTAAAAAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (26 bp):
TGGAGTTTAAGCTTTCAAACCAAGAC
Found at i:30124 original size:18 final size:18
Alignment explanation
Indices: 30098--30137 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30088 CCTCCAATTG
* *
30098 TTCTTCTCCTTCAGATTC
1 TTCTGCTCCTTCAGATGC
*
30116 TTCTGCTCCTTCGGATGC
1 TTCTGCTCCTTCAGATGC
30134 TTCT
1 TTCT
30138 TCTTCTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.33, G:0.12, T:0.47
Consensus pattern (18 bp):
TTCTGCTCCTTCAGATGC
Found at i:30139 original size:21 final size:21
Alignment explanation
Indices: 30113--30157 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
30103 CTCCTTCAGA
30113 TTCTTCTGCTCCTTCGGATGC
1 TTCTTCTGCTCCTTCGGATGC
* *
30134 TTCTTCTTCTCTTTCGGATGC
1 TTCTTCTGCTCCTTCGGATGC
30155 TTC
1 TTC
30158 CTCCCCTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.31, G:0.16, T:0.49
Consensus pattern (21 bp):
TTCTTCTGCTCCTTCGGATGC
Found at i:32040 original size:22 final size:20
Alignment explanation
Indices: 32005--32053 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
31995 ATAATATAAC
*
32005 AAAATTTCTCAAAAACAACAA
1 AAAATGTCTC-AAAACAACAA
* *
32026 ATAAATGTCTTAAAAGAACAA
1 A-AAATGTCTCAAAACAACAA
32047 AAAATGT
1 AAAATGT
32054 ACTGAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 11 0.46
22 7 0.29
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.22
Consensus pattern (20 bp):
AAAATGTCTCAAAACAACAA
Found at i:32981 original size:22 final size:22
Alignment explanation
Indices: 32951--32992 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
32941 AAGAACTACC
32951 ATCTTTCATG-AATAACAAGAT
1 ATCTTTCATGTAATAACAAGAT
*
32972 ATCTCTTCATGTCATAACAAG
1 ATCT-TTCATGTAATAACAAG
32993 TTCACCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 6 0.33
23 8 0.44
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCTTTCATGTAATAACAAGAT
Found at i:36898 original size:21 final size:22
Alignment explanation
Indices: 36858--36901 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
36848 CGCTTTAATT
36858 TTTATTTTATATGTATTTGTAC
1 TTTATTTTATATGTATTTGTAC
36880 TTTATTTTATATG-ATTTGTAC
1 TTTATTTTATATGTATTTGTAC
36901 T
1 T
36902 AATGTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTATTTTATATGTATTTGTAC
Found at i:38882 original size:37 final size:37
Alignment explanation
Indices: 38828--38924 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
38818 CCTTTTCGTC
38828 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* * * *
38865 TTGA-TAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CT-ACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* *
38902 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
38925 GATAGGATCC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
36 1 0.02
37 48 0.96
38 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
Found at i:39679 original size:21 final size:23
Alignment explanation
Indices: 39652--39699 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39642 CCAATTATCA
39652 TTATATATACT-TTTATATTTGGT
1 TTATATAT-CTATTTATATTTGGT
* *
39675 TTATATATTTATTTATTTTTGGT
1 TTATATATCTATTTATATTTGGT
39698 TT
1 TT
39700 TGGTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.67
Consensus pattern (23 bp):
TTATATATCTATTTATATTTGGT
Found at i:39731 original size:18 final size:19
Alignment explanation
Indices: 39705--39740 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39695 GGTTTTGGTT
*
39705 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
39723 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
39741 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:39784 original size:2 final size:2
Alignment explanation
Indices: 39777--39803 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39767 TTTACTCATT
39777 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
39804 TAATATTTTA
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:39854 original size:12 final size:12
Alignment explanation
Indices: 39809--39858 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
39799 TATATTAATA
39809 TTTTATTTATTT
1 TTTTATTTATTT
*
39821 ATTTATTTATTT
1 TTTTATTTATTT
*
39833 TTCCT-TTTATTT
1 TT-TTATTTATTT
*
39845 TTTTACTTATTT
1 TTTTATTTATTT
39857 TT
1 TT
39859 ATTCTTCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 1 0.03
12 29 0.94
13 1 0.03
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:44458 original size:23 final size:24
Alignment explanation
Indices: 44413--44459 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
44403 TCCAATCAAG
*
44413 AACAAAAAATAAAAGAAGCAAAAA
1 AACAAAAAATAAAAGAAGAAAAAA
44437 AACAAAAAA-AAACA-AAGAAAAAA
1 AACAAAAAATAAA-AGAAGAAAAAA
44460 GAGAAACAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.83, C:0.09, G:0.06, T:0.02
Consensus pattern (24 bp):
AACAAAAAATAAAAGAAGAAAAAA
Found at i:44864 original size:175 final size:163
Alignment explanation
Indices: 44534--44864 Score: 484
Period size: 175 Copynumber: 2.0 Consensus size: 163
44524 ACAAATGGTG
*
44534 CATCAAGCTTCAAACTATGAGATTGATCAAGCATAATCATTCCTGAATCACTTCACTCGAAGATC
1 CATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCTGAATCACTTCACTCGAAGATC
* *
44599 ATAGAGCATCAAGAGAGAGAAACATTTTGAGCAGGATTGAAGACATCATAATGAATTGTTCATTG
66 ATAGAGCATCAAGAGAGAG-AACATTTTGAGCAGGATTGAAGACATCAGAATGAATTGATCATTG
44664 GTTCAACACCCTGAAACACTTGTTTGAAATGTCA
130 GTTCAACACCCTGAAACACTTGTTTGAAATGTCA
44698 CATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATCACTTCACT
1 CATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCA-T------TC-CTGAATCACTTCACT
*
44763 CGAAGATCATAGAGCATCAAGAGAGAG-ACATTTTGAGCAGGACATGATTGAAGGCATCAGAATG
58 CGAAGATCATAGAGCATCAAGAGAGAGAACATTTTGAGCA-G----GATTGAAGACATCAGAATG
*
44827 AATTGATCCTTGGTTCAACACCCTGAAACACTTGTTTG
118 AATTGATCATTGGTTCAACACCCTGAAACACTTGTTTG
44865 GGCCTATTTA
Statistics
Matches: 149, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
164 38 0.26
165 1 0.01
170 12 0.08
171 3 0.02
172 42 0.28
175 53 0.36
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (163 bp):
CATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCTGAATCACTTCACTCGAAGATC
ATAGAGCATCAAGAGAGAGAACATTTTGAGCAGGATTGAAGACATCAGAATGAATTGATCATTGG
TTCAACACCCTGAAACACTTGTTTGAAATGTCA
Found at i:45302 original size:21 final size:22
Alignment explanation
Indices: 45267--45330 Score: 112
Period size: 21 Copynumber: 3.0 Consensus size: 22
45257 ATCAAATCGT
45267 TGAGCATCAAATGCCAAACCTA
1 TGAGCATCAAATGCCAAACCTA
*
45289 TGAGCATC-AATGCCAAACCTT
1 TGAGCATCAAATGCCAAACCTA
45310 TGAGCATCAAATGCCAAACCT
1 TGAGCATCAAATGCCAAACCT
45331 TTGACCAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 20 0.50
22 20 0.50
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (22 bp):
TGAGCATCAAATGCCAAACCTA
Found at i:45331 original size:22 final size:22
Alignment explanation
Indices: 45266--45334 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
45256 CATCAAATCG
45266 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
*
45288 ATGAGCATC-AATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
45309 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
45331 TTGA
1 TTGA
45335 CCAAACATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.45
22 24 0.55
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.23
Consensus pattern (22 bp):
TTGAGCATCAAATGCCAAACCT
Found at i:46270 original size:106 final size:106
Alignment explanation
Indices: 46113--47806 Score: 2490
Period size: 106 Copynumber: 16.0 Consensus size: 106
46103 ATATCGTGCC
* * * * * *
46113 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACCGCTAGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
46178 AATTTCAGATCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
46219 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
46284 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGCTATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
46325 ACTCCAGGCAATGCAAGTTCAAATTAACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
46390 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
46431 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
46496 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
46537 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
46602 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
46643 ACTCTAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
46708 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
46749 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
46814 AATTTCAGAGCCAATTTCGACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
46855 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
46920 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
46961 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
47026 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
47067 ACTCCAGACAATGCAAGTTCAACTTCACG-CTGAAGGTATCGCTAGTTGTCAACAAATAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGAC-GAAGGGACCGCTGGTTGTCAACAAACAACTTCC
*
47131 CAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
47173 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
47238 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
47279 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
47344 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
47385 ACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCACTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
47450 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
47491 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
47556 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
47597 AC-CCAAGACAACACAAGCTCAACTTCACGACGAAGGG-GCGACTGATTGTCAAC-AA-AA-TT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTC
* * *
47656 TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGAATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
47697 ACTCGAGACAACACAAGTTCAACTTTACAATGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * * *
47762 GGTTCCAAAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
47803 ACTC
1 ACTC
47807 AGAACAATGC
Statistics
Matches: 1436, Mismatches: 139, Indels: 26
0.90 0.09 0.02
Matches are distributed among these distances:
100 75 0.05
101 5 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 7 0.00
106 1338 0.93
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:48587 original size:37 final size:37
Alignment explanation
Indices: 48534--48638 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
48524 CATTTTCGTC
48534 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
48571 TTGCTAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
48608 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
48639 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:49179 original size:22 final size:22
Alignment explanation
Indices: 49154--49208 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
49144 ATTCATTTGG
*
49154 TTATTTTTTAATACTATATTTA-
1 TTATTTTTTAATA-TATATATAC
*
49176 TTATTTTATATATATATATATAC
1 TTATTTTTTA-ATATATATATAC
49199 TT-TTTTTTAA
1 TTATTTTTTAA
49209 AAATATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 22 0.79
23 5 0.18
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTTTTTAATATATATATAC
Found at i:49411 original size:5 final size:5
Alignment explanation
Indices: 49403--49440 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
49393 TTTGGTTTTT
49403 TTATA TTATA TTATA TTATA TT-T- TTATA TTACTA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA TTAT
49441 TATTGTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 21 0.70
6 5 0.17
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:49431 original size:18 final size:19
Alignment explanation
Indices: 49408--49455 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
49398 TTTTTTTATA
*
49408 TTATATTATATTA-TATTT
1 TTATATTATATTATTATTG
49426 TTATATTACTATTATTATTG
1 TTATATTA-TATTATTATTG
49446 TTATGATTAT
1 TTAT-ATTAT
49456 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 5 0.19
20 9 0.35
21 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TTATATTATATTATTATTG
Found at i:49531 original size:16 final size:16
Alignment explanation
Indices: 49512--49553 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
49502 CATTTATTTA
*
49512 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
*
49528 TTTATTTTTTTTTACT
1 TTTATTTATTTTTACT
49544 TATT-TTTATT
1 T-TTATTTATT
49554 CTTCATTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:51531 original size:16 final size:19
Alignment explanation
Indices: 51510--51551 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
51500 AACATTCCTA
51510 GTAATC-CTATT-CC-CTG
1 GTAATCTCTATTCCCACTG
*
51526 GTAATCTTTATTCCCACTG
1 GTAATCTCTATTCCCACTG
51545 GTAATCT
1 GTAATCT
51552 TACATTCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 2 0.09
19 10 0.45
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (19 bp):
GTAATCTCTATTCCCACTG
Done.