Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001886.1 Hibiscus syriacus cultivar Beakdansim tig00003829_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: 76638
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:179 original size:3 final size:3
Alignment explanation
Indices: 171--239 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
161 TTTGTATATC
* * * *
171 AAT AAT AAT AAT AAA AAT AAT AGT AGT AAT AAT TAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
219 AATT AA- AAT AAAT AAT AAT AA
1 AA-T AAT AAT -AAT AAT AAT AA
240 AAAAGACTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 49 0.86
4 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:642 original size:134 final size:133
Alignment explanation
Indices: 400--744 Score: 447
Period size: 134 Copynumber: 2.6 Consensus size: 133
390 ACACTGCTCA
* ** * * * * ** *
400 TACGTGATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGATCTTACATGATAAGGATATCTGATC
1 TACGTGATGAGGAGG-CTGGTTATCTAGGGGTGACACGGCTCATACATGATGAGGAGGTCTGGTC
* *
465 GGGGATGACACTACACATACGTGATAAAGAGTTTTTGGCCATCTTTAGGAAGGGTGATAACACGG
65 GGGGATGACACTACACATACATGATAAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACACGG
530 TTCC
130 TTCC
* *
534 TACGTGATGAGGACGGCTGGTTATCTAGGGGTGACACGGCTCCTACATGATGAGGAGGTATGGTC
1 TACGTGATGAGGA-GGCTGGTTATCTAGGGGTGACACGGCTCATACATGATGAGGAGGTCTGGTC
* * * *
599 GGGGATGACACTGCTCATACATGATGAAGAGTTCTTGGTCATCTTTAGGAAGGGTGATAACACGG
65 GGGGATGACACTACACATACATGATAAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACACGG
664 TTCC
130 TTCC
* * * *
668 TACGCGATGAGGATGGCTGGTTATCTAGGGATGACACGGCTCATACGTGATGAAGAGGTCTGGTC
1 TACGTGATGAGGA-GGCTGGTTATCTAGGGGTGACACGGCTCATACATGATGAGGAGGTCTGGTC
*
733 AGTGGATGACAC
65 -GGGGATGACAC
745 GGTTCTTATG
Statistics
Matches: 184, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
134 172 0.93
135 12 0.07
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (133 bp):
TACGTGATGAGGAGGCTGGTTATCTAGGGGTGACACGGCTCATACATGATGAGGAGGTCTGGTCG
GGGATGACACTACACATACATGATAAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACACGGT
TCC
Found at i:720 original size:43 final size:40
Alignment explanation
Indices: 658--770 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
648 AAGGGTGATA
* *
658 ACACGGTTCCTACGCGATGAGGATGGCTGGTTATCTAG-GGATG
1 ACACGGTTCATACGTGATGAGGATGGCTGG---TC-AGTGGATG
* *
701 ACACGGCTCATACGTGATGAAGA-GGTCTGGTCAGTGGATG
1 ACACGGTTCATACGTGATGAGGATGG-CTGGTCAGTGGATG
* *
741 ACACGGTTCTTATGTGATGAGGATGGCTGG
1 ACACGGTTCATACGTGATGAGGATGGCTGG
771 CCATTTTTAG
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
39 2 0.03
40 30 0.51
41 2 0.03
42 2 0.03
43 23 0.39
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (40 bp):
ACACGGTTCATACGTGATGAGGATGGCTGGTCAGTGGATG
Found at i:926 original size:63 final size:65
Alignment explanation
Indices: 850--973 Score: 155
Period size: 63 Copynumber: 1.9 Consensus size: 65
840 GATAATGTGT
**
850 TTTAAAATCAACTGTCTCGAA-AGAGACAAAATTAG-TTTAAAGAGAAACG-ACTCAAAGATGAC
1 TTTAAAAGAAACTGTCTC-AAGAGAGACAAAATTAGTTTTAAAGAGAAACGTACTCAAAGATGAC
912 G
65 G
* * * * *
913 TTTAAAAGAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGAT
1 TTTAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTTAAAGAGAAACGTACTCAAAGAT
974 CGGTGTTTCG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 28 0.55
64 12 0.24
65 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.26
Consensus pattern (65 bp):
TTTAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTTAAAGAGAAACGTACTCAAAGATGACG
Found at i:1024 original size:32 final size:34
Alignment explanation
Indices: 977--1074 Score: 110
Period size: 38 Copynumber: 2.8 Consensus size: 34
967 CAAAGATCGG
*
977 TGTTTCGAGAGAAACAAACTCAAAGATG-T-TTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTGTTT
* *
1009 TGTTTCAAGAAAAACATACTCAAAGATTTTGTTTGTTT
1 TGTTTCAAGAGAAACAAACTCAAAGA---TG-TTGTTT
*
1047 TGTTTCAAGGGAAACAAACTCAAAGATG
1 TGTTTCAAGAGAAACAAACTCAAAGATG
1075 GTAAATTTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
32 23 0.43
35 4 0.07
37 1 0.02
38 26 0.48
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTGTTT
Found at i:1223 original size:39 final size:39
Alignment explanation
Indices: 1145--1223 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
1135 AAGAGATAAA
* * *
1145 ATTTTGTTATCAAAGAAACATACTCAAAGATTTTTTTTC
1 ATTTTGTTATCAAAGAAACAAACTCAAAGACTTTGTTTC
* **
1184 ATTTTGTT-TCAAGTGAAACAAACTCAAATCCTTTGTTTC
1 ATTTTGTTATCAA-AGAAACAAACTCAAAGACTTTGTTTC
1223 A
1 A
1224 AAAGAAATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 4 0.12
39 29 0.88
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (39 bp):
ATTTTGTTATCAAAGAAACAAACTCAAAGACTTTGTTTC
Found at i:1320 original size:36 final size:36
Alignment explanation
Indices: 1280--1417 Score: 140
Period size: 36 Copynumber: 3.8 Consensus size: 36
1270 ATAATTTGGA
*
1280 AAATTATCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTATCTCAAGCGAGACAACATTTGTTTTTAGAG
* * *
1316 AAATTATCTCTAA-CAAGACAAAAATTGTTTTTAGAG
1 AAATTATCTC-AAGCGAGACAACATTTGTTTTTAGAG
*
1352 AAATTGTCTCAAGCGAGACAA-AGTTTGTTTTT-GAG
1 AAATTATCTCAAGCGAGACAACA-TTTGTTTTTAGAG
** *
1387 AAAAAGATCTCAAGTGAGATCAAC-TTTGTTT
1 -AAATTATCTCAAGCGAGA-CAACATTTGTTT
1418 AATGTGAAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
35 6 0.07
36 74 0.87
37 5 0.06
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (36 bp):
AAATTATCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:1757 original size:154 final size:155
Alignment explanation
Indices: 1516--1839 Score: 383
Period size: 154 Copynumber: 2.1 Consensus size: 155
1506 AAGTGAGATT
* *
1516 AATTTTTTTATCAAGTAAATCAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCCAGCAAG
1 AATTTTGTT-TCAAGTAAATCAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAGCAAG
* * * *
1581 ACGAAGTTTGTTTTAAGAAAATTGTCTTAAATAAGACAAAATTTATTTTAAAATTCTCAAAATTT
65 ACGAAATTTGTTTGAAGAAAATTGTCTCAAACAAGACAAAATTTATTTTAAAATTCTCAAAATTT
* *
1646 ATGG-GAACTATCTCAAGCGAGA-AA
130 ATGGAAAAATATCTCAAGCGAGACAA
* * * *
1670 GAATTTTGTTTCAAGTACAA-CAAATT-TAAATTTGTATCTTAGA-GAAATAAATGTCTCAAG-A
1 -AATTTTGTTTCAAGTA-AATCAAATTCGAAATTTGTATATCAAAGGAAA-AAATGTCTCAAGCA
* * *
1731 GAGACGAAATTTGCTTTGATAG-AAATTGTCTCAAGCGAGACAAAATTTGTTTTAAAATTCTCAA
63 -AGACGAAATTTG-TTTGA-AGAAAATTGTCTCAAACAAGACAAAATTTATTTTAAAATTCTCAA
* *
1795 AATTTTTGGAAAAATGTCTCAAGCGAGACAA
125 AATTTATGGAAAAATATCTCAAGCGAGACAA
1826 AATTTTGTTTCAAG
1 AATTTTGTTTCAAG
1840 AAAGAAAAAA
Statistics
Matches: 145, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
152 5 0.03
153 35 0.24
154 62 0.43
155 41 0.28
156 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (155 bp):
AATTTTGTTTCAAGTAAATCAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAGCAAGA
CGAAATTTGTTTGAAGAAAATTGTCTCAAACAAGACAAAATTTATTTTAAAATTCTCAAAATTTA
TGGAAAAATATCTCAAGCGAGACAA
Found at i:2135 original size:8 final size:8
Alignment explanation
Indices: 2122--2231 Score: 130
Period size: 8 Copynumber: 13.8 Consensus size: 8
2112 TAAATGTTTA
2122 ATGCATGT
1 ATGCATGT
2130 ATGCATGT
1 ATGCATGT
* *
2138 ACGCATGC
1 ATGCATGT
2146 ATGCATGT
1 ATGCATGT
2154 ATGCATGT
1 ATGCATGT
*
2162 ACGCATGT
1 ATGCATGT
* *
2170 ACGCATAT
1 ATGCATGT
2178 ATGCATGT
1 ATGCATGT
* *
2186 ACGTATGT
1 ATGCATGT
2194 ATGCATGT
1 ATGCATGT
*
2202 ATGCATGC
1 ATGCATGT
*
2210 ATGGATGT
1 ATGCATGT
*
2218 ATACATGT
1 ATGCATGT
2226 ATGCAT
1 ATGCAT
2232 ATATATATAT
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 84 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (8 bp):
ATGCATGT
Found at i:2154 original size:24 final size:24
Alignment explanation
Indices: 2122--2231 Score: 148
Period size: 24 Copynumber: 4.6 Consensus size: 24
2112 TAAATGTTTA
*
2122 ATGCATGTATGCATGTACGCATGC
1 ATGCATGTATGCATGTACGCATGT
2146 ATGCATGTATGCATGTACGCATGT
1 ATGCATGTATGCATGTACGCATGT
* * *
2170 ACGCATATATGCATGTACGTATGT
1 ATGCATGTATGCATGTACGCATGT
* * *
2194 ATGCATGTATGCATGCATGGATGT
1 ATGCATGTATGCATGTACGCATGT
*
2218 ATACATGTATGCAT
1 ATGCATGTATGCAT
2232 ATATATATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (24 bp):
ATGCATGTATGCATGTACGCATGT
Found at i:2250 original size:2 final size:2
Alignment explanation
Indices: 2245--2301 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2235 TATATATGTA
2245 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2287 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
2302 ATTCTCGATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:3832 original size:16 final size:16
Alignment explanation
Indices: 3811--3856 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3801 CTCTTTATCA
3811 TCTTTTTGTTCTTTTC
1 TCTTTTTGTTCTTTTC
* *
3827 TCTTTTCT-TTGTTTTG
1 TCTTTT-TGTTCTTTTC
3843 TCTTTTTG-TCTTTT
1 TCTTTTTGTTCTTTT
3857 TTTTTGCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.24
16 18 0.72
17 1 0.04
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TCTTTTTGTTCTTTTC
Found at i:3839 original size:19 final size:18
Alignment explanation
Indices: 3815--3869 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
3805 TTATCATCTT
3815 TTTGTTCTTTTCTCTTTTC
1 TTTGTT-TTTTCTCTTTTC
* *
3834 TTTGTTTTGTCTTTTTGTC
1 TTTGTTTTTTCTCTTT-TC
3853 TTT-TTTTTTGCTCTTTT
1 TTTGTTTTTT-CTCTTTT
3870 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (18 bp):
TTTGTTTTTTCTCTTTTC
Found at i:3862 original size:12 final size:13
Alignment explanation
Indices: 3845--3874 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3835 TTGTTTTGTC
3845 TTTTTG-TCTTTT
1 TTTTTGCTCTTTT
3857 TTTTTGCTCTTTT
1 TTTTTGCTCTTTT
3870 TTTTT
1 TTTTT
3875 ATTTTGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTTGCTCTTTT
Found at i:8668 original size:11 final size:11
Alignment explanation
Indices: 8639--8671 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
8629 ATAAATAAAG
*
8639 AAATACAATAT
1 AAATAAAATAT
8650 AAAT-AAATAT
1 AAATAAAATAT
8660 AAATAAAATAT
1 AAATAAAATAT
8671 A
1 A
8672 TGAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:10285 original size:4 final size:4
Alignment explanation
Indices: 10276--10974 Score: 1034
Period size: 4 Copynumber: 180.8 Consensus size: 4
10266 AATAAAAATA
*
10276 TATG TATG TATG TATG TATG TATA TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10324 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
10372 TATG TATG TATG TATG TATG TATA TATG TATG TATA TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
10420 TATG TATG TA-- TATG TATG TATA TATG TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
10466 TATG TATTA TATG TATA TATG TATA TATG TATG TATG TATG TAGG TATG
1 TATG TA-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10515 TATG TATG TATG TATG TATG TA-- TATG TA-G TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
10560 TA-- TATG TATG -ATG TATA TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10603 TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10649 TATG -ATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10694 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10740 TATG TATG TATG TAT- TATG TATG TATG TATG TA-G TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10786 TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10833 TATG TATG --TG TATG TATG TATG TATG TATG TATG TA-G TA-G TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
10877 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA TATA TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
10925 TATA TAT- TATA TATG TATA TATA CATG TATG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10972 TAT
1 TAT
10975 TCTCGATCTG
Statistics
Matches: 640, Mismatches: 30, Indels: 50
0.89 0.04 0.07
Matches are distributed among these distances:
2 16 0.03
3 27 0.04
4 594 0.93
5 3 0.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:10920 original size:2 final size:2
Alignment explanation
Indices: 10913--10962 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
10903 TGTATGTATG
* * *
10913 TA TA TA TA TA TA TA TA TA T- TA TA TA TG TA TA TA TA CA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
10954 TG TA TA TA T
1 TA TA TA TA T
10963 GTATGTATGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12132 original size:5 final size:5
Alignment explanation
Indices: 12122--12146 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12112 TATTAATCAT
12122 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
12147 TTGAATCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:14078 original size:52 final size:52
Alignment explanation
Indices: 13996--14119 Score: 178
Period size: 52 Copynumber: 2.4 Consensus size: 52
13986 TCGTTGGATG
13996 AGTTCTTCTCATTATGAACTCGCCACTGGAAAT-CTTGAACCAAGGTTGAACA
1 AGTTCTTCTCATTATGAACTCGCCACTGGAAATGC-TGAACCAAGGTTGAACA
* *** * *
14048 AGTTCTTCTCATTATGAACTCTCTGTTGGAAATGCTGAGCTAAGGTTGAACA
1 AGTTCTTCTCATTATGAACTCGCCACTGGAAATGCTGAACCAAGGTTGAACA
14100 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
14120 TCTTCTCCCT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 64 0.98
53 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (52 bp):
AGTTCTTCTCATTATGAACTCGCCACTGGAAATGCTGAACCAAGGTTGAACA
Found at i:14113 original size:143 final size:143
Alignment explanation
Indices: 13931--14210 Score: 470
Period size: 143 Copynumber: 2.0 Consensus size: 143
13921 GTCTTTCCAC
* *
13931 TGGAAATGATGATCTAAGGTTGAAGAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATG
1 TGGAAATGATGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATG
* *
13996 AGTTCTTCTCATTATGAACTCGCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATT
66 AGTTCTTCTCATTATGAACTCGCCACTGGAAATCTTGAACCAAGGCTAAACAAGTTCTTCTCATT
14061 ATGAACTCTCTGT
131 ATGAACTCTCTGT
* * **
14074 TGGAAATGCTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGATG
1 TGGAAATGATGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATG
* *
14139 AGTTCTTCTCATTATGAACTCTCCATTGGAAATCTTGAACCAAGGCTAAACAAGTTCTTCTCATT
66 AGTTCTTCTCATTATGAACTCGCCACTGGAAATCTTGAACCAAGGCTAAACAAGTTCTTCTCATT
14204 ATGAACT
131 ATGAACT
14211 TCTTTTCCCT
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
143 127 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (143 bp):
TGGAAATGATGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATG
AGTTCTTCTCATTATGAACTCGCCACTGGAAATCTTGAACCAAGGCTAAACAAGTTCTTCTCATT
ATGAACTCTCTGT
Found at i:14151 original size:91 final size:91
Alignment explanation
Indices: 14048--14254 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
14038 AGGTTGAACA
** * * * *
14048 AGTTCTTCTCATTATGAACTCTCTGTTGGAAATGC-TGAGCTAAGGTTGAACAAGTTCTTCTCAT
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAAT-CTTGAACCAAGGCTAAACAAGTTCTTCTCAT
** *
14112 TATGAACTTCTTCTCCCTTTTTGGATG
65 TATGAACTTCTTCTCCCTCGTTGGACG
14139 AGTTCTTCTCATTATGAACTCTCCATTGGAAATCTTGAACCAAGGCTAAACAAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATCTTGAACCAAGGCTAAACAAGTTCTTCTCATT
*
14204 ATGAACTTCTTTTCCCTCGTTGGACG
66 ATGAACTTCTTCTCCCTCGTTGGACG
14230 AGTTCTTCTCATTATGAACTCTCCA
1 AGTTCTTCTCATTATGAACTCTCCA
14255 CTGGCAATGT
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
90 1 0.01
91 104 0.99
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (91 bp):
AGTTCTTCTCATTATGAACTCTCCATTGGAAATCTTGAACCAAGGCTAAACAAGTTCTTCTCATT
ATGAACTTCTTCTCCCTCGTTGGACG
Found at i:14605 original size:30 final size:30
Alignment explanation
Indices: 14569--14739 Score: 119
Period size: 30 Copynumber: 5.5 Consensus size: 30
14559 TAAAATTTCT
*
14569 TGTTTCAAGGGAAACAATCTCAAAGGTTAG
1 TGTTTCAAGAGAAACAATCTCAAAGGTTAG
**
14599 TGTTTCAAGAGAAACTGTCTCAAAGGTTAG
1 TGTTTCAAGAGAAACAATCTCAAAGGTTAG
* ** * *
14629 TGTTTCAAGATAAACTGTCTCAAGAGAGATAAAACA
1 TGTTTCAAGAGAAACAATCTCAA-AG-G-T--TA-G
* * *
14665 TGTTTCAAGGGAAACAATCTCAAAGATTTTG
1 TGTTTCAAGAGAAACAATCTCAAAG-GTTAG
* * * * **
14696 TGTCTCAAGGGAAACATTTTCAAAATTTA-
1 TGTTTCAAGAGAAACAATCTCAAAGGTTAG
14725 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
14740 TGTCTCAAGG
Statistics
Matches: 114, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
29 13 0.11
30 52 0.46
31 23 0.20
32 1 0.01
33 1 0.01
34 1 0.01
35 4 0.04
36 19 0.17
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTAG
Found at i:14719 original size:31 final size:29
Alignment explanation
Indices: 14664--14739 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 29
14654 GAGATAAAAC
14664 ATGTTTCAAGGGAAACAATCTCAAAGATTT
1 ATGTTTCAAGGGAAACAATCTCAAA-ATTT
* *
14694 -TGTGTCTCAAGGGAAACATTTTCAAAATTT
1 ATGT-T-TCAAGGGAAACAATCTCAAAATTT
*
14724 ATGTTTCAAGAGAAAC
1 ATGTTTCAAGGGAAAC
14740 TGTCTCAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 13 0.32
30 6 0.15
31 21 0.52
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (29 bp):
ATGTTTCAAGGGAAACAATCTCAAAATTT
Found at i:14729 original size:96 final size:97
Alignment explanation
Indices: 14569--14775 Score: 267
Period size: 96 Copynumber: 2.1 Consensus size: 97
14559 TAAAATTTCT
* *
14569 TGTTTCAAGGGAAACAATCTCAAAGGTTAGTGTTTCAAGAGAAACTGTCTCAAAGGTTAGTGTTT
1 TGTTTCAAGGGAAACAATCTCAAAGGTTAGTGTCTCAAGAGAAACTGTCTCAAAAGTTAGTGTTT
* *
14634 CAAGATAAACTGTCTCAAGAGAGATAAAA-CA
66 CAAGAGAAACTGTCTCAAGAGAGACAAAATCA
* * * * *
14665 TGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTCTCAAGGGAAACAT-TTTCAAAATTTA-TGT
1 TGTTTCAAGGGAAACAATCTCAAAG-GTTAGTGTCTCAAGAGAAAC-TGTCTCAAAAGTTAGTGT
* **
14728 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
64 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATCA
14762 TGTTTCAAGGGAAA
1 TGTTTCAAGGGAAA
14776 TTGTCTCAGA
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
96 56 0.58
97 39 0.41
98 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (97 bp):
TGTTTCAAGGGAAACAATCTCAAAGGTTAGTGTCTCAAGAGAAACTGTCTCAAAAGTTAGTGTTT
CAAGAGAAACTGTCTCAAGAGAGACAAAATCA
Found at i:14881 original size:66 final size:65
Alignment explanation
Indices: 14725--14974 Score: 229
Period size: 65 Copynumber: 3.7 Consensus size: 65
14715 TCAAAATTTA
*
14725 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA-GGGAAATTGTCTCAGAAAC
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGGAAAGTGTCTCAGAAAC
14789 T
65 T
* * ** * *
14790 TGTTTCAAGAGAATCTGTCTCAAGGGAAACAAAATTCATTTCAAGGGGAACGT-TCTCA-AAGTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGGAAAGTGTCTCAGAA--A
*
14853 TT
64 CT
* * *
14855 GTGTTTCAAGAGAAACTATCTCAAGGGAGATAAAATTTGTTTCAA-GGGAAACTGTCTCAAGAGA
1 -TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGGAAAGTGTCTC-----A
*
14919 GGCAAAATT
60 -G--AAACT
* * *
14928 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG
14975 AAACTATCTC
Statistics
Matches: 148, Mismatches: 22, Indels: 22
0.77 0.11 0.11
Matches are distributed among these distances:
63 2 0.01
64 13 0.09
65 45 0.30
66 42 0.28
71 1 0.01
72 39 0.26
73 4 0.03
75 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGGAAAGTGTCTCAGAAACT
Found at i:15200 original size:39 final size:38
Alignment explanation
Indices: 14856--15196 Score: 415
Period size: 39 Copynumber: 9.0 Consensus size: 38
14846 CAAAGTTTTG
* *
14856 TGTTTCAAGAGAAACTATCTCAAGGGAGATAAAA--TT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
* * **
14892 TGTTTCAAGGGAAACTGTCTCAAGAGAGGCAAAA--TT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
* * *
14928 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
*
14964 TATTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
* * *
15002 TGTTTCGAGGAAAACTATCTCAAGCGAGGTAAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGAT-AAAATC-TT
* * *
15042 TGTTTCGAGGAAAACTACCTCAAGCGAGATAAAATCTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
* *
15080 CTGTTTAAAGGGAAACTACCTCAAGCGAGATAAAATCTTT
1 -TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC-TT
*
15120 TGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
*
15158 CTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTT
1 -TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
15197 CTGTAAAAAC
Statistics
Matches: 276, Mismatches: 22, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
36 96 0.35
38 32 0.12
39 116 0.42
40 32 0.12
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (38 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
Found at i:15288 original size:76 final size:76
Alignment explanation
Indices: 15170--15355 Score: 222
Period size: 76 Copynumber: 2.5 Consensus size: 76
15160 GTTTCAAGGG
* *
15170 AAACTATCTCAAGCGAGACAAA--ATCTTCT--GTAAAAACAATCTTGAGTAAAATGAAAT-GTC
1 AAACTATCTCAAGCGAGACAAATTATGTTTTAAG-AAAAACAATCTTGAGTAAAAT-AAATCGTC
15230 TTCTTTCGAGTAA
64 TTCTTTCGAGTAA
* * * * *
15243 AAATTGTCTCAAGCGAGATAAATCT-TGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCT
1 AAACTATCTCAAGCGAGACAAAT-TATGTTTTAAGAAAAACAATCTTGAGTAAAATAAATCGTCT
*
15307 TGTTTCGAGTAA
65 TCTTTCGAGTAA
*
15319 AAACTATCTCAAGTGAGACAAATTATGTTTTAAGAAA
1 AAACTATCTCAAGCGAGACAAATTATGTTTTAAGAAA
15356 GATAAATCCT
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
73 19 0.20
75 9 0.10
76 65 0.69
77 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (76 bp):
AAACTATCTCAAGCGAGACAAATTATGTTTTAAGAAAAACAATCTTGAGTAAAATAAATCGTCTT
CTTTCGAGTAA
Found at i:27664 original size:2 final size:2
Alignment explanation
Indices: 27657--27699 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
27647 TATTTTAGTC
* *
27657 AT AT AT AT AT AT AT AGC AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
27700 TTAAAAGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 35 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30734 original size:3 final size:3
Alignment explanation
Indices: 30728--30797 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
30718 TTTACTCATT
* *
30728 TTA TTA TTA TTA TTA CTA ATA TTA TTA TTA TTAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
*
30774 TAA TTA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA
30798 AAAAAATTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.03
3 51 0.86
4 6 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:30787 original size:37 final size:37
Alignment explanation
Indices: 30728--30798 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
30718 TTTACTCATT
*
30728 TTATTATTATTATTACTAATATTATTATTATTAATTA
1 TTATTATTATAATTACTAATATTATTATTATTAATTA
30765 TTATTATTATAATTA-TATATATTATTATTATTAA
1 TTATTATTATAATTACTA-ATATTATTATTATTAA
30799 AAAAATTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 2 0.06
37 30 0.94
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (37 bp):
TTATTATTATAATTACTAATATTATTATTATTAATTA
Found at i:32384 original size:26 final size:26
Alignment explanation
Indices: 32355--32407 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
32345 TATATTTTAA
32355 ATAAATAAATATTTATTTATAAATAT
1 ATAAATAAATATTTATTTATAAATAT
* * *
32381 ATAAATTAATATTTTTTTATAATTAT
1 ATAAATAAATATTTATTTATAAATAT
32407 A
1 A
32408 ATTTCGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATAAATAAATATTTATTTATAAATAT
Found at i:32393 original size:22 final size:21
Alignment explanation
Indices: 32344--32395 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
32334 GTCCTTTCTG
32344 ATATATTTTAAATAAATAAAT
1 ATATATTTTAAATAAATAAAT
* *
32365 ATTTATTTATAAATATATAAAT
1 ATATATTT-TAAATAAATAAAT
32387 -TAATATTTT
1 AT-ATATTTT
32396 TTTATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATTTTAAATAAATAAAT
Found at i:39822 original size:9 final size:9
Alignment explanation
Indices: 39808--39866 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
39798 ATGCTTGAAT
39808 AAAAAGAAA
1 AAAAAGAAA
39817 AAAAAGAAA
1 AAAAAGAAA
*
39826 AAAAAG-GA
1 AAAAAGAAA
*
39834 AGAAAGAAA
1 AAAAAGAAA
39843 AGAAAAGAAAA
1 A-AAAAG-AAA
39854 AAGAAAGAAA
1 AA-AAAGAAA
39864 AAA
1 AAA
39867 GGGGGTCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 6 0.14
9 18 0.43
10 10 0.24
11 8 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:39839 original size:17 final size:16
Alignment explanation
Indices: 39816--39865 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 16
39806 ATAAAAAGAA
39816 AAAAAAGAAAAAAAAGG
1 AAAAAAGAAAAAAAA-G
*
39833 AAGAAAGAAAAGAAAAG
1 AAAAAAGAAAA-AAAAG
39850 AAAAAAGAAAGAAAAA
1 AAAAAAGAAA-AAAAA
39866 AGGGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 24 0.83
18 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:41401 original size:93 final size:93
Alignment explanation
Indices: 41240--41624 Score: 578
Period size: 93 Copynumber: 4.1 Consensus size: 93
41230 AACAAGTGCC
* * *
41240 ATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTTATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* *
41305 AAACCCCATCATTGGACTTGAAAGATGA
66 AAACCCAATCATTAGACTTGAAAGATGA
* *
41333 GTGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACC-CT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC-
*
41397 AAAACCCCATCATTAGACTTGAAAGATGA
65 AAAACCCAATCATTAGACTTGAAAGATGA
*
41426 GTGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
* *
41491 AAACCCAATCATTAGATTTAGAAATATGA
66 AAACCCAATCATTAGACTT-GAAAGATGA
*
41520 ATGCGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCAC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG-AACCAC
* *
41585 AGAA-CCAATCATT-GAATTTGAAAGATGA
65 AAAACCCAATCATTAG-ACTTGAAAGATGA
*
41613 ATGTGATCATAG
1 ATGTGCTCATAG
41625 TAGAAATAAG
Statistics
Matches: 272, Mismatches: 15, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
92 1 0.00
93 184 0.68
94 78 0.29
95 9 0.03
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (93 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
AAACCCAATCATTAGACTTGAAAGATGA
Found at i:42826 original size:228 final size:229
Alignment explanation
Indices: 42411--43196 Score: 1066
Period size: 228 Copynumber: 3.5 Consensus size: 229
42401 TAGCAAAGAT
*
42411 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
42476 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
*
42541 TGGATTAACATTG-AAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAA
131 TGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAA
*
42605 ATTCATAATGAGAAGAATTTATTCAACCTTTCGC
196 ATTCATAATGAGAAGAATTTATTCAACCTTTTGC
42639 TCAAATCCATCATTTGA-AGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
42703 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATAATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
42768 TGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAA
131 TGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAA
*
42833 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
196 ATTCATAATGAGAAGAATTTATTCAACCTTTTGC
* * * ****
42867 TCAAATCCATCACTTGATGGATCAGCTTTTCAAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * * *
42932 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
* *** *
42997 TGGATCAGTTTTTCCA-G-AGAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA-GAA-AATG
131 TGGATTAACATTGCCAGGTAG-AGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAA-G
* ** *
43055 ---TTCACAATGAGAAGAGCTTATTCAACATTTTTGC
194 AAATTCATAATGAGAAGAATTTATTCAAC-CTTTTGC
* ** * * * * *
43089 AT-AATTTTATCA---CA-ACATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 -TCAAATCCATCATTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * ** *
43149 AAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
43197 AATGACTCTA
Statistics
Matches: 505, Mismatches: 47, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
218 79 0.16
219 1 0.00
221 22 0.04
222 13 0.03
223 3 0.01
224 4 0.01
225 12 0.02
226 1 0.00
227 125 0.25
228 134 0.27
229 111 0.22
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (229 bp):
TCAAATCCATCATTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
TGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAA
ATTCATAATGAGAAGAATTTATTCAACCTTTTGC
Found at i:42981 original size:113 final size:113
Alignment explanation
Indices: 42411--43196 Score: 912
Period size: 113 Copynumber: 7.0 Consensus size: 113
42401 TAGCAAAGAT
* *
42411 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
*
42476 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * ** *
42524 TTAAATTCATCATTTGATGGATTAAC-ATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAA--C-TCATC
* * *
42588 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTCGC
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
42639 TCAAATCCATCATTTGA-AGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
*
42703 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * * *
42751 TTAAATTCATAATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAA--C-TCATC
*
42816 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
42867 TCAAATCCATCACTTGATGGATCAGCTTTTCAAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
*
42932 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
42980 TCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
* * ** * *
43044 AGAA-G-A-AA-ATGTTCACAATGAGAAGAGCTTATTCAACATTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC-CTTTTGC
* ** * ** * * * *
43089 AT-AATTTTATCA---CA-ACATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 -TCAAATCCATCATTTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTG
* * ** *
43149 AAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
43197 AATGACTCTA
Statistics
Matches: 579, Mismatches: 79, Indels: 34
0.84 0.11 0.05
Matches are distributed among these distances:
105 14 0.02
106 31 0.05
108 25 0.04
109 23 0.04
110 29 0.05
111 1 0.00
112 120 0.21
113 139 0.24
114 7 0.01
115 91 0.16
116 99 0.17
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:43418 original size:3 final size:3
Alignment explanation
Indices: 43412--43492 Score: 110
Period size: 3 Copynumber: 27.0 Consensus size: 3
43402 TTTTACCCAT
* * *
43412 TTA TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
43460 TTA TAA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
43493 AAAAAATAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 63 0.93
4 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:45089 original size:27 final size:27
Alignment explanation
Indices: 45057--45109 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
45047 GATATATTTT
45057 TAAATAAATAAATATTTTATTTATAAA
1 TAAATAAATAAATATTTTATTTATAAA
* *
45084 TAAATAAATTAATATTTTTTTTATAA
1 TAAATAAATAAATATTTTATTTATAA
45110 TTATAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAAATAAATAAATATTTTATTTATAAA
Found at i:46845 original size:23 final size:21
Alignment explanation
Indices: 46818--46860 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
46808 GATATAAAAA
46818 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
46839 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
46860 T
1 T
46861 AAATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:47985 original size:17 final size:18
Alignment explanation
Indices: 47963--47999 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
47953 GTCAACAATC
47963 AGTGGTATATCT-AAACA
1 AGTGGTATATCTAAAACA
47980 AGTGGTATATCTAAAACA
1 AGTGGTATATCTAAAACA
47998 AG
1 AG
48000 CTTATTAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (18 bp):
AGTGGTATATCTAAAACA
Found at i:48757 original size:41 final size:41
Alignment explanation
Indices: 48712--48791 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
48702 TAATTAAATC
* **
48712 TATGATCCATGTTTCATGTAATTACTATGGTTCAAGTTTAG
1 TATGATCCATATTTCACATAATTACTATGGTTCAAGTTTAG
*
48753 TATGATCCATATTTCACATAATTATTATGGTTCAAGTTT
1 TATGATCCATATTTCACATAATTACTATGGTTCAAGTTT
48792 TTGTTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (41 bp):
TATGATCCATATTTCACATAATTACTATGGTTCAAGTTTAG
Found at i:52048 original size:90 final size:90
Alignment explanation
Indices: 51895--52075 Score: 353
Period size: 90 Copynumber: 2.0 Consensus size: 90
51885 CAACAATTTG
51895 TATCATAGTTTGACTCATTAGAAGGTCTAACAACCTTGAGACGATATTTGAAGAAACTATATCCA
1 TATCATAGTTTGACTCATTAGAAGGTCTAACAACCTTGAGACGATATTTGAAGAAACTATATCCA
*
51960 TTTTTGACACAACCGAAAAGATGGT
66 TTTTCGACACAACCGAAAAGATGGT
51985 TATCATAGTTTGACTCATTAGAAGGTCTAACAACCTTGAGACGATATTTGAAGAAACTATATCCA
1 TATCATAGTTTGACTCATTAGAAGGTCTAACAACCTTGAGACGATATTTGAAGAAACTATATCCA
52050 TTTTCGACACAACCGAAAAGATGGT
66 TTTTCGACACAACCGAAAAGATGGT
52075 T
1 T
52076 TCCACCTCTA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (90 bp):
TATCATAGTTTGACTCATTAGAAGGTCTAACAACCTTGAGACGATATTTGAAGAAACTATATCCA
TTTTCGACACAACCGAAAAGATGGT
Found at i:52691 original size:16 final size:15
Alignment explanation
Indices: 52670--52703 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
52660 CTTTAAAAAA
52670 TGAAAAATGAAAATTT
1 TGAAAAA-GAAAATTT
*
52686 TGAAAAAGAAAGTTT
1 TGAAAAAGAAAATTT
52701 TGA
1 TGA
52704 TTTAAAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (15 bp):
TGAAAAAGAAAATTT
Found at i:57953 original size:65 final size:65
Alignment explanation
Indices: 57864--57999 Score: 184
Period size: 65 Copynumber: 2.1 Consensus size: 65
57854 CACTAATTAT
* * *
57864 ATTCGATGTTTTAAAAGAACCAAGAGTGTATCGATGCATGG-TCTGTGCATCGATACAAAAAATG
1 ATTCGATGTTTCAAAAGAACCAAGAGTGCATCAATGCATGGCT-TGTGCATCGATACAAAAAATG
57928 C
65 C
* ** * *
57929 ATTCGATGTTTCAAAATATTCAAGAGTGCATCAATGCATGGCTTGTGCATCGGTACACAAAATGC
1 ATTCGATGTTTCAAAAGAACCAAGAGTGCATCAATGCATGGCTTGTGCATCGATACAAAAAATGC
57994 ATTCGA
1 ATTCGA
58000 AATAGGTGTG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 61 0.98
66 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (65 bp):
ATTCGATGTTTCAAAAGAACCAAGAGTGCATCAATGCATGGCTTGTGCATCGATACAAAAAATGC
Found at i:58728 original size:16 final size:16
Alignment explanation
Indices: 58691--58721 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58681 CATCAAATTC
58691 AAACATAACAATCCAA
1 AAACATAACAATCCAA
*
58707 AAACATATCAATCCA
1 AAACATAACAATCCA
58722 TCAACATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (16 bp):
AAACATAACAATCCAA
Found at i:72697 original size:42 final size:40
Alignment explanation
Indices: 72607--72704 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 40
72597 TGCACAGCAG
* * *
72607 AGTGCATCGATGCACATTCAAGGAATGCATTGGCATCTTC
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGCATCGTC
*
72647 ATGATGTATCGATGCACATTCAAGGGATGCATCGATGCA-CGTC
1 A-G-TGTATCGATGCACATTCAAGGAATGCATCG--GCATCGTC
72690 TAGTGTATCGATGCA
1 -AGTGTATCGATGCA
72705 TTATGCACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
40 1 0.02
41 1 0.02
42 39 0.80
43 4 0.08
44 4 0.08
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (40 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGCATCGTC
Done.