Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006326.1 Hibiscus syriacus cultivar Beakdansim tig00015121_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: 111479
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1481 original size:23 final size:22
Alignment explanation
Indices: 1437--1499 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
1427 ACAGCTCTAT
1437 AATTGCACGAAGTGCCACGTAG
1 AATTGCACGAAGTGCCACGTAG
* **
1459 AATTGCACTGGAGTGCCGTGTAG
1 AATTGCAC-GAAGTGCCACGTAG
*
1482 AATTGCACCATAGTGCCA
1 AATTGCACGA-AGTGCCA
1500 TATAATATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 8 0.24
23 25 0.76
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (22 bp):
AATTGCACGAAGTGCCACGTAG
Found at i:1695 original size:102 final size:98
Alignment explanation
Indices: 1519--1723 Score: 313
Period size: 102 Copynumber: 2.0 Consensus size: 98
1509 TCCATAAGAC
* *
1519 CATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGGTCCACCATACTTCACAC
1 CATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGGTCCACCAGACTTCACAC
*
1584 ATATTCCAAAGAATACATATATGTCCCGAAGGACCA
66 A-ATGCCAAAGAATAC--ATATGTCCCGAAGGACCA
*
1620 CATATCATTTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1 CATATCA-TTCCTTAAGAATCATATACATATACCAAGGATCAAGTATG-GTC-CACCAGACTTCA
1685 CAC-ATGCCAAAGAATACATATGTCCCGAAGGACCA
63 CACAATGCCAAAGAATACATATGTCCCGAAGGACCA
1720 CATA
1 CATA
1724 GGACCCGACT
Statistics
Matches: 97, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
100 22 0.23
101 7 0.07
102 51 0.53
103 3 0.03
104 14 0.14
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (98 bp):
CATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGGTCCACCAGACTTCACAC
AATGCCAAAGAATACATATGTCCCGAAGGACCA
Found at i:8101 original size:18 final size:18
Alignment explanation
Indices: 8078--8113 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
8068 ACGCAAAAGG
8078 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
8096 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
8114 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:8563 original size:25 final size:25
Alignment explanation
Indices: 8525--8574 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
8515 AAATCAATTA
*
8525 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
8550 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
8575 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:9004 original size:24 final size:24
Alignment explanation
Indices: 8953--9005 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
8943 TTTCATATGT
* * *
8953 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
8977 AATTTGAGTTTGAATTTTAATATA
1 AATTTGAGTTTGAATTTAAATATA
9001 AATTT
1 AATTT
9006 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:9309 original size:39 final size:39
Alignment explanation
Indices: 9266--9352 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
9256 TCCGATGCTC
*
9266 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATCGTGCCAAGCAAAAGGAA
*
9305 ATCAAAATCCAAATCTCATATCGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATCGTGCCAAGCAAAAGGAA
9344 ATCAAAATC
1 ATCAAAATC
9353 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATCGTGCCAAGCAAAAGGAA
Found at i:9590 original size:20 final size:20
Alignment explanation
Indices: 9558--9613 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
9548 TAACCGAAAA
*
9558 TCGCGTTGCGAATTTGACTT
1 TCGCATTGCGAATTTGACTT
*
9578 TCGCATTGTGAATTTGACTT
1 TCGCATTGCGAATTTGACTT
*
9598 TCGCGTTGCGAATTTG
1 TCGCATTGCGAATTTG
9614 TACCTTCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGAATTTGACTT
Found at i:9804 original size:62 final size:63
Alignment explanation
Indices: 9672--9813 Score: 180
Period size: 62 Copynumber: 2.2 Consensus size: 63
9662 TTTTAGAAAC
*
9672 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
9737 A
63 A
* * ** *
9738 AACAAATCAACTTTTACAAATCAATT-AATCAAAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
9800 AACAAATCAACTTT
1 AACAAATCAACTTT
9814 CAATGTAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
61 4 0.06
62 39 0.57
66 26 0.38
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:11214 original size:21 final size:21
Alignment explanation
Indices: 11190--11262 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
11180 GGCGGGACTA
*
11190 CTTGAACGATGACAGTGGCCT
1 CTTGAACGATGACAGGGGCCT
* ** *
11211 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGACAGGGGCCT
* *
11232 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAACGATGACAGGGGCCT
11253 CTTGAACGAT
1 CTTGAACGAT
11263 AGGAGACGCC
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (21 bp):
CTTGAACGATGACAGGGGCCT
Found at i:11243 original size:42 final size:42
Alignment explanation
Indices: 11167--11260 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
11157 ATGAATCGGG
* *
11167 CTCTTGAACGGTGGGCGGGACTACTTGAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACTACTTGAACGATGACAGGGGC
* * * *
11209 CTCTTGAACGGTGGGAGGGGCTTCTTCG-ATGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGACTACTT-GAACGATGACAGGGGC
11251 CTCTTGAACG
1 CTCTTGAACG
11261 ATAGGAGACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.36, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACTACTTGAACGATGACAGGGGC
Found at i:11283 original size:42 final size:42
Alignment explanation
Indices: 11190--11289 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
11180 GGCGGGACTA
* * * * * ** *
11190 CTTGAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGACGCCT
11232 CTTCG-ATGATGATAGGGGCCTCTTGAACGATAGGAGACGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGATAGGAGACGCCT
11274 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
11290 TGCATCGGGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGACGCCT
Found at i:13521 original size:13 final size:13
Alignment explanation
Indices: 13503--13527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13493 TTTTTTCAAC
13503 AAAAAGACAAAAT
1 AAAAAGACAAAAT
13516 AAAAAGACAAAA
1 AAAAAGACAAAA
13528 CAAAGACAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAGACAAAAT
Found at i:13774 original size:22 final size:22
Alignment explanation
Indices: 13746--13796 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
13736 GATGGAGATA
*
13746 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCAGAAATGGG
*
13768 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGTCAGAAATGGG
13790 GACGGAT
1 GACGGAT
13797 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGGG
Found at i:13949 original size:20 final size:20
Alignment explanation
Indices: 13924--13968 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
13914 GCGTAAAAAC
*
13924 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
13944 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
13964 ATTTG
1 ATTTG
13969 GAATGTCGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:14021 original size:21 final size:21
Alignment explanation
Indices: 13960--14013 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
13950 CTATCGCGTT
13960 GCGAATTTGGAATGTCGCAAC
1 GCGAATTTGGAATGTCGCAAC
13981 GCGAATTTGGAATGTCGCAAC
1 GCGAATTTGGAATGTCGCAAC
*
14002 GTGAATTTGGAA
1 GCGAATTTGGAA
14014 AATCGCAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (21 bp):
GCGAATTTGGAATGTCGCAAC
Found at i:14083 original size:20 final size:20
Alignment explanation
Indices: 14034--14087 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
14024 CGATTTACAT
14034 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* * *
14054 A-ACTGGGTTGTGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
14074 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
14088 TTTGTTAGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:18728 original size:30 final size:30
Alignment explanation
Indices: 18680--18795 Score: 86
Period size: 30 Copynumber: 4.1 Consensus size: 30
18670 GCACAAATTT
* *
18680 AAACATAAAGGGA-AAAAATAATAAAAACAG
1 AAAC-TAAAGGGACTAAAATAATAAAAACAA
* *
18710 AAACTAAAGGGACTAAAAT-A-GAAAA-AT
1 AAACTAAAGGGACTAAAATAATAAAAACAA
*
18737 AAA-T-TAGGGACTAAAATAATAAAAACAA
1 AAACTAAAGGGACTAAAATAATAAAAACAA
** *
18765 AAAC-CCAGAGGACTAAAATGATAAAAA-AA
1 AAACTAAAG-GGACTAAAATAATAAAAACAA
18794 AA
1 AA
18796 GAAATTTAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
25 12 0.17
26 2 0.03
27 8 0.11
28 8 0.11
29 15 0.21
30 26 0.37
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.13
Consensus pattern (30 bp):
AAACTAAAGGGACTAAAATAATAAAAACAA
Found at i:18920 original size:30 final size:30
Alignment explanation
Indices: 18884--18955 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
18874 AAGAAAGTAG
*
18884 AGAAACTTTAGGGACCAAAATAGATGAAAT
1 AGAAACTTTAGGGACCAAAATAGATAAAAT
** * * *
18914 AGAAACTAAAGGGACTAAATTGGATAAAAT
1 AGAAACTTTAGGGACCAAAATAGATAAAAT
18944 AGAAAC-TTAGGG
1 AGAAACTTTAGGG
18956 GGCTAAATAG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.19
Consensus pattern (30 bp):
AGAAACTTTAGGGACCAAAATAGATAAAAT
Found at i:21395 original size:149 final size:149
Alignment explanation
Indices: 21021--21401 Score: 557
Period size: 149 Copynumber: 2.6 Consensus size: 149
21011 GCGATACAAT
* * *
21021 ATTCACATATGTGACTGACACCATAATCGTAAATTAGTATTATGAATCAAATAACATTAAATTTG
1 ATTCACATATGTGACTGACACCGTAATCGTAATTTAGTATTATGAATCAAATAACATTGAATTTG
** * * *
21086 TACAAAAAATTTAAAAATAAATCACACTCGTAATGACCGTTACGCGTTATATAACTTCTGTAGTA
66 TACAAAATTTTTAGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACTTCTGTAGTA
21151 TCCACAACCGCGATACTGC
131 TCCACAACCGCGATACTGC
* * *
21170 ATTCACATATGTGACTGACACCGTAATTGTAATTTAGTATTGTGAATCAGATAACATTGAATTTG
1 ATTCACATATGTGACTGACACCGTAATCGTAATTTAGTATTATGAATCAAATAACATTGAATTTG
*
21235 TACAAAATTTTTTGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACGTT-TGTAGT
66 TACAAAATTTTTAGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAAC-TTCTGTAGT
* * *
21299 ATTCACAATCGTGATACTGC
130 ATCCACAACCGCGATACTGC
* * **
21319 ATTCACATATGTGACTAACGCCGTAATCGTAATTTAGTATTATGAATCCTATAACATTGAATTTG
1 ATTCACATATGTGACTGACACCGTAATCGTAATTTAGTATTATGAATCAAATAACATTGAATTTG
**
21384 TACAACCTTTTTAGAAAC
66 TACAAAATTTTTAGAAAC
21402 GACTGTTACG
Statistics
Matches: 207, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
149 205 0.99
150 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (149 bp):
ATTCACATATGTGACTGACACCGTAATCGTAATTTAGTATTATGAATCAAATAACATTGAATTTG
TACAAAATTTTTAGAAACAAATCACACTAGTAATGACCGTTACGCGTTATATAACTTCTGTAGTA
TCCACAACCGCGATACTGC
Found at i:22605 original size:84 final size:84
Alignment explanation
Indices: 22474--22801 Score: 489
Period size: 84 Copynumber: 3.9 Consensus size: 84
22464 CTATACACCA
* * * * *
22474 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
22537 ACAGCAAAGGGACCTGGGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
* * *
22560 GTAAGGTTTACTCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
22625 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
* *
22644 GTAAGGCTTACCCTTGCACACAGCAAAGGGGCCTGGTAAATTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
22709 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
* * *
22728 GTAAGGCTTACCCTTGCACACAGCAAAGGGACATGGTAAACTGTAAGGCTTACATTCGCACACAA
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
22793 CAAAGGGAC
66 CAAAGGGAC
22802 ATGATAATAC
Statistics
Matches: 222, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
83 4 0.02
84 191 0.86
85 13 0.06
86 14 0.06
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:22804 original size:42 final size:41
Alignment explanation
Indices: 22474--22801 Score: 424
Period size: 42 Copynumber: 7.8 Consensus size: 41
22464 CTATACACCA
* * *
22474 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
*
22518 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* * *
22560 GTAAGGTTTACTCTTGCACACAACAAAGGGACCTGGTAAACT
1 GTAAGGCTTAC-CTTGCACACAGCAAAGGGACCTGGGAAACT
22602 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
* * *
22644 GTAAGGCTTACCCTTGCACACAGCAAAGGGGCCTGGTAAATT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
22686 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
* *
22728 GTAAGGCTTACCCTTGCACACAGCAAAGGGACATGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* *
22770 GTAAGGCTTACATTCGCACACAACAAAGGGAC
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGAC
22802 ATGATAATAC
Statistics
Matches: 257, Mismatches: 19, Indels: 18
0.87 0.06 0.06
Matches are distributed among these distances:
41 11 0.04
42 209 0.81
43 23 0.09
44 14 0.05
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:23783 original size:28 final size:28
Alignment explanation
Indices: 23741--23891 Score: 139
Period size: 29 Copynumber: 5.4 Consensus size: 28
23731 CATTTTACAC
* *
23741 AAATAGCACTCTTTTTAAAATAATTACCA
1 AAATAGCAC-CTTTTTAAATTAATTCCCA
*
23770 AAATAGCACCTTTTTGAATTAATTCCCA
1 AAATAGCACCTTTTTAAATTAATTCCCA
*
23798 AAATAGCA-CTAATTTCAAATTAATTCCCA
1 AAATAGCACCT--TTTTAAATTAATTCCCA
* * *
23827 GAATATCA-CTTTTTGAAA--AATTACCA
1 AAATAGCACCTTTTT-AAATTAATTCCCA
* * *
23853 AAATTGCACACATTTCAAATTAATTCCCA
1 AAATAGCAC-CTTTTTAAATTAATTCCCA
23882 AAATAGCACC
1 AAATAGCACC
23892 AAAATTGAAT
Statistics
Matches: 99, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
26 12 0.12
27 8 0.08
28 32 0.32
29 47 0.47
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (28 bp):
AAATAGCACCTTTTTAAATTAATTCCCA
Found at i:23868 original size:55 final size:57
Alignment explanation
Indices: 23741--23891 Score: 182
Period size: 55 Copynumber: 2.7 Consensus size: 57
23731 CATTTTACAC
** * * * * *
23741 AAATAGCACTCTTTTTAAAATAATTACCAAAATAGCACCTTTTTGAATTAATTCCCA
1 AAATAGCACTAATTTCAAATTAATTCCCAAAATAGCACCTTTTTGAATAAATTACCA
* *
23798 AAATAGCACTAATTTCAAATTAATTCCCAGAATATCA-CTTTTTGAA-AAATTACCA
1 AAATAGCACTAATTTCAAATTAATTCCCAAAATAGCACCTTTTTGAATAAATTACCA
*
23853 AAATTGCAC-ACATTTCAAATTAATTCCCAAAATAGCACC
1 AAATAGCACTA-ATTTCAAATTAATTCCCAAAATAGCACC
23892 AAAATTGAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
54 1 0.01
55 39 0.49
56 10 0.12
57 30 0.38
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (57 bp):
AAATAGCACTAATTTCAAATTAATTCCCAAAATAGCACCTTTTTGAATAAATTACCA
Found at i:23907 original size:84 final size:84
Alignment explanation
Indices: 23751--23915 Score: 208
Period size: 84 Copynumber: 2.0 Consensus size: 84
23741 AAATAGCACT
* ** * *
23751 CTTTTTAAAATAATTACCAAAATAGCACCTTTTTGAATTAATTCCCAAAATAGCACTAATTTCAA
1 CTTTTTAAAATAATTACCAAAATAGCACCATTTCAAATTAATTCCCAAAATAGCACAAAATTCAA
*
23816 ATTAATTCCCAGAATATCA
66 ATAAATTCCCAGAATATCA
* *
23835 CTTTTTGAAA-AATTACCAAAATTGCACACATTTCAAATTAATTCCCAAAATAGCACCAAAATT-
1 CTTTTTAAAATAATTACCAAAATAGCAC-CATTTCAAATTAATTCCCAAAATAGCA-CAAAATTC
* *
23898 GAATAAATTCTCAGAATA
64 AAATAAATTCCCAGAATA
23916 GCACCGGTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 16 0.23
84 48 0.70
85 5 0.07
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (84 bp):
CTTTTTAAAATAATTACCAAAATAGCACCATTTCAAATTAATTCCCAAAATAGCACAAAATTCAA
ATAAATTCCCAGAATATCA
Found at i:23939 original size:13 final size:13
Alignment explanation
Indices: 23921--23950 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
23911 GAATAGCACC
23921 GGTCAACGGGTCG
1 GGTCAACGGGTCG
23934 GGTCAACGGGTCG
1 GGTCAACGGGTCG
23947 GGTC
1 GGTC
23951 GGGTCGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:30127 original size:42 final size:41
Alignment explanation
Indices: 30064--30355 Score: 413
Period size: 42 Copynumber: 7.0 Consensus size: 41
30054 GAGCCTAGGA
* * *
30064 AAACAGTAAGGTTTATCCTTGCACACAGCAAAGGGACTTGGG
1 AAACTGTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGG
*
30106 AAACTGTAAGGCTTACTCTTGCACACAGCAAAGGGACCTGGT
1 AAACTGTAAGGCTTAC-CTTGCACACAGCAAAGGGACCTGGG
*
30148 AAACTGTAAGGTTTACCTTCGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGG
* * * *
30190 AAACTGTAAGGCTTTCCCTTGCACACAGTAAAGGGGCCTGGT
1 AAACTGTAAGGC-TTACCTTGCACACAGCAAAGGGACCTGGG
* *
30232 AAACTATAAGGCTTACCTTCGCATACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGG
*
30274 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGT
1 AAACTGTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGG
30316 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 AAACTGTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
30356 ATAATACTTC
Statistics
Matches: 224, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
41 14 0.06
42 200 0.89
43 10 0.04
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (41 bp):
AAACTGTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGG
Found at i:30172 original size:84 final size:84
Alignment explanation
Indices: 30064--30355 Score: 478
Period size: 84 Copynumber: 3.5 Consensus size: 84
30054 GAGCCTAGGA
* * * *
30064 AAACAGTAAGGTTTATCCTT-GCACACAGCAAAGGGACTTGGGAAACTGTAAGGCTTACTCTTGC
1 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGC
30128 ACACAGCAAAGGGACCTGGT
65 ACACAGCAAAGGGACCTGGT
* *
30148 AAACTGTAAGGTTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTTCCCTTGCA
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCA
* *
30213 CACAGTAAAGGGGCCTGGT
66 CACAGCAAAGGGACCTGGT
* *
30232 AAACTATAAGGCTTACCTTCGCATACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCA
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCA
30297 CACAGCAAAGGGACCTGGT
66 CACAGCAAAGGGACCTGGT
30316 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
30356 ATAATACTTC
Statistics
Matches: 193, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
83 4 0.02
84 189 0.98
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (84 bp):
AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCA
CACAGCAAAGGGACCTGGT
Found at i:31333 original size:29 final size:29
Alignment explanation
Indices: 31281--31438 Score: 151
Period size: 29 Copynumber: 5.4 Consensus size: 29
31271 CACTTTACAC
* * *
31281 AAATAGCACC-TTTTTAAAATAATTACCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
31309 AAATAGCACCATTTTTGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
* *
31338 AAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
* * ** *
31367 AAATATCA-CTTTTTTGAAGAAAAAAATTTACCA
1 AAATAGCACCATTTTT---G-AATTAA-TTCCCA
*
31400 AAATAGCACCA-TTTCGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
31428 AAATAGCACCA
1 AAATAGCACCA
31439 AAATCAAATA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
28 30 0.29
29 53 0.50
30 1 0.01
31 1 0.01
32 4 0.04
33 15 0.14
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (29 bp):
AAATAGCACCATTTTTGAATTAATTCCCA
Found at i:42362 original size:110 final size:110
Alignment explanation
Indices: 42198--42415 Score: 301
Period size: 110 Copynumber: 2.0 Consensus size: 110
42188 TGCTTCATCC
* * * * *
42198 GACAAATTGACACTTCTATGCAGTTAAAAATGATTGAGCACCTCTATGCTTCAGTCTAGAATCTG
1 GACAAACTAACACCTCTATGCAGTTAAAAATGACTGAGCACCTATATGCTTCAGTCTAGAATCTG
*
42263 ACACCTATGTGTTTTGTAATGATTCAATACATATATGCTTCAATG
66 ACACCTATGTGCTTTGTAATGATTCAATACATATATGCTTCAATG
* * *
42308 GACAAACTAACACCTCTGTGCAGTTAAAAATGACTGAGCACCTATGTGCTTCAGTCTAGAATTTG
1 GACAAACTAACACCTCTATGCAGTTAAAAATGACTGAGCACCTATATGCTTCAGTCTAGAATCTG
* * * * * *
42373 GCACCTTTGTGCTTTGTAATGATTGAGTACCTATGTGCTTCAA
66 ACACCTATGTGCTTTGTAATGATTCAATACATATATGCTTCAA
42416 ATTAGGATAT
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
110 93 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (110 bp):
GACAAACTAACACCTCTATGCAGTTAAAAATGACTGAGCACCTATATGCTTCAGTCTAGAATCTG
ACACCTATGTGCTTTGTAATGATTCAATACATATATGCTTCAATG
Found at i:42412 original size:54 final size:54
Alignment explanation
Indices: 42335--42570 Score: 197
Period size: 54 Copynumber: 4.3 Consensus size: 54
42325 GTGCAGTTAA
* * * *
42335 AAATGACTGAGCACCTATGTGCTTCAGTCTAGAATTTGGCACCTTTGTGCTTTG
1 AAATGATTGAGCACCTATGTGCTTCAATCTAGAATCTGGAACCTTTGTGCTTTG
* * * * * * *
42389 TAATGATTGAGTACCTATGTGCTTCAAAT-TAGGATAT-GACATCTTTATGATTTG
1 AAATGATTGAGCACCTATGTGCTTC-AATCTAGAATCTGGA-ACCTTTGTGCTTTG
** * * * * *
42443 GGATGATTGAGCACCTCTGTCCTTCAATCTAAAATCTGGAACCTATGTGCTTTA
1 AAATGATTGAGCACCTATGTGCTTCAATCTAGAATCTGGAACCTTTGTGCTTTG
* * * *
42497 AAATTGATTAAGCACCTATGTGCATCAATCTAGAGTCTAGAACCTTTGTGCTTTG
1 AAA-TGATTGAGCACCTATGTGCTTCAATCTAGAATCTGGAACCTTTGTGCTTTG
* *
42552 ACAAACGATTGAGTACCTA
1 --AAATGATTGAGCACCTA
42571 AATGTTGCAA
Statistics
Matches: 138, Mismatches: 37, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
53 4 0.03
54 74 0.54
55 46 0.33
56 11 0.08
57 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (54 bp):
AAATGATTGAGCACCTATGTGCTTCAATCTAGAATCTGGAACCTTTGTGCTTTG
Found at i:42511 original size:55 final size:55
Alignment explanation
Indices: 42446--42550 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 55
42436 TGATTTGGGA
* * * *
42446 TGATTGAGCACCTCTGTCCTTCAATCTAAAATCTGGAACCTATGTGCTTTAAAAT
1 TGATTAAGCACCTATGTCCATCAATCTAAAATCTAGAACCTATGTGCTTTAAAAT
* * * *
42501 TGATTAAGCACCTATGTGCATCAATCTAGAGTCTAGAACCTTTGTGCTTT
1 TGATTAAGCACCTATGTCCATCAATCTAAAATCTAGAACCTATGTGCTTT
42551 GACAAACGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (55 bp):
TGATTAAGCACCTATGTCCATCAATCTAAAATCTAGAACCTATGTGCTTTAAAAT
Found at i:44601 original size:6 final size:6
Alignment explanation
Indices: 44590--44640 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
44580 TCAATCCCTA
** * *
44590 AATCCC AATCCC AATCCC AATATC AATCCC AACACCC AATCCA AATCCC
1 AATCCC AATCCC AATCCC AATCCC AATCCC AA-TCCC AATCCC AATCCC
44639 AA
1 AA
44641 CCCTAGATCC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (6 bp):
AATCCC
Found at i:44631 original size:31 final size:32
Alignment explanation
Indices: 44580--44640 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
44570 ATATATGATT
*
44580 TCAATCCCTAAATCCCAATCCCAATCCCAATA
1 TCAATCCCTAAATCCCAATCCAAATCCCAATA
44612 TCAATCCC-AACA-CCCAATCCAAATCCCAA
1 TCAATCCCTAA-ATCCCAATCCAAATCCCAA
44641 CCCTAGATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (32 bp):
TCAATCCCTAAATCCCAATCCAAATCCCAATA
Found at i:45275 original size:21 final size:21
Alignment explanation
Indices: 45251--45295 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
45241 AAGTTGCATG
*
45251 AAAGACTTCAAAAATCACTCC
1 AAAGACTTCAAAAACCACTCC
*
45272 AAAGACTTCAGAAACCACTCC
1 AAAGACTTCAAAAACCACTCC
45293 AAA
1 AAA
45296 ACTCTATCTT
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:0.49, C:0.29, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAGACTTCAAAAACCACTCC
Found at i:50501 original size:42 final size:42
Alignment explanation
Indices: 50438--50537 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
50428 GTAGGTAGTG
* *
50438 GGCGGGTGTGGATTTAGAAAGTGGTACCCATCGCGGGTTGTA
1 GGCGGGTGTGGATTTAAAAAGTGGTACCCATCGCGAGTTGTA
*
50480 GGCGGGTGTGGATTTAAAAAGTGGTACCCTTCGCGAGTTGTA
1 GGCGGGTGTGGATTTAAAAAGTGGTACCCATCGCGAGTTGTA
50522 GGCGGGTGATGGATTT
1 GGCGGGTG-TGGATTT
50538 GAGACCTTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 47 0.87
43 7 0.13
ACGTcount: A:0.19, C:0.13, G:0.40, T:0.28
Consensus pattern (42 bp):
GGCGGGTGTGGATTTAAAAAGTGGTACCCATCGCGAGTTGTA
Found at i:50960 original size:43 final size:43
Alignment explanation
Indices: 50897--51048 Score: 198
Period size: 43 Copynumber: 3.6 Consensus size: 43
50887 ATGTACCAGC
* *
50897 GTGGGCGGGT-GTAGATTTGAAAAATTTTACCCATCATGGGTG
1 GTGGGCGGATGGTGGATTTGAAAAATTTTACCCATCATGGGTG
* *
50939 GTGGGCGGATGGTGGATTTGAAAAATTTTACACATAATGGGTG
1 GTGGGCGGATGGTGGATTTGAAAAATTTTACCCATCATGGGTG
* * * *
50982 GTGAGCGTATGGTGGATTTGAAAATTTTTACCCATCATGAGTG
1 GTGGGCGGATGGTGGATTTGAAAAATTTTACCCATCATGGGTG
* * *
51025 ATGGACGGATGGTCGATTTGAAAA
1 GTGGGCGGATGGTGGATTTGAAAA
51049 TATTAGATAT
Statistics
Matches: 94, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 9 0.10
43 85 0.90
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.31
Consensus pattern (43 bp):
GTGGGCGGATGGTGGATTTGAAAAATTTTACCCATCATGGGTG
Found at i:55828 original size:2 final size:2
Alignment explanation
Indices: 55821--55847 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55811 TGTATTTTTG
55821 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
55848 TTGTAAAACT
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:58011 original size:3 final size:3
Alignment explanation
Indices: 57996--58039 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
57986 TGGCAAGTGT
*
57996 AGA AGA TGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA GAGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA A
58040 AACCCCTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:60079 original size:2 final size:2
Alignment explanation
Indices: 60072--60099 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60062 CTCATCTATG
60072 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
60100 TTCAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62335 original size:30 final size:30
Alignment explanation
Indices: 62299--62383 Score: 143
Period size: 30 Copynumber: 2.8 Consensus size: 30
62289 GGATTACACA
62299 ATGATTTCTAAAAAACATGTTGACTGCACG
1 ATGATTTCTAAAAAACATGTTGACTGCACG
62329 ATGATTTCTAAAAAACATGTTGACTGCACG
1 ATGATTTCTAAAAAACATGTTGACTGCACG
** *
62359 ATGATTTCTGGAAAACGTGTTGACT
1 ATGATTTCTAAAAAACATGTTGACT
62384 ACAGGAGGAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (30 bp):
ATGATTTCTAAAAAACATGTTGACTGCACG
Found at i:79842 original size:35 final size:35
Alignment explanation
Indices: 79796--79862 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
79786 AGAAATTATC
79796 TTATAATTATCC-AACTATTAAAAAAACTATATTTA
1 TTATAATTATCCAAACTATT-AAAAAACTATATTTA
79831 TTATAATTATCCAAACTATTAAAAAACTATAT
1 TTATAATTATCCAAACTATTAAAAAACTATAT
79863 GGATAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 24 0.77
36 7 0.23
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (35 bp):
TTATAATTATCCAAACTATTAAAAAACTATATTTA
Found at i:79874 original size:36 final size:35
Alignment explanation
Indices: 79798--79874 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
79788 AAATTATCTT
** *
79798 ATAATTATCCAACTATTAAAAAAACTATATTTATT
1 ATAATTATCCAACTATTAAAAAAACTATATGGATA
79833 ATAATTATCCAAACTATT-AAAAAACTATATGGATA
1 ATAATTATCC-AACTATTAAAAAAACTATATGGATA
79868 ATTAATT
1 A-TAATT
79875 GATTGTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 25 0.68
36 12 0.32
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (35 bp):
ATAATTATCCAACTATTAAAAAAACTATATGGATA
Found at i:85929 original size:21 final size:21
Alignment explanation
Indices: 85886--85930 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
85876 TATCGCATTA
**
85886 CGATTTTCCAAATTCACGTTG
1 CGATTTTCCAAATTCACAATG
* *
85907 CGATTTTCCTAATTCGCAATG
1 CGATTTTCCAAATTCACAATG
85928 CGA
1 CGA
85931 ATACGTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (21 bp):
CGATTTTCCAAATTCACAATG
Found at i:85945 original size:20 final size:20
Alignment explanation
Indices: 85920--86032 Score: 217
Period size: 20 Copynumber: 5.7 Consensus size: 20
85910 TTTTCCTAAT
85920 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
85940 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
85960 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
85980 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
86000 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
86020 TCGCAACGCGAAT
1 TCGCAATGCGAAT
86033 CTGACTATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 92 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:86254 original size:22 final size:22
Alignment explanation
Indices: 86229--86294 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
86219 GGCGACATCC
*
86229 GTCCCCATCTCCGACGAAATTA
1 GTCCCCATCTCCGACGAAATCA
*
86251 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* **
86273 GTCTCCATCTCTTACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
86295 TTCACAGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.26, C:0.36, G:0.12, T:0.26
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:86733 original size:40 final size:39
Alignment explanation
Indices: 86629--86736 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 39
86619 GCGATTCTGT
86629 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCAAATTCG
** * **
86668 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTC-ATTTCGCGTTGCGATAGTCAAATTCG
* *
86708 TGTTGCGATTTTCATTTTCGTGTTGCGAT
1 CGTTGCGATTTTCA-TTTCGCGTTGCGAT
86737 TTTAAGTTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
39 12 0.21
40 45 0.79
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.41
Consensus pattern (39 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATAGTCAAATTCG
Found at i:86739 original size:20 final size:20
Alignment explanation
Indices: 86629--86736 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
86619 GCGATTCTGT
**
86629 CGTTGCGATTTTC-ATTTCG
1 CGTTGCGATAGTCAATTTCG
*
86648 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
86668 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
86688 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
* ** *
86708 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
*
86728 TGTTGCGAT
1 CGTTGCGAT
86737 TTTAAGTTTC
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
19 11 0.14
20 69 0.86
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:86746 original size:20 final size:20
Alignment explanation
Indices: 86703--86746 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
86693 CGATAGTCAT
* *
86703 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
86723 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
86743 TTTC
1 TTTC
86747 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:88632 original size:20 final size:20
Alignment explanation
Indices: 88607--88763 Score: 126
Period size: 20 Copynumber: 8.5 Consensus size: 20
88597 AGAATAGTTT
88607 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
88627 ACTATCGCAACGCGAAAATT
1 ACTATCGCAATGCGAAAATG
*
88647 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
88663 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
88680 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
88696 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
88714 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
88734 ACTATCACAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
88754 ACTATCGCAA
1 ACTATCGCAA
88764 CGAAAGAATC
Statistics
Matches: 113, Mismatches: 10, Indels: 28
0.75 0.07 0.19
Matches are distributed among these distances:
14 14 0.12
16 9 0.08
17 8 0.07
18 5 0.04
19 7 0.06
20 70 0.62
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:88676 original size:34 final size:34
Alignment explanation
Indices: 88630--88784 Score: 134
Period size: 34 Copynumber: 4.4 Consensus size: 34
88620 GAAAATGACT
* *
88630 ATCGCAACGCGAAAATTACTATCGCAACGAGAGA
1 ATCGCAACGCGAAAATGACTATCGCAACGAAAGA
* ** *
88664 ATCGCAATGCG-AAATGAAAATCGCAAC-AACAAA
1 ATCGCAACGCGAAAATGACTATCGCAACGAA-AGA
88697 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAACGCGAAAATGACTATCGCAA--CG-AAA-GA
* * **
88735 CTATCACAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAACGCGAAAATGACTATCGCAACGAAAGA
*
88771 ATCGCAAAGCGAAA
1 ATCGCAACGCGAAA
88785 TGAAAATTGC
Statistics
Matches: 95, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
32 1 0.01
33 25 0.26
34 34 0.36
36 3 0.03
37 4 0.04
38 5 0.05
40 23 0.24
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACGAAAGA
Found at i:88835 original size:20 final size:20
Alignment explanation
Indices: 88808--88876 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
88798 GCGATTCTCT
**
88808 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
88828 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
88848 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
88868 CGTTGCGAT
1 CGTTGCGAT
88877 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:88886 original size:20 final size:20
Alignment explanation
Indices: 88808--88886 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
88798 GCGATTCTCT
*
88808 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* * *
88828 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
88848 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
88868 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
88887 AGATTCTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:89417 original size:21 final size:21
Alignment explanation
Indices: 89326--89423 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 21
89316 GACTCACCTG
**
89326 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTA
89348 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
** * *
89368 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * *
89389 CCACCGTTCAAGAGGCCACTA
1 TCATCGTTCAAGAGGCCCCTA
*
89410 TCATCGTTGAAGAG
1 TCATCGTTCAAGAG
89424 ATCCCTCCCA
Statistics
Matches: 59, Mismatches: 16, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
20 3 0.05
21 55 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:89423 original size:42 final size:42
Alignment explanation
Indices: 89351--89433 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
89341 CCTCCCCTAT
*
89351 CGTTCAAGAGGCCCCTATCATCCCTCAAGAG-TCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGAT-CCCTCCCAC
** *
89393 CGTTCAAGAGGCCACTATCATCGTTGAAGAGATCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGATCCCTCCCA
89434 ACATTCTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGATCCCTCCCAC
Found at i:90832 original size:14 final size:14
Alignment explanation
Indices: 90813--90848 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
90803 ATTGTTTAAT
90813 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
90827 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
90841 TGATTTGT
1 TGATTTGT
90849 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:90997 original size:34 final size:34
Alignment explanation
Indices: 90954--91049 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
90944 AAAACAGACT
**
90954 ATCGCAATGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
90988 ATCGCAATGC-GAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
91021 AGCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGGAAATGAAAATCGCAACG
91050 CGAAACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:91148 original size:33 final size:33
Alignment explanation
Indices: 91064--91148 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
91054 ACTAAATTCG
91064 CGTTGCGATTTTCATTTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCACATTGCGATTCTCT
* *
91098 CGTCGCGATTTTTATTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCACATTGCGATTCTCT
**
91131 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
91149 CGTGTTGCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 33 0.73
34 12 0.27
ACGTcount: A:0.15, C:0.24, G:0.16, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCACATTGCGATTCTCT
Found at i:91175 original size:20 final size:20
Alignment explanation
Indices: 91131--91198 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
91121 GCGATTCTCT
91131 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
91151 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
91171 CGTT--G-T-G--ATTTCCG
1 CGTTGCGATAGTCATTTCCG
91185 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
91199 AATGAATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
13 2 0.05
14 8 0.21
16 2 0.05
17 2 0.05
18 2 0.05
20 20 0.53
21 2 0.05
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:93618 original size:24 final size:24
Alignment explanation
Indices: 93584--93637 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
93574 CTGAAAAATC
93584 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
93608 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
93632 ATCAAA
1 ATCAAA
93638 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:94504 original size:20 final size:20
Alignment explanation
Indices: 94479--94525 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
94469 AAATTCAGTA
94479 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
94499 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
94519 TTGCGAT
1 TTGCGAT
94526 TTACGTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:94550 original size:20 final size:20
Alignment explanation
Indices: 94519--94584 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
94509 CAGAATCTCG
94519 TTGCGATTTACGTATTCGAA
1 TTGCGATTTACGTATTCGAA
* * *
94539 TTTCGATATACGTATTCGCA
1 TTGCGATTTACGTATTCGAA
*
94559 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGAA
94579 TTGCGA
1 TTGCGA
94585 ATTAAGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGAA
Found at i:94605 original size:21 final size:21
Alignment explanation
Indices: 94581--94626 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
94571 TATTCGCATT
94581 GCGAATTAAGAAAATCGCAAC
1 GCGAATTAAGAAAATCGCAAC
** *
94602 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAAGAAAATCGCAAC
94623 GCGA
1 GCGA
94627 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAAGAAAATCGCAAC
Found at i:99785 original size:2 final size:2
Alignment explanation
Indices: 99778--99872 Score: 172
Period size: 2 Copynumber: 47.5 Consensus size: 2
99768 GTTTCAAAAC
99778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
99862 GT AT AT GT AT A
1 AT AT AT AT AT A
99873 ATAAATCTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:102501 original size:23 final size:23
Alignment explanation
Indices: 102475--102520 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
102465 ATAATGCACT
102475 CAAGCATAAAGAGAAAAATGAGA
1 CAAGCATAAAGAGAAAAATGAGA
*
102498 CAAGCATAAAGAGAAACATGAGA
1 CAAGCATAAAGAGAAAAATGAGA
102521 ATAATTGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.59, C:0.11, G:0.22, T:0.09
Consensus pattern (23 bp):
CAAGCATAAAGAGAAAAATGAGA
Found at i:104026 original size:16 final size:17
Alignment explanation
Indices: 103997--104047 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
103987 AAAATATTTT
103997 ATATATAATTAATATAAA
1 ATATATAA-TAATATAAA
* *
104015 ATATATAA-AATATTAT
1 ATATATAATAATATAAA
104031 ATATATATATATATATA
1 ATATATA-ATA-ATATA
104048 TAATCGGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 13 0.48
17 1 0.04
18 9 0.33
19 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAATAATATAAA
Found at i:104048 original size:16 final size:15
Alignment explanation
Indices: 103996--104051 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 15
103986 GAAAATATTT
103996 TATATATA-AT-TAA
1 TATATATATATATAA
*
104009 TATA-AAATATATAA
1 TATATATATATATAA
*
104023 AATAT-TATATAT-A
1 TATATATATATATAA
104036 TATATATATATATAA
1 TATATATATATATAA
104051 T
1 T
104052 CGGGGCGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 2 0.06
13 11 0.32
14 19 0.56
15 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATATATATAA
Done.