Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2435
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: 91710
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:2552 original size:79 final size:78
Alignment explanation
Indices: 2408--2870 Score: 325
Period size: 79 Copynumber: 5.8 Consensus size: 78
2398 TGGAGATAAA
* * * * *
2408 AACGGGGTTGGAGTAT-CTCCGA-GATGAAAATTTCAATATTTTAGAAACAAAAATGAGATTAGA
1 AACGAGGTTGGAGTATCCT-CGAGGATAAAAATTT-AATATTTTAGAAA-TAAAATGAGGTTGGA
*
2471 GTACCCCCTCAAAAAT
63 GTATCCCCTCAAAAAT
* *
2487 AACGAGATTAGAGTATCCTCGA-GATAAGAAATTTAATATTTTAGAAATAAAATCGAGGTTGGAG
1 AACGAGGTTGGAGTATCCTCGAGGATAA-AAATTTAATATTTTAGAAATAAAAT-GAGGTTGGAG
* *
2551 TATTCCCTAAAAAAT
64 TATCCCCTCAAAAAT
* * * * * * * *
2566 AACAAGGTTGGTGCATCCTCGAGGGTAAAAAATTGATATTTTGGAAATAAAACTGGGGTTGGAGT
1 AACGAGGTTGGAGTATCCTCGAGGATAAAAATTTAATATTTTAGAAATAAAA-TGAGGTTGGAGT
**
2631 ATCCCCTCGGAAAT
65 ATCCCCTCAAAAAT
* * * * **
2645 AACGGGGTTGGATTATCC-CTGATGATGAAAAACTCGATATTTTAGAAATAAAAATGAGGTTGGA
1 AACGAGGTTGGAGTATCCTC-GAGGAT-AAAAATTTAATATTTTAGAAAT-AAAATGAGGTTGGA
** * *
2709 GTATCCGTTCGAAAGT
63 GTATCCCCTCAAAAAT
* * * ** **
2725 AAC-AGGGTTGGAGTATCCCCAATGGAGAAAAA-TCGATATTTGGGAAATAAAAATGAGGTTGGA
1 AACGA-GGTTGGAGTATCCTCGA-GGATAAAAATTTAATATTTTAGAAAT-AAAATGAGGTTGGA
*
2788 GTATCCCCTCGAAAAT
63 GTATCCCCTCAAAAAT
* * * *
2804 AAC-AGGGTTGGAGTATCCCCGATGG-TGAAAAA-TTGATATTTT-GAAAATAAAAAAGGGGTTG
1 AACGA-GGTTGGAGTATCCTCGA-GGAT-AAAAATTTAATATTTTAG-AAAT-AAAATGAGGTTG
2865 GAGTAT
61 GAGTAT
2871 TGCCTCGGAA
Statistics
Matches: 316, Mismatches: 55, Indels: 26
0.80 0.14 0.07
Matches are distributed among these distances:
78 7 0.02
79 228 0.72
80 74 0.23
81 7 0.02
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.27
Consensus pattern (78 bp):
AACGAGGTTGGAGTATCCTCGAGGATAAAAATTTAATATTTTAGAAATAAAATGAGGTTGGAGTA
TCCCCTCAAAAAT
Found at i:2734 original size:159 final size:157
Alignment explanation
Indices: 2451--2870 Score: 429
Period size: 159 Copynumber: 2.7 Consensus size: 157
2441 CAATATTTTA
* * * * * * * *
2451 GAAACAAAAATGAGATTAGAGTACCCCCTCAAAAATAAC-GAGATTAGAGTATCCTCGA-GAT-A
1 GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCCCGATGATGA
**
2513 AGAAATTTAATATTTTAGAAAT-AAAATCGAGGTTGGAGTATTCCCTAAAAAATAACAAGGTTGG
65 A-AAA-TCGATATTTTAGAAATAAAAAT-GAGGTTGGAGTA-TCCCTAAAAAATAACAAGGTTGG
* * * * *
2577 TGCATCCTCGAGGGTA-AAAAATTGATATTTTG
126 AGCATCCCCAAGGG-AGAAAAATCGATATTTGG
* * * * * *
2609 GAAATAAAACTGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGATTATCCCTGATGATGAA
1 GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGATGAA
* ** * * *
2674 AAACTCGATATTTTAGAAATAAAAATGAGGTTGGAGTATCCGTTCGAAAGTAACAGGGTTGGAGT
66 AAA-TCGATATTTTAGAAATAAAAATGAGGTTGGAGTATCC-CTAAAAAATAACAAGGTTGGAGC
*
2739 ATCCCCAATGGAGAAAAATCGATATTTGG
129 ATCCCCAAGGGAGAAAAATCGATATTTGG
*
2768 GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGGTGAA
1 GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGATGAA
* * *
2833 AAATTGATATTTT-GAAAATAAAAAAGGGGTTGGAGTAT
66 AAATCGATATTTTAG-AAATAAAAATGAGGTTGGAGTAT
2871 TGCCTCGGAA
Statistics
Matches: 217, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
157 1 0.00
158 77 0.35
159 132 0.61
160 7 0.03
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (157 bp):
GAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGATGAA
AAATCGATATTTTAGAAATAAAAATGAGGTTGGAGTATCCCTAAAAAATAACAAGGTTGGAGCAT
CCCCAAGGGAGAAAAATCGATATTTGG
Found at i:2877 original size:79 final size:79
Alignment explanation
Indices: 2522--2902 Score: 410
Period size: 79 Copynumber: 4.8 Consensus size: 79
2512 AAGAAATTTA
** * * * *
2522 ATATTTT-AGAAAT-AAAATCGAGGTTGGAGTATTCCCTAAAAAATAACAAGGTTGGTGCATCCT
1 ATATTTTGA-AAATAAAAAT-GAGGTTGGAGTATTCCCTCGAAAATAACAGGGTTGGAGTATCCC
* * *
2585 CGAGGGTAAAAAATTG
64 CGATGGTGAAAAATCG
* * * * * * * *
2601 ATATTTTGGAAATAAAACTGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGATTATCCCTG
1 ATATTTTGAAAATAAAAATGAGGTTGGAGTATTCCCTCGAAAATAACAGGGTTGGAGTATCCCCG
*
2666 ATGATGAAAAACTCG
66 ATGGTGAAAAA-TCG
* *
2681 ATATTTT-AGAAATAAAAATGAGGTTGGAGTA-TCCGTTCGAAAGTAACAGGGTTGGAGTATCCC
1 ATATTTTGA-AAATAAAAATGAGGTTGGAGTATTCC-CTCGAAAATAACAGGGTTGGAGTATCCC
* *
2744 CAATGGAGAAAAATCG
64 CGATGGTGAAAAATCG
* * *
2760 ATATTTGGGAAATAAAAATGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCG
1 ATATTTTGAAAATAAAAATGAGGTTGGAGTATTCCCTCGAAAATAACAGGGTTGGAGTATCCCCG
*
2825 ATGGTGAAAAATTG
66 ATGGTGAAAAATCG
* * * * *
2839 ATATTTTGAAAATAAAAAAGGGGTTGGAGTATTGCCTCGGAAACAACAGGGTTGGAGTATCCCC
1 ATATTTTGAAAATAAAAATGAGGTTGGAGTATTCCCTCGAAAATAACAGGGTTGGAGTATCCCC
2903 TTGGTTTTAT
Statistics
Matches: 248, Mismatches: 47, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
79 181 0.73
80 67 0.27
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (79 bp):
ATATTTTGAAAATAAAAATGAGGTTGGAGTATTCCCTCGAAAATAACAGGGTTGGAGTATCCCCG
ATGGTGAAAAATCG
Found at i:2995 original size:79 final size:78
Alignment explanation
Indices: 2907--3101 Score: 239
Period size: 79 Copynumber: 2.5 Consensus size: 78
2897 ATCCCCTTGG
* * ** * *
2907 TTTTATTTCTAAAATATTAAATTTCTCGTCTCGGGGATACTCCAACCCTATTATTTTTTAGGGGG
1 TTTTATTTCTAAAATATTAAATTT-TCGTCTCAGGGATACTCCAACCCCATTATTTTCGAGAGGA
* *
2972 TGCTCCAATCCCCT
65 TACTCCAATCCCAT
*
2986 TTTTATTTCTAAAATATTTAAATTTTCGTCTCAGGGATACTCCAACCCCGTTATTTTCGAGAGGA
1 TTTTATTTCTAAAATA-TTAAATTTTCGTCTCAGGGATACTCCAACCCCATTATTTTCGAGAGGA
3051 TACTCCAATCCCAT
65 TACTCCAATCCCAT
* * * *
3065 TTTTATCTCCAAAGTATTAAAGTTTTCATCT-AGGGAT
1 TTTTATTTCTAAAATATTAAA-TTTTCGTCTCAGGGAT
3102 GTGCTCCAAC
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
78 11 0.11
79 82 0.81
80 8 0.08
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (78 bp):
TTTTATTTCTAAAATATTAAATTTTCGTCTCAGGGATACTCCAACCCCATTATTTTCGAGAGGAT
ACTCCAATCCCAT
Found at i:9153 original size:49 final size:49
Alignment explanation
Indices: 9096--10097 Score: 1409
Period size: 49 Copynumber: 20.8 Consensus size: 49
9086 TGGGGACAAT
* *
9096 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
9145 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
9188 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * * *
9237 ATTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
9286 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
9335 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-CCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
9383 ATTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
9432 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATC
*
9484 -TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * *
9532 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
9581 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * *
9630 ATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
9679 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
9722 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * * * *
9771 ATTAAGCCCAATGTCGCTGGCCTTGAATCAGCATATTGGCATCATCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
9820 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
9869 TTTAAGTCCAATGTAGCTGGCCTTG-ATCAGCACATTGGCACC-TCAAC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
9916 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
9965 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * *
10008 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATC
*
10060 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
10098 ACATCCTTTT
Statistics
Matches: 844, Mismatches: 81, Indels: 53
0.86 0.08 0.05
Matches are distributed among these distances:
43 121 0.14
45 1 0.00
47 31 0.04
48 79 0.09
49 531 0.63
50 1 0.00
51 41 0.05
52 39 0.05
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
Found at i:9211 original size:22 final size:22
Alignment explanation
Indices: 9144--9211 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
9134 GCACCTTTAT
9144 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
* * *
9166 CTTGAA-TCAGCACAT-TGGC--AC
1 CTTTAAGTC--CA-ATGTAGCTGGC
9187 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
9209 CTT
1 CTT
9212 GACTCAGCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATGTAGCTGGC
Found at i:9745 original size:22 final size:22
Alignment explanation
Indices: 9678--9745 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
9668 GCACCTTTAT
9678 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
* * *
9700 CTTGAA-TCAGCACAT-TGGC--AC
1 CTTTAAGTC--CA-ATGTAGCTGGC
9721 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
9743 CTT
1 CTT
9746 GACTCAGCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATGTAGCTGGC
Found at i:10143 original size:56 final size:52
Alignment explanation
Indices: 10007--10145 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 52
9997 ACATTGGCAC
* *
10007 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCCAT
* * *
10059 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACA-CC-TTTTC--CAT
* * * *
10115 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
10146 ACATATTGGC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
52 37 0.51
53 2 0.03
54 5 0.07
56 28 0.39
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCCAT
Found at i:10966 original size:33 final size:33
Alignment explanation
Indices: 10929--10995 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10919 TTCAATGATT
10929 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
10962 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
10995 T
1 T
10996 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:10967 original size:13 final size:13
Alignment explanation
Indices: 10949--10973 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10939 CATAAAATGT
10949 TGTATCGATACAA
1 TGTATCGATACAA
10962 TGTATCGATACA
1 TGTATCGATACA
10974 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11057 original size:13 final size:13
Alignment explanation
Indices: 11039--11063 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11029 ATTACTCACA
11039 TGTATCGATACAT
1 TGTATCGATACAT
11052 TGTATCGATACA
1 TGTATCGATACA
11064 CTGATTTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11128 original size:52 final size:52
Alignment explanation
Indices: 11072--11192 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
11062 CACTGATTTT
*
11072 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
11124 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
11176 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
11193 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:17492 original size:4 final size:4
Alignment explanation
Indices: 17477--17506 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
17467 AAACAAAACA
*
17477 AAAT ATAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
17507 GCACCTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:19691 original size:79 final size:78
Alignment explanation
Indices: 19564--19822 Score: 326
Period size: 79 Copynumber: 3.3 Consensus size: 78
19554 TACTTTGGAG
* * * *
19564 ATAAAAACGGGGTTGGAGTATTCCCTTGAAAATAACG-GAGTT-AGAGTATCCCCGATGGTAAAA
1 ATAAAAACGGGGTTGGAGTA-TCCCTCGGAAACAACGAG-GTTGA-AGTATCCCCGATGGTGAAA
*
19627 AATTTGATATTTTGGAA
63 AA-TTGATATTTTGAAA
* *
19644 ATAAAAA-GGGGTTGAAGTATCCTCTCGGAAACAACGAGGTTGAAGTATCCCCGATAGTGAAAAA
1 ATAAAAACGGGGTTGGAGTATCC-CTCGGAAACAACGAGGTTGAAGTATCCCCGATGGTGAAAAA
19708 TTGATATTTTGAAA
65 TTGATATTTTGAAA
* * **
19722 ATAAAAAAGGGGTTGGAGTATCCCTTCGGAAACAACAAGGTTGGTGTATCCCCGATGGTGAAAAA
1 ATAAAAACGGGGTTGGAGTATCCC-TCGGAAACAACGAGGTTGAAGTATCCCCGATGGTGAAAAA
*
19787 TCGATATTTTGAAA
65 TTGATATTTTGAAA
*
19801 ATAAAAACGGGATTGGAGTATC
1 ATAAAAACGGGGTTGGAGTATC
19823 TTTAATAGTG
Statistics
Matches: 159, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
78 24 0.15
79 126 0.79
80 9 0.06
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.26
Consensus pattern (78 bp):
ATAAAAACGGGGTTGGAGTATCCCTCGGAAACAACGAGGTTGAAGTATCCCCGATGGTGAAAAAT
TGATATTTTGAAA
Found at i:19884 original size:50 final size:51
Alignment explanation
Indices: 19759--19925 Score: 214
Period size: 51 Copynumber: 3.3 Consensus size: 51
19749 GGAAACAACA
*
19759 AGGTTGGTGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAAACG
1 AGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAAACG
**** * *
19810 -GGATTGGAGTATCTTTAATAGTGAAAAATCGATATTTTGGAAAT-AAAACG
1 AGG-TTGGAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAAACG
* *
19860 AGGTTGGAGTATCCCGGATGGTGAAAAAGT-AATATTTTGAAAATAAAAACG
1 AGGTTGGAGTATCCCCGATGGTGAAAAA-TCGATATTTTGAAAATAAAAACG
19911 AGGTTGGAGTATCCC
1 AGGTTGGAGTATCCC
19926 TCAAAAATAA
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
50 40 0.41
51 58 0.59
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (51 bp):
AGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTGAAAATAAAAACG
Found at i:20086 original size:79 final size:78
Alignment explanation
Indices: 19856--20161 Score: 373
Period size: 79 Copynumber: 3.9 Consensus size: 78
19846 TTGGAAATAA
* * * * *
19856 AACGAGGTTGGAGTATCCCGGATGGTGAAAAAGTAATATTTTGAAAATAAAAACGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAATGAGGTTGGAGT
*** *
19921 ATCCCTCAAAAAT
66 ATCCCTTGGAAAC
* * * *
19934 AATGGGGTTGGAGTATCCCCGATGGTG-AAAATTGATAGTTTGGAAATAAAAATGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAATGAGGTTGGAG-
*
19998 TTTCCCTTGGAAAC
65 TATCCCTTGGAAAC
* * *
20012 AACGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGGAAATAAAAATGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAATGAGGTTGGAGT
20077 ATCCTCTTGGAAAC
66 ATCC-CTTGGAAAC
* * * * *
20091 AACAGGGTTGGAGTATCCTCGATGGAGAAAAATTGATATTTTGGAAAT-AAAATCGAGGTTAGAG
1 AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAAT-GAGGTTGGAG
20155 TATCCCT
65 TATCCCT
20162 GAGATAAGGA
Statistics
Matches: 196, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
77 30 0.15
78 69 0.35
79 97 0.49
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGGAAATAAAAATGAGGTTGGAGT
ATCCCTTGGAAAC
Found at i:20087 original size:31 final size:28
Alignment explanation
Indices: 20052--20110 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
20042 AATCAATATT
20052 TTGGAAATAAAAATGGGGTTGGAGTATCCTC
1 TTGGAAA-AAAAA--GGGTTGGAGTATCCTC
* *
20083 TTGGAAACAACAGGGTTGGAGTATCCTC
1 TTGGAAAAAAAAGGGTTGGAGTATCCTC
20111 GATGGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
30 3 0.12
31 7 0.27
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (28 bp):
TTGGAAAAAAAAGGGTTGGAGTATCCTC
Found at i:20260 original size:130 final size:130
Alignment explanation
Indices: 20046--20291 Score: 298
Period size: 130 Copynumber: 1.9 Consensus size: 130
20036 GTGAAAAATC
* * * *** ** *
20046 AATATTTTGGAAATAAAAATGGGGTTGGAGTATCCTCTTGGAAACAACAGGGTTGGAGTATCCTC
1 AATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAACAACAGGGTTAAAGTATCCTA
* * * * *
20111 GATGGAGAAAAATTGATATTTTGGAAATAAAATCGAGGTTAGAGTATCCCTGAGATAAGGAATTT
66 GATGGAGAAAAATTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCTGAGATAAGGAATTT
* *
20176 AATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAAAGTATCCCT
1 AATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAACAACAGGGTTAAAGTAT-CCT
* *
20241 GAGAT-GAG-GAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCT
65 -AGATGGAGAAAAATTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCT
20292 TTAAAATTAA
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
130 87 0.91
131 6 0.06
132 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (130 bp):
AATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAACAACAGGGTTAAAGTATCCTA
GATGGAGAAAAATTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCTGAGATAAGGAATTT
Found at i:20287 original size:79 final size:79
Alignment explanation
Indices: 20147--20353 Score: 245
Period size: 79 Copynumber: 2.6 Consensus size: 79
20137 ATAAAATCGA
* ** **
20147 GGTTAGAGTATCCCTGAGATAAGGAATTTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTAGAGTATCCCTGAGATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCC
20212 CTCAAAAATAACAG
66 CTCAAAAATAACAG
*
20226 GGTTAAAGTATCCCTGAGATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCC
1 GGTTAGAGTATCCCTGAGATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCC
* * * *
20291 TTTAAAATTAACGG
66 CTCAAAAATAACAG
* * * * * * *
20305 GGTTGGTGTATCCCCGATGGTGA-AAAATTGATATTTTAGAAATAAAACC
1 GGTTAGAGTATCCCTGA-GATGAGGAATTTAATATTTTAGAAATAAAACC
20354 GAGATTGTAG
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 105 0.96
80 4 0.04
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (79 bp):
GGTTAGAGTATCCCTGAGATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCC
CTCAAAAATAACAG
Found at i:20341 original size:288 final size:285
Alignment explanation
Indices: 19809--20431 Score: 657
Period size: 288 Copynumber: 2.2 Consensus size: 285
19799 AAATAAAAAC
* ** * * *
19809 GGGATTGGAGTATCTTTAATAGTGAAAAATCGATATTTTGGAAATAAAACGAGGTTGGAGTATCC
1 GGGATTGGAGTATCCTCGATGGAGAAAAATCGATATTTTGGAAATAAAACGAGGTTAGAGTATCC
* **
19874 CGGATGGTGAAAAAGTAATATTTTGAAAATAAAAACGAGGTTGGAGTATCCCTCAAAAATAATGG
66 CGGATGATGAAAAAGTAATATTTTGAAAATAAAAACGAGGTTGGAGTATCCCTCAAAAATAACAG
** * * * *** ** *
19939 GGTTGGAGTATCCCCGATGGTGAAAATTGATAGTTTGGAAATAAAAATGGGGTTGGAGTTTTCCC
131 GGTTAAAGTATCCCCGATGATGAAAATTAATAGTTTAGAAATAAAAACAAGGTTAAAGTTATCCC
* * * *
20004 TTGGAAACAACGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGGAAATAAAAATGGG
196 TTGAAAACAACGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTAGAAATAAAAACGAG
* **
20069 GTTGGAGTA-TCCTCTTGGAAACAACA
261 ATTGGAGTATTCCT-TCAGAAACAA-A
*
20095 GGG-TTGGAGTATCCTCGATGGAGAAAAATTGATATTTTGGAAATAAAATCGAGGTTAGAGTATC
1 GGGATTGGAGTATCCTCGATGGAGAAAAATCGATATTTTGGAAATAAAA-CGAGGTTAGAGTATC
* ** * *
20159 CCTGA-GAT-AAGGAATTTAATATTTT-AGAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAAT
65 CCGGATGATGAA--AAAGTAATATTTTGA-AAATAAAAACGAGGTTGGAGTAT-CCCTCAAAAAT
* * * *
20221 AACAGGGTTAAAGTATCCCTGA-GATGAGGAATTTAATATTTTAGAAATAAAACCAAGGTTAAAG
126 AACAGGGTTAAAGTATCCCCGATGATGA--AAATTAATAGTTTAGAAATAAAAACAAGGTTAAAG
* * * * **
20285 -TATCCCTTTAAAATTAACGGGGTTGGTGTATCCCCGATGGTGAAAAATTGATATTTTAGAAATA
189 TTATCCCTTGAAAA-CAACGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTAGAAATA
* * * *
20349 AAACCGAGATTGTAGTATTCCTTCAGAAATAAT
253 AAAACGAGATTGGAGTATTCCTTCAGAAACAAA
* * *
20382 GGGATTGGAGTATCCTCGATGGTGAAAAATCAATATTTTGAAAATAAAAC
1 GGGATTGGAGTATCCTCGATGGAGAAAAATCGATATTTTGGAAATAAAAC
20432 TGGGATTGGA
Statistics
Matches: 276, Mismatches: 51, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
284 2 0.01
285 42 0.15
286 57 0.21
287 42 0.15
288 129 0.47
289 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (285 bp):
GGGATTGGAGTATCCTCGATGGAGAAAAATCGATATTTTGGAAATAAAACGAGGTTAGAGTATCC
CGGATGATGAAAAAGTAATATTTTGAAAATAAAAACGAGGTTGGAGTATCCCTCAAAAATAACAG
GGTTAAAGTATCCCCGATGATGAAAATTAATAGTTTAGAAATAAAAACAAGGTTAAAGTTATCCC
TTGAAAACAACGGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTAGAAATAAAAACGAG
ATTGGAGTATTCCTTCAGAAACAAA
Found at i:20366 original size:79 final size:78
Alignment explanation
Indices: 20174--20476 Score: 270
Period size: 79 Copynumber: 3.8 Consensus size: 78
20164 GATAAGGAAT
* * * * **
20174 TTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAAAGTATCC
1 TTAATATTTTAGAAATAAAACCGAGATTGGAGTATCCCTTC-AAAATAACGGGGTTGGAGTATCC
* * * *
20239 CTGA-GATGAGGAAT
65 CCGATGGTGA-AAAA
* * ** * *
20253 TTAATATTTTAGAAATAAAACCAAGGTTAAAGTATCCCTTTAAAATTAACGGGGTTGGTGTATCC
1 TTAATATTTTAGAAATAAAACCGAGATTGGAGTATCCCTTCAAAA-TAACGGGGTTGGAGTATCC
20318 CCGATGGTGAAAAA
65 CCGATGGTGAAAAA
* * * * *
20332 TTGATATTTTAGAAATAAAACCGAGATTGTAGTATTCCTTCAGAAATAATGGGATTGGAGTATCC
1 TTAATATTTTAGAAATAAAACCGAGATTGGAGTATCCCTTCA-AAATAACGGGGTTGGAGTATCC
*
20397 TCGATGGTGAAAAA
65 CCGATGGTGAAAAA
* * * * * *
20411 TCAATATTTT-GAAAATAAAACTGGGATTGGAGTAT-CTTCTCGGAAATAACGGGGTTTGAGTAT
1 TTAATATTTTAG-AAATAAAACCGAGATTGGAGTATCCCT-TC-AAAATAACGGGGTTGGAGTAT
20474 CCC
63 CCC
20477 TAATGGTAAA
Statistics
Matches: 182, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
78 7 0.04
79 168 0.92
80 7 0.04
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (78 bp):
TTAATATTTTAGAAATAAAACCGAGATTGGAGTATCCCTTCAAAATAACGGGGTTGGAGTATCCC
CGATGGTGAAAAA
Found at i:21924 original size:2 final size:2
Alignment explanation
Indices: 21917--21942 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21907 TGAGATAAAG
21917 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
21943 AGAAGGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:23050 original size:20 final size:21
Alignment explanation
Indices: 23025--23078 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
23015 CATTTTAGGC
23025 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTGT
*
23045 ATGTATCGATACATTTACTGT
1 ATGTATCGATACATTCACTGT
* *
23066 TTCTATCGATACA
1 ATGTATCGATACA
23079 AATTATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTGT
Found at i:25748 original size:28 final size:29
Alignment explanation
Indices: 25727--25783 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
25717 AATATTATTT
25727 TATTTTTAT-ATTAATATTAATATTAAAA
1 TATTTTTATAATTAATATTAATATTAAAA
*
25755 TATTTTTCTAATTAATATTAA-A-TAAAA
1 TATTTTTATAATTAATATTAATATTAAAA
25782 TA
1 TA
25784 ATAATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.26
28 9 0.33
29 11 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTTTTATAATTAATATTAATATTAAAA
Found at i:27484 original size:23 final size:23
Alignment explanation
Indices: 27458--27501 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27448 TTATGTATTT
27458 TATTATATCATAATTATATTTAA
1 TATTATATCATAATTATATTTAA
* * *
27481 TATTATTTTATATTTATATTT
1 TATTATATCATAATTATATTT
27502 TTAATACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATATCATAATTATATTTAA
Found at i:28345 original size:2 final size:2
Alignment explanation
Indices: 28279--28325 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
28269 ACTAAAATGT
28279 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28320 TA TA TA
1 TA TA TA
28326 AGGTAAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29401 original size:16 final size:18
Alignment explanation
Indices: 29360--29403 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
29350 GTTTTAAAAA
*
29360 TATATAATGTATATTAAT
1 TATATAATTTATATTAAT
*
29378 TTTATAATTTATA-T-AT
1 TATATAATTTATATTAAT
29394 TATATAATTT
1 TATATAATTT
29404 TTACCATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 11 0.48
17 1 0.04
18 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATATAATTTATATTAAT
Found at i:32594 original size:2 final size:2
Alignment explanation
Indices: 32587--32615 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32577 CAAGATTGTA
32587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32616 AACAAATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33630 original size:122 final size:122
Alignment explanation
Indices: 33491--33736 Score: 474
Period size: 122 Copynumber: 2.0 Consensus size: 122
33481 TGCTGATAAA
*
33491 ATATTGATGTGTCATGTGATGTAAAATTTTAAATTTTATATAAAAAAAGATTTAAGTTATGTGTC
1 ATATTGATGTGTCATGTGATGTAAAATTTTAAATTTTATACAAAAAAAGATTTAAGTTATGTGTC
33556 GAGTTTAGGTAATTTTTCTTATAAAATTTTAAATCCCATATGATATAGCATATTAGC
66 GAGTTTAGGTAATTTTTCTTATAAAATTTTAAATCCCATATGATATAGCATATTAGC
33613 ATATTGATGTGTCATGTGATGTAAAATTTTAAATTTTATACAAAAAAAGATTTAAGTTATGTGTC
1 ATATTGATGTGTCATGTGATGTAAAATTTTAAATTTTATACAAAAAAAGATTTAAGTTATGTGTC
*
33678 GAGTTTAGGTAATTTTTCTTATAAAATTTTAAATCTCATATGATATAGCATATTAGC
66 GAGTTTAGGTAATTTTTCTTATAAAATTTTAAATCCCATATGATATAGCATATTAGC
33735 AT
1 AT
33737 TTTATCAGCA
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.43
Consensus pattern (122 bp):
ATATTGATGTGTCATGTGATGTAAAATTTTAAATTTTATACAAAAAAAGATTTAAGTTATGTGTC
GAGTTTAGGTAATTTTTCTTATAAAATTTTAAATCCCATATGATATAGCATATTAGC
Found at i:33835 original size:29 final size:29
Alignment explanation
Indices: 33793--33851 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
33783 TTATTTGTTC
*
33793 TAACTTTTAAAGTATAAAAATTAAAATAT
1 TAACTTTTAAAGTACAAAAATTAAAATAT
*
33822 TAAC-TTTAATAGTACAAGAATTAAAATAT
1 TAACTTTTAA-AGTACAAAAATTAAAATAT
33851 T
1 T
33852 TTTTTCACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (29 bp):
TAACTTTTAAAGTACAAAAATTAAAATAT
Found at i:34169 original size:14 final size:14
Alignment explanation
Indices: 34150--34184 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
34140 TCGTAATGTA
34150 ATTTTATAATCATT
1 ATTTTATAATCATT
*
34164 ATTTTATAATCGTT
1 ATTTTATAATCATT
34178 ATTTTAT
1 ATTTTAT
34185 GATTTCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (14 bp):
ATTTTATAATCATT
Found at i:37285 original size:22 final size:23
Alignment explanation
Indices: 37238--37283 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
37228 TTAAATTGAG
*
37238 TTAAATATTAAATAATATTTTAAA
1 TTAAATA-TAAATAATAATTTAAA
37262 TTAAATA-AAATAAATAATTTAA
1 TTAAATATAAAT-AATAATTTAA
37284 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAATATAAATAATAATTTAAA
Found at i:37312 original size:30 final size:31
Alignment explanation
Indices: 37250--37359 Score: 81
Period size: 29 Copynumber: 3.7 Consensus size: 31
37240 AAATATTAAA
37250 TAATATTTTAAATTAAATAAAATAAATAATT
1 TAATATTTTAAATTAAATAAAATAAATAATT
** *
37281 TAAT-TTTTAAA-TAAATTTAATATAATTATT
1 TAATATTTTAAATTAAATAAAATA-AATAATT
* *
37311 TAA-A-TATATAA--AAATAAAATAAA-AAAT
1 TAATATTTTA-AATTAAATAAAATAAATAATT
* *
37338 AAATATATTTATATTAAATAAA
1 TAATAT-TTTAAATTAAATAAA
37360 TATTGACATT
Statistics
Matches: 60, Mismatches: 11, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
27 4 0.07
28 3 0.05
29 21 0.35
30 21 0.35
31 11 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TAATATTTTAAATTAAATAAAATAAATAATT
Found at i:39007 original size:20 final size:20
Alignment explanation
Indices: 38971--39008 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38961 TATAATGAAT
*
38971 ATTTACAAATATTTTCATTG
1 ATTTACAAAGATTTTCATTG
38991 ATTTA-AAAGATTATTCAT
1 ATTTACAAAGATT-TTCAT
39009 ATTCGTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (20 bp):
ATTTACAAAGATTTTCATTG
Found at i:42387 original size:22 final size:22
Alignment explanation
Indices: 42359--42413 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
42349 TGGACATGTT
42359 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
42381 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
42403 AAAAATGCATG
1 AAAAATGCATG
42414 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:43373 original size:20 final size:20
Alignment explanation
Indices: 43326--43400 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
43316 AAAAAGACAT
*
43326 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
43345 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
43366 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
43386 AATGTATCGATACAT
1 AATGTATCGATACAT
43401 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:43394 original size:40 final size:39
Alignment explanation
Indices: 43323--43400 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
43313 GGTAAAAAGA
* *
43323 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
43362 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
43401 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:44491 original size:29 final size:32
Alignment explanation
Indices: 44452--44522 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
44442 AAATAATAAA
*
44452 AAAATATTATATGACATG-ATTAC-ATGTATC
1 AAAATATTATATAACATGAATTACAATGTATC
*
44482 AAAATA-TATATAACATGAATTACTAATGTATT
1 AAAATATTATATAACATGAATTAC-AATGTATC
44514 AAAAT-TTAT
1 AAAATATTAT
44523 TTAAATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 10 0.29
30 11 0.31
32 14 0.40
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (32 bp):
AAAATATTATATAACATGAATTACAATGTATC
Found at i:47083 original size:2 final size:2
Alignment explanation
Indices: 47071--47120 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
47061 GCCACTTTGT
*
47071 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47113 TA TA TA TA
1 TA TA TA TA
47121 CACGTTCATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:49192 original size:42 final size:41
Alignment explanation
Indices: 49100--49193 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 41
49090 TTAAAACTCA
* * *
49100 TTTATTA-TTAGATTATAATTAATAATGTTATTTTTTGTGT
1 TTTATTATTTATAATATAATTAATAATGTTATTTTTTGTAT
*
49140 TTTATTTATTTATAATATAATTAATAATATTTATATTTTAT-TAT
1 TTTA-TTATTTATAATATAATTAATAAT-GTTAT-TTTT-TGTAT
49184 TTTA-TATTTA
1 TTTATTATTTA
49194 AAACTAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
40 4 0.09
41 3 0.07
42 23 0.51
43 4 0.09
44 10 0.22
45 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (41 bp):
TTTATTATTTATAATATAATTAATAATGTTATTTTTTGTAT
Found at i:50347 original size:24 final size:22
Alignment explanation
Indices: 50310--50353 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
50300 AATTTTCATG
50310 TAATAAAAATATATATAAATAT
1 TAATAAAAATATATATAAATAT
*
50332 TAATATAAAATAATATTTAAAT
1 TAATA-AAAAT-ATATATAAAT
50354 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 5 0.26
24 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATAAAAATATATATAAATAT
Found at i:60038 original size:11 final size:11
Alignment explanation
Indices: 60006--60043 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
59996 AAAATTATAT
60006 TATTTATTTAAA
1 TATTTATTT-AA
60018 TATATT-TTTAA
1 TAT-TTATTTAA
60029 TATTTATTTAA
1 TATTTATTTAA
60040 TATT
1 TATT
60044 AAAAACGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 14 0.58
12 6 0.25
13 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:61673 original size:27 final size:27
Alignment explanation
Indices: 61620--61674 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
61610 TAATAAAATT
* * **
61620 ATATATATTTAAATAATTTGATTTTTA
1 ATATAAATTTAAAAAATTTGAAGTTTA
*
61647 ATATAAATTTAAAAAATTTTAAGTTTA
1 ATATAAATTTAAAAAATTTGAAGTTTA
61674 A
1 A
61675 ATCTCGTGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
ATATAAATTTAAAAAATTTGAAGTTTA
Found at i:61845 original size:14 final size:14
Alignment explanation
Indices: 61823--61883 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
61813 TTAATTTTTT
* *
61823 TATACTAAAAATAA
1 TATAATAAATATAA
61837 TATAATAAATATAA
1 TATAATAAATATAA
* *
61851 AATAATAAATTTAAA
1 TATAATAAATAT-AA
* *
61866 TATAATTAACATAA
1 TATAATAAATATAA
61880 TATA
1 TATA
61884 TTTTACAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 28 0.74
15 10 0.26
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
TATAATAAATATAA
Found at i:61854 original size:19 final size:19
Alignment explanation
Indices: 61830--61870 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
61820 TTTTATACTA
61830 AAAATAATATAA-TAAATAT
1 AAAATAATA-AATTAAATAT
61849 AAAATAATAAATTTAAATAT
1 AAAATAATAAA-TTAAATAT
61869 AA
1 AA
61871 TTAACATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.10
19 9 0.45
20 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATAATAAATTAAATAT
Found at i:63592 original size:13 final size:13
Alignment explanation
Indices: 63574--63635 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
63564 TTTAAAAAAT
*
63574 TTTAAATTTTATA
1 TTTAAATTTTAAA
63587 TTTAAA-TTTAAA
1 TTTAAATTTTAAA
63599 TTTAAATTAATTAAA
1 TTTAAATT--TTAAA
* *
63614 TTT-AGTTTATAGA
1 TTTAAATTT-TAAA
63627 TTTAAATTT
1 TTTAAATTT
63636 ATTATTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 12 0.30
13 13 0.32
14 7 0.17
15 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
TTTAAATTTTAAA
Found at i:63595 original size:6 final size:6
Alignment explanation
Indices: 63574--63636 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
63564 TTTAAAAAAT
* *
63574 TTTAAA TTTTATA TTTAAA TTTAAA TTTAAA -TT-AA -TTAAA TTT-AG
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
63619 TTTATAGA TTTAAA TTTA
1 TTTA-A-A TTTAAA TTTA
63637 TTATTTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
4 4 0.09
5 8 0.17
6 24 0.51
7 7 0.15
8 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:63680 original size:14 final size:14
Alignment explanation
Indices: 63661--63688 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63651 TAAAATTAAA
63661 AATATTTTTATATT
1 AATATTTTTATATT
63675 AATATTTTTATATT
1 AATATTTTTATATT
63689 TTATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:64363 original size:17 final size:17
Alignment explanation
Indices: 64320--64366 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
64310 ATTTAAATAA
*
64320 AAATATATTATTTTAATTT
1 AAAT-TATTA-TTTAAGTT
64339 ATAATTATTATTTAAGTT
1 A-AATTATTATTTAAGTT
64357 AAATTATTAT
1 AAATTATTAT
64367 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 9 0.35
18 8 0.31
19 6 0.23
20 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AAATTATTATTTAAGTT
Found at i:65483 original size:2 final size:2
Alignment explanation
Indices: 65476--65501 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65466 TTCATTAATT
65476 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
65502 GAAGGAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72256 original size:1 final size:1
Alignment explanation
Indices: 72250--72275 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
72240 AATTGAGAGG
72250 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
72276 CATCTAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:77572 original size:21 final size:23
Alignment explanation
Indices: 77548--77589 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
77538 TAAATTTAAA
77548 AAATA-ATTT-TAAAAATATATT
1 AAATATATTTATAAAAATATATT
*
77569 AAATATATTTATATAAATATA
1 AAATATATTTATAAAAATATA
77590 AATTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATATATTTATAAAAATATATT
Found at i:77798 original size:9 final size:8
Alignment explanation
Indices: 77784--77820 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
77774 AATTGGGTAG
77784 AAAAAAAT
1 AAAAAAAT
77792 AAAAAAAT
1 AAAAAAAT
77800 AAAAAAAT
1 AAAAAAAT
*
77808 -GAAAAAT
1 AAAAAAAT
77815 AAAAAA
1 AAAAAA
77821 CATGAACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:77803 original size:15 final size:16
Alignment explanation
Indices: 77784--77820 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
77774 AATTGGGTAG
77784 AAAAAAATAAAAAAAT
1 AAAAAAATAAAAAAAT
*
77800 AAAAAAAT-GAAAAAT
1 AAAAAAATAAAAAAAT
77815 AAAAAA
1 AAAAAA
77821 CATGAACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:77825 original size:16 final size:15
Alignment explanation
Indices: 77784--77826 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
77774 AATTGGGTAG
*
77784 AAAAAAATAAAAAAAT
1 AAAAAAAT-GAAAAAT
77800 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
77815 AAAAAACATGAA
1 AAAAAA-ATGAA
77827 CCCTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (15 bp):
AAAAAAATGAAAAAT
Found at i:78544 original size:22 final size:22
Alignment explanation
Indices: 78513--78566 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
78503 AGTATTTAAA
* *
78513 AATATGATTAAATTTTTTTAATT
1 AATAT-ATTAAAATTTTATAATT
* *
78536 ATTATATTAAAATTTTATATTT
1 AATATATTAAAATTTTATAATT
78558 AATATATTA
1 AATATATTA
78567 TTTTTATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATATATTAAAATTTTATAATT
Found at i:79638 original size:11 final size:12
Alignment explanation
Indices: 79611--79637 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
79601 GTGTCTCAAA
79611 TTTTCTTTCTTT
1 TTTTCTTTCTTT
79623 TTTTCTTTCTTT
1 TTTTCTTTCTTT
79635 TTT
1 TTT
79638 CCACCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:80332 original size:22 final size:21
Alignment explanation
Indices: 80290--80362 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
80280 TTGTATACAA
*
80290 TTTAAATAAAT-TTATTATTT
1 TTTAAATAAATATTATTTTTT
80310 TTTAAATTAAATATTATTTTTT
1 TTTAAA-TAAATATTATTTTTT
** *
80332 TAAAAAATAAATA-TATTTTTA
1 T-TTAAATAAATATTATTTTTT
80353 TTTATAATAA
1 TTTA-AATAA
80363 CAATATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
20 7 0.16
21 18 0.42
22 15 0.35
23 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAATAAATATTATTTTTT
Found at i:80508 original size:16 final size:17
Alignment explanation
Indices: 80482--80523 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
80472 AATTTTTTAA
80482 AAAATTTTAAATAAAATT
1 AAAA-TTTAAATAAAATT
* *
80500 -AAATTTAAATTAATTT
1 AAAATTTAAATAAAATT
80516 AAAATTTA
1 AAAATTTA
80524 TTTTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTTAAATAAAATT
Found at i:80572 original size:21 final size:22
Alignment explanation
Indices: 80527--80577 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
80517 AAATTTATTT
*
80527 TATTATTTATAGTAATATTAAA
1 TATTATTTTTAGTAATATTAAA
* *
80549 TATTATTTTTA-TATTATTATA
1 TATTATTTTTAGTAATATTAAA
80570 TA-TATTTT
1 TATTATTTT
80578 ATTAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.23
21 10 0.38
22 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTATTTTTAGTAATATTAAA
Found at i:81323 original size:15 final size:15
Alignment explanation
Indices: 81294--81331 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
81284 TAAATAAATT
*
81294 TTTAAA-TAGTTTAA
1 TTTAAATTAATTTAA
81308 TTTAAATTAATTTAA
1 TTTAAATTAATTTAA
81323 TTTAAATTA
1 TTTAAATTA
81332 TTATGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTAAATTAATTTAA
Found at i:81411 original size:6 final size:7
Alignment explanation
Indices: 81394--81419 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
81384 TAATATAAAT
81394 TTTTTTA
1 TTTTTTA
81401 TTTTTTA
1 TTTTTTA
81408 TTTTTTA
1 TTTTTTA
81415 TTTTT
1 TTTTT
81420 GCTACGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:81750 original size:19 final size:17
Alignment explanation
Indices: 81709--81768 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 17
81699 AATGTATGTA
*
81709 TTATAATTATATTTTTAT
1 TTATAA-TATATTTATAT
81727 ATTATAATATATTTAATAAT
1 -TTATAATATATTT-AT-AT
**
81747 TTATTTTATATTTATAT
1 TTATAATATATTTATAT
81764 TTATA
1 TTATA
81769 TAATTATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 6 0.17
18 9 0.26
19 18 0.51
20 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATAATATATTTATAT
Found at i:81762 original size:6 final size:6
Alignment explanation
Indices: 81709--81769 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
81699 AATGTATGTA
* * *
81709 TTATAA TTATAT TTTTAT ATTATA- ATATAT TTAATAAT TTAT-T TTATAT
1 TTATAT TTATAT TTATAT -TTATAT TTATAT TT-AT-AT TTATAT TTATAT
81758 TTATAT TTATAT
1 TTATAT TTATAT
81770 AATTATATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
5 9 0.20
6 24 0.53
7 8 0.18
8 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTATAT
Found at i:82580 original size:2 final size:2
Alignment explanation
Indices: 82573--82598 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
82563 CTTTTTATTT
82573 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
82599 AATTAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83190 original size:19 final size:18
Alignment explanation
Indices: 83166--83207 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
83156 TAGGTCAAGA
83166 ATATAAATATGATATAAAT
1 ATATAAATATGATA-AAAT
**
83185 ATATAAATATTTTAAAAT
1 ATATAAATATGATAAAAT
83203 ATATA
1 ATATA
83208 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATAAATATGATAAAAT
Found at i:83418 original size:5 final size:5
Alignment explanation
Indices: 83408--83490 Score: 84
Period size: 5 Copynumber: 16.8 Consensus size: 5
83398 AGATCATCTG
83408 ATATT ATATT ATATT ATATT ATATT ATATT ATATTT ATATT AT-TT -T-TT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATA-TT ATATT ATATT ATATT
* **
83456 ATATT TTAATAT ATATT -TAAA ATATT ATATT ATAT
1 ATATT AT-AT-T ATATT ATATT ATATT ATATT ATAT
83491 AAATTTTAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
3 3 0.05
4 5 0.08
5 47 0.71
6 9 0.14
7 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:83467 original size:26 final size:26
Alignment explanation
Indices: 83408--83490 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
83398 AGATCATCTG
83408 ATATTATA-TTATATTATATTATATT
1 ATATTATATTTATATTATATTATATT
83433 ATATTATATTTATATTAT-TT-T-TT
1 ATATTATATTTATATTATATTATATT
* * **
83456 ATATTTTAATATATATT-TAAAATATT
1 ATATTAT-ATTTATATTATATTATATT
83482 ATATTATAT
1 ATATTATAT
83491 AAATTTTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
23 9 0.19
24 9 0.19
25 13 0.27
26 17 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTATATTTATATTATATTATATT
Found at i:83470 original size:12 final size:12
Alignment explanation
Indices: 83455--83504 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
83445 TATTATTTTT
83455 TATATTTTAATA
1 TATATTTTAATA
*
83467 TATA-TTTAAAA
1 TATATTTTAATA
*
83478 TATTATATT-ATA
1 TA-TATTTTAATA
*
83490 TAAATTTTAATA
1 TATATTTTAATA
83502 TAT
1 TAT
83505 TAATAATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
11 12 0.41
12 15 0.52
13 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATTTTAATA
Found at i:83497 original size:35 final size:33
Alignment explanation
Indices: 83458--83563 Score: 112
Period size: 33 Copynumber: 3.2 Consensus size: 33
83448 TATTTTTTAT
83458 ATTTTAATATATATTTAA-AATATTATATTATATAA
1 ATTTTAA-ATATA-TTAATAAT-TTATATTATATAA
*
83493 ATTTT-AATATATTAATAATTTATTTTATATAA
1 ATTTTAAATATATTAATAATTTATATTATATAA
* *
83525 ATTTTAACATAT-TT-ATATATTTATATCATATTA
1 ATTTTAA-ATATATTAATA-ATTTATATTATATAA
83558 ATTTTA
1 ATTTTA
83564 TTTTTTTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
32 24 0.38
33 29 0.46
34 5 0.08
35 5 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (33 bp):
ATTTTAAATATATTAATAATTTATATTATATAA
Found at i:83526 original size:32 final size:32
Alignment explanation
Indices: 83466--83563 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
83456 ATATTTTAAT
83466 ATATATTTAA-AATATTATATTATATAAATTTTA
1 ATATA-TTAATAAT-TTATATTATATAAATTTTA
*
83499 ATATATTAATAATTTATTTTATATAAATTTTA
1 ATATATTAATAATTTATATTATATAAATTTTA
* * * *
83531 ACATATTTATATATTTATATCATATTAATTTTA
1 ATATATTAATA-ATTTATATTATATAAATTTTA
83564 TTTTTTTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
32 31 0.54
33 26 0.46
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATATTAATAATTTATATTATATAAATTTTA
Found at i:83530 original size:16 final size:16
Alignment explanation
Indices: 83475--83530 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
83465 TATATATTTA
* *
83475 AAATATTATATTATAT
1 AAATTTTATTTTATAT
* *
83491 AAATTTTAATATAT-T
1 AAATTTTATTTTATAT
*
83506 AATAATTTATTTTATAT
1 AA-ATTTTATTTTATAT
83523 AAATTTTA
1 AAATTTTA
83531 ACATATTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTTTATTTTATAT
Found at i:83539 original size:65 final size:62
Alignment explanation
Indices: 83413--83563 Score: 144
Period size: 65 Copynumber: 2.4 Consensus size: 62
83403 ATCTGATATT
* * * * * *
83413 ATATTATATTATATTATATTATATTATATTTATATTATTTTTTATATTTTAATATATATTTAAA
1 ATATTATATTATA-TAAATTTTAATATATTAATATTATTTTTTAAATTTTAATACATATTT-AA
83477 ATATTATATTATATAAATTTTAATATATTAATAATTTATTTTATATAAATTTT-A-ACATATTTA
1 ATATTATATTATATAAATTTTAATATATTAAT-A-TTATTTT-T-TAAATTTTAATACATATTTA
*
83540 T
62 A
* *
83541 ATATTTATATCATATTAATTTTA
1 ATA-TTATATTATATAAATTTTA
83564 TTTTTTTATA
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
63 15 0.21
64 18 0.25
65 31 0.42
66 2 0.03
67 7 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (62 bp):
ATATTATATTATATAAATTTTAATATATTAATATTATTTTTTAAATTTTAATACATATTTAA
Found at i:83910 original size:24 final size:25
Alignment explanation
Indices: 83882--83940 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
83872 AATTATATAA
* *
83882 ATAATATAATATGTTAA-ATAAAAT
1 ATAATATAATATATAAATATAAAAT
83906 ATAATATAAATATATAAATATAAAAT
1 ATAATAT-AATATATAAATATAAAAT
83932 A-AATA-AATA
1 ATAATATAATA
83941 AATTATGCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 4 0.13
24 7 0.23
25 12 0.39
26 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
ATAATATAATATATAAATATAAAAT
Found at i:83924 original size:19 final size:19
Alignment explanation
Indices: 83896--83943 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
83886 TATAATATGT
*
83896 TAAATAAAATATAATATAAA
1 TAAAT-AAATATAAAATAAA
*
83916 TATATAAATATAAAATAAA
1 TAAATAAATATAAAATAAA
83935 TAAATAAAT
1 TAAATAAAT
83944 TATGCGATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAATAAATATAAAATAAA
Found at i:83937 original size:15 final size:14
Alignment explanation
Indices: 83876--83940 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 14
83866 ATTAAAAATT
83876 ATATAAATAATATAA
1 ATATAAATAA-ATAA
*
83891 TATGTTAAATAAAATATA
1 -AT-ATAAAT-AAATA-A
*
83909 ATATAAATATATAA
1 ATATAAATAAATAA
83923 ATATAAAATAAATAA
1 ATAT-AAATAAATAA
83938 ATA
1 ATA
83941 AATTATGCGA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.12
15 16 0.39
16 7 0.17
17 10 0.24
18 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
ATATAAATAAATAA
Found at i:85712 original size:29 final size:29
Alignment explanation
Indices: 85670--85728 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
85660 CCTAGCTTTG
85670 GTTATGAAATAATA-AAAACAAAAAAAAAA
1 GTTATGAAATAATAGAAAA-AAAAAAAAAA
*
85699 GTTAT-AAATAAATAGAAAAATAAAAAAAA
1 GTTATGAAAT-AATAGAAAAAAAAAAAAAA
85728 G
1 G
85729 ATAATTTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 4 0.15
29 19 0.70
30 4 0.15
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (29 bp):
GTTATGAAATAATAGAAAAAAAAAAAAAA
Found at i:86852 original size:15 final size:15
Alignment explanation
Indices: 86822--86865 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
86812 TGGTTTTCAA
*
86822 AAAAATAATAATAAAT
1 AAAAA-AATAAAAAAT
**
86838 AAGTAAATAAAAAAT
1 AAAAAAATAAAAAAT
86853 AAAAAAATAAAAA
1 AAAAAAATAAAAA
86866 GTGTTTTTCG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:90258 original size:28 final size:28
Alignment explanation
Indices: 90216--90286 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
90206 GGAATTAAGC
** *
90216 CGGGGTT-GAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
90243 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
90271 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
90287 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 7 0.18
28 31 0.82
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:90337 original size:51 final size:51
Alignment explanation
Indices: 90279--90401 Score: 135
Period size: 50 Copynumber: 2.4 Consensus size: 51
90269 AACGAGGTTG
* * *
90279 GAGTATCCTCGATTGTGA-AAAATTGGTATTTTTGAAAAT-AAATCGGAGTTA
1 GAGTATCCCCGATTGTGAGAAAATTAG--TGTTTGAAAATAAAATCGGAGTTA
** *
90330 GAGTATCCCCGATT-AAAGAAAATTAGTGTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAGAAAATTAGTGTTTGAAAATAAAATCGGAGTTA
*
90380 GAATATCCCCGATTGTGGAGAA
1 GAGTATCCCCGATTGT-GAGAA
90402 TTGAGAAACT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
49 10 0.17
50 25 0.42
51 20 0.34
52 4 0.07
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAAATTAGTGTTTGAAAATAAAATCGGAGTTA
Done.