Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 28 of 32
Found at i:3984621 original size:23 final size:23
Alignment explanation
Indices: 3984593--3984641 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
3984583 TGAAGTTATA
3984593 TCATGAAGAAAACTTAAAGAAAG
1 TCATGAAGAAAACTTAAAGAAAG
*
3984616 TCATGAAGAAAACTTGAAGAAAG
1 TCATGAAGAAAACTTAAAGAAAG
3984639 TCA
1 TCA
3984642 CATAAAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.53, C:0.10, G:0.18, T:0.18
Consensus pattern (23 bp):
TCATGAAGAAAACTTAAAGAAAG
Found at i:3984954 original size:10 final size:9
Alignment explanation
Indices: 3984936--3984976 Score: 55
Period size: 10 Copynumber: 4.2 Consensus size: 9
3984926 ATCCACTATC
3984936 TTTTCTTTT
1 TTTTCTTTT
3984945 TTTCTCTTTT
1 TTT-TCTTTT
3984955 TTTTCTTTTT
1 TTTTC-TTTT
3984965 CTTTTCTTTT
1 -TTTTCTTTT
3984975 TT
1 TT
3984977 GGTTTTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.24
10 17 0.59
11 5 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:3984954 original size:15 final size:15
Alignment explanation
Indices: 3984934--3984976 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3984924 AAATCCACTA
3984934 TCTTTTCTTTTTTTC
1 TCTTTTCTTTTTTTC
*
3984949 TCTTTT-TTTTCTTTT
1 TCTTTTCTTTT-TTTC
3984964 TCTTTTCTTTTTT
1 TCTTTTCTTTTTT
3984977 GGTTTTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TCTTTTCTTTTTTTC
Found at i:3984957 original size:11 final size:10
Alignment explanation
Indices: 3984936--3984976 Score: 57
Period size: 11 Copynumber: 4.1 Consensus size: 10
3984926 ATCCACTATC
3984936 TTTTCTTTTT
1 TTTTCTTTTT
*
3984946 TTCTC-TTTT
1 TTTTCTTTTT
3984955 TTTTCTTTTT
1 TTTTCTTTTT
3984965 CTTTTCTTTTT
1 -TTTTCTTTTT
3984976 T
1 T
3984977 GGTTTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.30
10 9 0.33
11 10 0.37
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:3984960 original size:19 final size:20
Alignment explanation
Indices: 3984936--3984976 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3984926 ATCCACTATC
3984936 TTTTCTTTTT-TTCTCTTTT
1 TTTTCTTTTTCTTCTCTTTT
*
3984955 TTTTCTTTTTCTTTTCTTTT
1 TTTTCTTTTTCTTCTCTTTT
3984975 TT
1 TT
3984977 GGTTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTCTTTTTCTTCTCTTTT
Found at i:3984963 original size:17 final size:17
Alignment explanation
Indices: 3984943--3984975 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3984933 ATCTTTTCTT
3984943 TTTTTCTCTTT-TTTTTC
1 TTTTTCT-TTTCTTTTTC
3984960 TTTTTCTTTTCTTTTT
1 TTTTTCTTTTCTTTTT
3984976 TGGTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTC
Found at i:3985677 original size:21 final size:21
Alignment explanation
Indices: 3985652--3985741 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
3985642 ACATTGTGTT
3985652 AATACAATATGGCCTTGTATC
1 AATACAATATGGCCTTGTATC
*
3985673 GATAC-A-AT-GCCATTGTATC
1 AATACAATATGGCC-TTGTATC
* * *
3985692 AATACAATATGGCATTGCATT
1 AATACAATATGGCCTTGTATC
* *
3985713 AATATAATATGGCTTTGTATC
1 AATACAATATGGCCTTGTATC
*
3985734 GATACAAT
1 AATACAAT
3985742 CCATGTTTCT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
18 3 0.06
19 13 0.24
20 2 0.04
21 34 0.63
22 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (21 bp):
AATACAATATGGCCTTGTATC
Found at i:3986575 original size:13 final size:13
Alignment explanation
Indices: 3986554--3986583 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3986544 ATACAATGTT
*
3986554 CATTGTATCGATA
1 CATTATATCGATA
3986567 CATTATATCGATA
1 CATTATATCGATA
3986580 CATT
1 CATT
3986584 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:3986624 original size:20 final size:19
Alignment explanation
Indices: 3986599--3986686 Score: 89
Period size: 20 Copynumber: 4.8 Consensus size: 19
3986589 TTTACCTAGA
3986599 TGTATCGATACATTCTGCAT
1 TGTATCGATACATTCT-CAT
3986619 TGTATCGAT--A----CAT
1 TGTATCGATACATTCTCAT
3986632 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
* *
3986652 TGTATCGATACATTTTACAA
1 TGTATCGATACATTCT-CAT
3986672 TGTATCGATACATTC
1 TGTATCGATACATTC
3986687 AAGCATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
13 12 0.21
15 1 0.02
18 1 0.02
19 1 0.02
20 42 0.74
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATTCTCAT
Found at i:3986641 original size:33 final size:33
Alignment explanation
Indices: 3986536--3986665 Score: 144
Period size: 33 Copynumber: 4.1 Consensus size: 33
3986526 TTTTCACAAT
* * *
3986536 TTGTATCGATACAATGTTCATTGTATCGATACA
1 TTGTATCGATACATTCTGCATTGTATCGATACA
* ** * *
3986569 TTATATCGATACATTCTGGGTT-TA-C-CTAGA
1 TTGTATCGATACATTCTGCATTGTATCGATACA
3986599 -TGTATCGATACATTCTGCATTGTATCGATACA
1 TTGTATCGATACATTCTGCATTGTATCGATACA
3986631 TTGTATCGATACATTGCT-CATTGTATCGATACA
1 TTGTATCGATACATT-CTGCATTGTATCGATACA
3986664 TT
1 TT
3986666 TTACAATGTA
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
29 18 0.23
30 5 0.06
31 2 0.03
32 5 0.06
33 47 0.59
34 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (33 bp):
TTGTATCGATACATTCTGCATTGTATCGATACA
Found at i:3986665 original size:13 final size:13
Alignment explanation
Indices: 3986616--3986646 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3986606 ATACATTCTG
3986616 CATTGTATCGATA
1 CATTGTATCGATA
3986629 CATTGTATCGATA
1 CATTGTATCGATA
3986642 CATTG
1 CATTG
3986647 CTCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3988483 original size:13 final size:13
Alignment explanation
Indices: 3988465--3988490 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3988455 CAATTTTTTG
3988465 TGTATCGATACAT
1 TGTATCGATACAT
3988478 TGTATCGATACAT
1 TGTATCGATACAT
3988491 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3990304 original size:50 final size:51
Alignment explanation
Indices: 3990230--3990345 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
3990220 GTTATTTCCG
* * * *
3990230 AGGGGATACTCCAACCCCAGTTTTA-TTTCTAAATACCAATTTTCCACAAT
1 AGGGGATACTCCAACACCAATTTTATTTTCAAAACACCAATTTTCCACAAT
* *
3990280 CGGGGATACTCCAACACCAATTTTATTTTCAAAACACCAATTTTTCACAAT
1 AGGGGATACTCCAACACCAATTTTATTTTCAAAACACCAATTTTCCACAAT
3990331 AGGGGATACTCCAAC
1 AGGGGATACTCCAAC
3990346 CCCGTTATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
50 22 0.38
51 36 0.62
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (51 bp):
AGGGGATACTCCAACACCAATTTTATTTTCAAAACACCAATTTTCCACAAT
Found at i:3990385 original size:129 final size:128
Alignment explanation
Indices: 3990174--3990551 Score: 397
Period size: 129 Copynumber: 2.9 Consensus size: 128
3990164 TCAATCCCGG
* * * ** *
3990174 TTTCATTTTCAAAACATCAATTTTT-C-ATCGAGGATACTTTAACCCCGTTATTTCCGAGGGGAT
1 TTTCATTTTCAAAACACCAATTTTTACAATAGGGGATACTCCAACCCCGTTATTTCCAAGGGGAT
*
3990237 ACTCCAACCCCAGTTTTATTTCTAAATACCAATTTTCCACAATCGGGGATACTCCAACACCAA
66 ACTCCAACCCCGGTTTTATTTCTAAATACCAATTTTCCACAATCGGGGATACTCCAACACCAA
*
3990300 TTTTATTTTCAAAACACCAATTTTTCACAATAGGGGATACTCCAACCCCGTTATTTCCAAGGGGA
1 TTTCATTTTCAAAACACCAATTTTT-ACAATAGGGGATACTCCAACCCCGTTATTTCCAAGGGGA
* ** * * * ** * *
3990365 TACTTCAACCCCGGCCTTATTTTTAAATCATCGATTTTTTACAATCGGGGATACTCCAACCCCGA
65 TACTCCAACCCCGGTTTTATTTCTAAAT-ACCAATTTTCCACAATCGGGGATACTCCAACACCAA
* ** * * **
3990430 TTTCATTTTCAAAATACTGATTTTTATAATCA-GGGATACTCCAACCCTGTTATTTTTGAA-GGG
1 TTTCATTTTCAAAACACCAATTTTTACAAT-AGGGGATACTCCAACCCCGTTA-TTTCCAAGGGG
* * * **
3990493 ATACTCCAAACCCGATTTTATTTCTGGAACT-CCAATTTTCCGTAATCGGGGATACTCCA
64 ATACTCCAACCCCGGTTTTATTTCT--AAATACCAATTTTCCACAATCGGGGATACTCCA
3990552 GCCCCGTTGT
Statistics
Matches: 205, Mismatches: 39, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
126 23 0.11
128 1 0.00
129 121 0.59
130 57 0.28
131 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (128 bp):
TTTCATTTTCAAAACACCAATTTTTACAATAGGGGATACTCCAACCCCGTTATTTCCAAGGGGAT
ACTCCAACCCCGGTTTTATTTCTAAATACCAATTTTCCACAATCGGGGATACTCCAACACCAA
Found at i:3990438 original size:51 final size:50
Alignment explanation
Indices: 3990360--3990476 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 50
3990350 TTATTTCCAA
* * *
3990360 GGGGATACTTCAACCCCGGCCTTATTTT-TAAAT-CATCGATTTTTTACAATC
1 GGGGATACTCCAACCCCGGACTTATTTTCAAAATAC-T-GA-TTTTTACAATC
* *
3990411 GGGGATACTCCAACCCC-GATTTCATTTTCAAAATACTGATTTTTATAATC
1 GGGGATACTCCAACCCCGGACTT-ATTTTCAAAATACTGATTTTTACAATC
*
3990461 AGGGATACTCCAACCC
1 GGGGATACTCCAACCC
3990477 TGTTATTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
50 28 0.49
51 23 0.40
52 5 0.09
53 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGGACTTATTTTCAAAATACTGATTTTTACAATC
Found at i:3991437 original size:248 final size:248
Alignment explanation
Indices: 3990999--3991448 Score: 900
Period size: 248 Copynumber: 1.8 Consensus size: 248
3990989 AAACCTTTTC
3990999 TATAAAAAATCATCGTGTCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAA
1 TATAAAAAATCATCGTGTCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAA
3991064 CCCGGATTTGTAGTTTTCACAAAACTTCATGCATTAGAGGGAGTTACATCTAAGTAATGATAAAA
66 CCCGGATTTGTAGTTTTCACAAAACTTCATGCATTAGAGGGAGTTACATCTAAGTAATGATAAAA
3991129 ATGGAACCGAGAAATTCGAGATTTTAGTAAGACGTAGTTAGAAGGTACCAATTTCGGGCGTCGTG
131 ATGGAACCGAGAAATTCGAGATTTTAGTAAGACGTAGTTAGAAGGTACCAATTTCGGGCGTCGTG
3991194 GGGGTGCCCTCACTTCTCCGAGGTGCATAGGTGAAAAAATCACTTCTCCGAGG
196 GGGGTGCCCTCACTTCTCCGAGGTGCATAGGTGAAAAAATCACTTCTCCGAGG
3991247 TATAAAAAATCATCGTGTCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAA
1 TATAAAAAATCATCGTGTCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAA
3991312 CCCGGATTTGTAGTTTTCACAAAACTTCATGCATTAGAGGGAGTTACATCTAAGTAATGATAAAA
66 CCCGGATTTGTAGTTTTCACAAAACTTCATGCATTAGAGGGAGTTACATCTAAGTAATGATAAAA
3991377 ATGGAACCGAGAAATTCGAGATTTTAGTAAGACGTAGTTAGAAGGTACCAATTTCGGGCGTCGTG
131 ATGGAACCGAGAAATTCGAGATTTTAGTAAGACGTAGTTAGAAGGTACCAATTTCGGGCGTCGTG
3991442 GGGGTGC
196 GGGGTGC
3991449 TAATCTTTCC
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
248 202 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (248 bp):
TATAAAAAATCATCGTGTCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAA
CCCGGATTTGTAGTTTTCACAAAACTTCATGCATTAGAGGGAGTTACATCTAAGTAATGATAAAA
ATGGAACCGAGAAATTCGAGATTTTAGTAAGACGTAGTTAGAAGGTACCAATTTCGGGCGTCGTG
GGGGTGCCCTCACTTCTCCGAGGTGCATAGGTGAAAAAATCACTTCTCCGAGG
Found at i:3997073 original size:61 final size:59
Alignment explanation
Indices: 3996974--3997583 Score: 606
Period size: 55 Copynumber: 10.5 Consensus size: 59
3996964 TAGCCCTTCC
* * *
3996974 AGTCCTTAAAGAGCAGGACGTTTTTTTCCTTTTTAAAGCCCATACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACG--CTTTT-C-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
3997037 AGTCCTCAAAAAGCAAGACGTCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
3997098 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACAAAAGTTGGTGGCACCTTCT
1 AGTCCTCAAAGAGCAGGACG-CTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
*
3997159 AGTCCTCAAAGAGTAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTT
* * * *
3997220 AGTCCTCAAAGAGTAGGATGC----CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
3997275 AGTCCTCAAAGAGCAGGACGC----CTTTTAGAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * **
3997330 AATCCTCAAAGAGCAGGACGC----CTTTCAAAGCCCACACAAGTTTGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
3997385 AGTCCTCAAAGAGCAGGACGC----CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCT
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-T
* * * * *
3997440 AGTTCTGAAAGAGTAGGACGC----CTTTTAAAGCCCACACAAGTTAGTGGCA-TTTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * **
3997494 CAATCCTCAAAGAGCAGGATGCTTTCTCCTTTCAAAGCCCACACAAG-T--TGGCA-CTTCCC
1 -AGTCCTCAAAGAGCAGGACGCTTT-T-CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TT
*
3997553 AGTCCTCAAAGAGCAGGACGCTCTCTCTTTT
1 AGTCCTCAAAGAGCAGGACGCT-TTTCTTTT
3997584 CGCCCTTTTA
Statistics
Matches: 488, Mismatches: 47, Indels: 30
0.86 0.08 0.05
Matches are distributed among these distances:
54 5 0.01
55 239 0.49
56 4 0.01
57 4 0.01
58 28 0.06
59 1 0.00
60 7 0.01
61 177 0.36
62 6 0.01
63 17 0.03
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (59 bp):
AGTCCTCAAAGAGCAGGACGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
Found at i:4000834 original size:52 final size:52
Alignment explanation
Indices: 4000701--4000841 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
4000691 TGAAAAGTTA
4000701 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
4000753 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
4000805 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
4000842 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:4000848 original size:13 final size:13
Alignment explanation
Indices: 4000830--4000854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4000820 CAAAAATCAG
4000830 TGTATCGATACAA
1 TGTATCGATACAA
4000843 TGTATCGATACA
1 TGTATCGATACA
4000855 TGTGAGTAAT
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:4000938 original size:13 final size:13
Alignment explanation
Indices: 4000920--4000944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4000910 CAAAAAAATA
4000920 TGTATCGATACAT
1 TGTATCGATACAT
4000933 TGTATCGATACA
1 TGTATCGATACA
4000945 ACATTTTATG
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:4000940 original size:33 final size:33
Alignment explanation
Indices: 4000898--4000964 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4000888 AGTAGCTTAA
4000898 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
4000931 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
4000964 A
1 A
4000965 AATCATTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:4001043 original size:21 final size:21
Alignment explanation
Indices: 4001002--4001043 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4000992 GTTGGGACCT
*
4001002 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
4001023 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
4001044 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:4001921 original size:171 final size:167
Alignment explanation
Indices: 4001576--4002596 Score: 1195
Period size: 171 Copynumber: 6.1 Consensus size: 167
4001566 CCTGCCACAC
* * * * * * *
4001576 TGGACTTAAAGATGATGAGGATGAAGAGCGATAAA-AGGACCAACACGTTGATTCACGGCCAACG
1 TGGACTTAAAGATGATGATGA-GAAAAGTGATAAAGATG-CCAATATGTTGATTCATGGCCAACG
* * * ** * *
4001640 ATATTGGG-TTCAAAGATGAGAAAAAGGA--TAAAAGAGCCAATATGC--GGCTAGCAATATTGG
64 ATATTGGGCTT-AAAGATGAGAAAAAGGATGTCAACGTGCTGAT-T-CAAGGCCAGCTA-ATT-G
* *
4001700 ACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACAT
124 ACTTAAAGAT-AA-GTGCCAATATGCTGATTCAAGGCCAGCGATAT
*
4001746 TGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGAT
1 TGGACTTAAAGATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGAT
*
4001811 ATTGGGCCTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTA
66 ATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTA-ATTG-ACTTA
4001876 AAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
129 AAGAT-AAG-TGCCAATATGCTGATTCAAGGCCAGCGATAT
*
4001917 TGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGAT
1 TGGACTTAAAGATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGAT
* *
4001982 ATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTTAA-AGA-TGGA
66 ATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGC-TAATTGACT-TA
*
4002045 AA-AT--GTGCCAATATGCTGATTCAAGGCCAGCTATAT
129 AAGATAAGTGCCAATATGCTGATTCAAGGCCAGCGATAT
* * * * * * * *
4002081 TGGACTTAAAGGTGATGAGGATGAAGAGCGATAAA-AGGACCAACACGTTGATTCACGGCCAACG
1 TGGACTTAAAGATGATGATGA-GAAAAGTGATAAAGATG-CCAATATGTTGATTCATGGCCAACG
* * * ** * * *
4002145 ATATTGGG-TTCAAAGATGAGAAAAAGGA--TAAAAGAGCCAATATGC--GACTAGCGATATTGG
64 ATATTGGGCTT-AAAGATGAGAAAAAGGATGTCAACGTGCTGAT-T-CAAGGCCAGCTA-ATT-G
* *
4002205 ACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACAT
124 ACTTAAAGAT-AA-GTGCCAATATGCTGATTCAAGGCCAGCGATAT
*
4002251 TGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGAT
1 TGGACTTAAAGATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGAT
*
4002316 ATTGGGCCTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTA
66 ATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTA-ATTG-ACTTA
4002381 AAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
129 AAGAT-AAG-TGCCAATATGCTGATTCAAGGCCAGCGATAT
* *
4002422 TGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAATGAT
1 TGGACTTAAAGATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGAT
* *
4002487 ATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTTAA-AGA-TGGA
66 ATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGC-TAATTGACT-TA
*
4002550 AA-AT--GTGCCAATATGCTGATTCAAGGCCAGCTATAT
129 AAGATAAGTGCCAATATGCTGATTCAAGGCCAGCGATAT
4002586 TGGACTTAAAG
1 TGGACTTAAAG
4002597 GTGCCAATGT
Statistics
Matches: 739, Mismatches: 78, Indels: 74
0.83 0.09 0.08
Matches are distributed among these distances:
162 1 0.00
163 14 0.02
164 93 0.13
165 66 0.09
166 3 0.00
168 6 0.01
169 126 0.17
170 80 0.11
171 346 0.47
172 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (167 bp):
TGGACTTAAAGATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGAT
ATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTAATTGACTTAAA
GATAAGTGCCAATATGCTGATTCAAGGCCAGCGATAT
Found at i:4001924 original size:49 final size:49
Alignment explanation
Indices: 4001778--4001936 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
4001768 AAAAGTGATA
* * * * *
4001778 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
4001829 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
4001882 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
4001931 ATGATG
1 AAGATG
4001937 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
49 45 0.53
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:4002039 original size:45 final size:42
Alignment explanation
Indices: 4001987--4002076 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
4001977 ACGATATTGG
* *
4001987 GCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCA
1 GCTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCA
* *
4002032 GCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
1 GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
4002074 GCT
1 GCT
4002077 ATATTGGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 24 0.59
43 5 0.12
44 1 0.02
45 11 0.27
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.22
Consensus pattern (42 bp):
GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
Found at i:4002255 original size:334 final size:330
Alignment explanation
Indices: 4001714--4002736 Score: 1191
Period size: 334 Copynumber: 3.1 Consensus size: 330
4001704 AAAGATAAAG
* * *
4001714 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGAGAAAAGTGATAA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGAGAAAAGTGATAA
*
4001779 AGATGCCAATATGTTGATTCATGGCCAACGATATTGGG-CCTAAAGATGAGAAAAAGGATGTCAA
66 AGATGCCAATATGTTGATTCATGGCCAACGATATTGGGTTC-AAAGATGAGAAAAAGGA-GTCAA
* * * * *
4001843 CGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGC
129 CGTGCTGATTC---GACAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGC
*
4001908 CAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATG
191 CAGCGACATTGGACTT-AAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATG
4001973 GCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTTAA
255 GCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTTAA
4002038 AGATGGAAAAT
320 AGATGGAAAAT
* * * * *
4002049 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGATGAGGATGAAGAGCGATA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGA-GAAAAGTGATA
* * * * *
4002114 AA-AGGACCAACACGTTGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGGA-TAAA
65 AAGATG-CCAATATGTTGATTCATGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGGAGTCAA
* * ** * *
4002177 AGAGCCAATATGCGACTAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGC
129 CGTGCTGAT-T-CGAC-AGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGC
*
4002242 CAGCGACATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATG
191 CAGCGACATTGGACTTAAA-ATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATG
*
4002307 GCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGC-TAC
255 GCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTTA-
* *
4002371 ATTGAACT-TAAAGAT
319 A-AG-A-TGGAAA-AT
*
4002386 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTG
1 ---G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGAGAAAAGTG
*
4002451 ATAAAGATGCCAATATGTTGATTCATGGCCAATGATATTGGGCTT-AAAGATGAGAAAAAGGATG
62 ATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGG-TTCAAAGATGAGAAAAAGGA-G
* *
4002515 TCAACGTGCTGATTC-A-AG-GCCA---G-CTTAAAGATGGAAAATGTGCCAATATGCTGATTCA
125 TCAACGTGCTGATTCGACAGCGACATTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATTCA
* * * *
4002573 A-G---GC--CA---G-C-T---AT-AT--TG-G---ACT--TAAAGGTGCCAATGTGCTGATTC
187 AGGCCAGCGACATTGGACTTAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTC
* *
4002615 AAGGCCAATGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCT
252 ATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCT
4002680 TAAAGATGGAAAAT
317 TAAAGATGGAAAAT
*
4002694 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
4002737 GTGCCAATGT
Statistics
Matches: 601, Mismatches: 62, Indels: 81
0.81 0.08 0.11
Matches are distributed among these distances:
304 40 0.07
305 1 0.00
308 3 0.00
309 4 0.01
310 1 0.00
311 82 0.14
312 2 0.00
313 2 0.00
316 1 0.00
317 2 0.00
319 1 0.00
320 2 0.00
324 1 0.00
325 1 0.00
326 1 0.00
329 2 0.00
331 2 0.00
332 9 0.01
333 8 0.01
334 171 0.28
335 73 0.12
336 65 0.11
337 6 0.01
339 1 0.00
340 59 0.10
341 53 0.09
342 8 0.01
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (330 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGAGAAAAGTGATAA
AGATGCCAATATGTTGATTCATGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGGAGTCAACG
TGCTGATTCGACAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCG
ACATTGGACTTAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAAC
GATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGG
AAAAT
Found at i:4002429 original size:49 final size:49
Alignment explanation
Indices: 4002283--4002441 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
4002273 AAAAGTGATA
* * * * *
4002283 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
4002334 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
4002387 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
4002436 ATGATG
1 AAGATG
4002442 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
49 45 0.53
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:4002493 original size:505 final size:505
Alignment explanation
Indices: 4001576--4002599 Score: 2012
Period size: 505 Copynumber: 2.0 Consensus size: 505
4001566 CCTGCCACAC
*
4001576 TGGACTTAAAGATGATGAGGATGAAGAGCGATAAAAGGACCAACACGTTGATTCACGGCCAACGA
1 TGGACTTAAAGGTGATGAGGATGAAGAGCGATAAAAGGACCAACACGTTGATTCACGGCCAACGA
*
4001641 TATTGGGTTCAAAGATGAGAAAAAGGATAAAAGAGCCAATATGCGGCTAGCAATATTGGACTTAA
66 TATTGGGTTCAAAGATGAGAAAAAGGATAAAAGAGCCAATATGCGACTAGCAATATTGGACTTAA
4001706 AGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGAGAAA
131 AGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGAGAAA
4001771 AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGG
196 AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGG
4001836 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGAT
261 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGAT
4001901 TCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTG
326 TCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTG
4001966 ATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCC
391 ATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCC
4002031 AGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATAT
456 AGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATAT
4002081 TGGACTTAAAGGTGATGAGGATGAAGAGCGATAAAAGGACCAACACGTTGATTCACGGCCAACGA
1 TGGACTTAAAGGTGATGAGGATGAAGAGCGATAAAAGGACCAACACGTTGATTCACGGCCAACGA
*
4002146 TATTGGGTTCAAAGATGAGAAAAAGGATAAAAGAGCCAATATGCGACTAGCGATATTGGACTTAA
66 TATTGGGTTCAAAGATGAGAAAAAGGATAAAAGAGCCAATATGCGACTAGCAATATTGGACTTAA
4002211 AGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGAGAAA
131 AGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGAGAAA
4002276 AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGG
196 AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGG
4002341 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGAT
261 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGAT
4002406 TCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTG
326 TCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTG
*
4002471 ATTCATGGCCAATGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCC
391 ATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCC
4002536 AGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATAT
456 AGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATAT
4002586 TGGACTTAAAGGTG
1 TGGACTTAAAGGTG
4002600 CCAATGTGCT
Statistics
Matches: 515, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
505 515 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.23
Consensus pattern (505 bp):
TGGACTTAAAGGTGATGAGGATGAAGAGCGATAAAAGGACCAACACGTTGATTCACGGCCAACGA
TATTGGGTTCAAAGATGAGAAAAAGGATAAAAGAGCCAATATGCGACTAGCAATATTGGACTTAA
AGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGAGAAA
AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGG
ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGAT
TCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTG
ATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCC
AGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATAT
Found at i:4002573 original size:42 final size:42
Alignment explanation
Indices: 4002492--4002764 Score: 212
Period size: 43 Copynumber: 6.1 Consensus size: 42
4002482 ATGATATTGG
* *
4002492 GCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCA
1 GCTTAAAGATG-G-AAAAGG-TGCCAATGTGCTGATTCAAGGCCA
* *
4002537 GCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
1 GCTTAAAGATGGAAAAGGTGCCAATGTGCTGATTCAAGGCCA
* *
4002579 GC-TATA-TTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAATGATA
1 GCTTAAAGATGGA---AAAGGTGCCAATGTGCTGATTCAAGGCC------A
* *
4002628 TTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCA
1 ----GCTTAAAGATG-G-AAAAGG-TGCCAATGTGCTGATTCAAGGCCA
* *
4002677 GCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
1 GCTTAAAGATGGAAAAGGTGCCAATGTGCTGATTCAAGGCCA
* *
4002719 GC-TATA-TTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
1 GCTTAAAGATGGA---AAAGGTGCCAATGTGCTGATTCAAGGCCA
4002762 GCT
1 GCT
4002765 ACATTGGACT
Statistics
Matches: 186, Mismatches: 20, Indels: 45
0.74 0.08 0.18
Matches are distributed among these distances:
40 8 0.04
41 6 0.03
42 46 0.25
43 65 0.35
44 2 0.01
45 22 0.12
49 2 0.01
53 2 0.01
54 8 0.04
55 23 0.12
56 1 0.01
57 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (42 bp):
GCTTAAAGATGGAAAAGGTGCCAATGTGCTGATTCAAGGCCA
Found at i:4002675 original size:98 final size:95
Alignment explanation
Indices: 4002538--4003068 Score: 568
Period size: 98 Copynumber: 5.6 Consensus size: 95
4002528 TCAAGGCCAG
* * * *
4002538 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG-G-TGC
1 CTTAAAGAT-G-AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAGATGC
* ** *
4002601 CAATGTGCTGATTCAAGGCCAATGATATTGGG
64 CAATATGCTGATTCAAGGCCAGCGATATTGGA
* * * * * *
4002633 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGA---AAA-T
1 CTTAAAGAT--G--AAAGG-TGCCAATGTGCTGAGTCAAGGCCAGC-TACA-TTGGACTTAAAGA
*
4002694 G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
59 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
*
4002730 C-T-----T-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAT
1 CTTAAAGATGAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA-G---AT
4002788 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA
62 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA
4002822 C-T-----T-AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGAT
1 CTTAAAGATGAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AA-A-G-AGAT
4002880 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA
62 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA
4002914 CTTAAAGATG-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGAT
1 CTTAAAGATGAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AA-A-G-AGAT
4002978 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA
62 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA
4003012 CTTAAAGATG-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
1 CTTAAAGATGAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
4003069 TGAAGATGCC
Statistics
Matches: 391, Mismatches: 19, Indels: 53
0.84 0.04 0.11
Matches are distributed among these distances:
83 4 0.01
84 3 0.01
85 24 0.06
86 8 0.02
88 1 0.00
91 1 0.00
92 116 0.30
93 3 0.01
94 2 0.01
95 12 0.03
96 4 0.01
97 42 0.11
98 164 0.42
99 3 0.01
100 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (95 bp):
CTTAAAGATGAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAGATGCCA
ATATGCTGATTCAAGGCCAGCGATATTGGA
Found at i:4002704 original size:140 final size:140
Alignment explanation
Indices: 4002452--4002924 Score: 604
Period size: 140 Copynumber: 3.4 Consensus size: 140
4002442 AGAAAAGTGA
* * * *
4002452 TAAAGATGCCAATATGTTGATTCATGGCCAATGATATTGGGCTTAAAGATGAGAAAAAGGATGTC
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAGAAAAAGGATGTC
4002517 AACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCT
66 AACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCT
4002582 ATATTGGACT
131 ATATTGGACT
* *
4002592 TAAAGGTGCCAATGTGCTGATTCAAGGCCAATGATATTGGGCTTAAAGATGAGAAAAAGGATGTC
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAGAAAAAGGATGTC
4002657 AACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCT
66 AACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCT
4002722 ATATTGGACT
131 ATATTGGACT
* * * *
4002732 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCT-ACATTGGACTTAAAGAT--G--AAA--ATGC
1 TAAAGGTGCCAATATGCTGATTCAAGGCCA-ATGATATTGGACTTAAAGATGAGAAAAAGGATGT
** * * * * * *
4002790 CAATATGCTGATTCAAGGCCAGC-GATA-TTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCC
65 CAACGTGCTGATTCAAGGCCAGCTTAAAGATGGA---AAATGTGCCAATATGCTGATTCAAGGCC
*
4002853 AGCTACATTGGACT
127 AGCTATATTGGACT
**
4002867 TAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA
1 T-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGA
4002925 AGGTGCCAAT
Statistics
Matches: 299, Mismatches: 21, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
132 4 0.01
133 2 0.01
134 24 0.08
135 39 0.13
136 5 0.02
137 1 0.00
138 2 0.01
140 182 0.61
141 40 0.13
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (140 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAGAAAAAGGATGTC
AACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCT
ATATTGGACT
Found at i:4002793 original size:49 final size:49
Alignment explanation
Indices: 4002695--4003079 Score: 533
Period size: 49 Copynumber: 8.1 Consensus size: 49
4002685 ATGGAAAATG
*
4002695 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
4002738 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
4002787 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
4002830 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
4002879 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
4002928 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
4002977 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
4003026 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
4003075 TGCCA
1 TGCCA
4003080 GCTATATTGG
Statistics
Matches: 299, Mismatches: 31, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
43 70 0.23
44 4 0.01
45 2 0.01
46 3 0.01
47 1 0.00
48 3 0.01
49 216 0.72
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:4002818 original size:92 final size:94
Alignment explanation
Indices: 4002695--4003079 Score: 643
Period size: 98 Copynumber: 4.1 Consensus size: 94
4002685 ATGGAAAATG
* *
4002695 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A-AAGGTGCCAATGTGCTGATTCAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAG
*
4002758 GCCAGCTACATTGGACTTAAAGATGAAAA
66 GCCAGCTACATTGGACTTAAAGATGAAGA
4002787 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A-AAGGTGCCAATGTGCTGAGTCAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAG
4002850 GCCAGCTACATTGGACTTAAAGATGAAGA
66 GCCAGCTACATTGGACTTAAAGATGAAGA
4002879 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A-GAAGGTGCCAATGTGCTGAGT
4002944 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
62 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
4002977 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A-GAAGGTGCCAATGTGCTGAGT
4003042 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
62 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
4003075 TGCCA
1 TGCCA
4003080 GCTATATTGG
Statistics
Matches: 284, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
92 127 0.45
96 1 0.00
98 156 0.55
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (94 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAG
GCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:4003138 original size:33 final size:34
Alignment explanation
Indices: 4003099--4003163 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
4003089 GGCTTAGAGG
4003099 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
4003132 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
4003164 GGAGAAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (34 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
Found at i:4003206 original size:34 final size:33
Alignment explanation
Indices: 4003168--4003581 Score: 423
Period size: 34 Copynumber: 12.8 Consensus size: 33
4003158 AGGAAGGGAG
* *
4003168 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-GGAA
*
4003202 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
4003237 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
4003267 --A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
4003298 AAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* **
4003332 AAAGAGTGCCACAGAGTTGTGGGCTTTTAA--AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
4003364 AAA-GTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
4003397 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
4003431 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
4003463 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AGGAA
* *
4003497 AAAAGTGCCACGGAATTGTGGGCTTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
4003528 ---GGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
4003557 AAAGGTGCCACGGAGTTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTT
4003582 TGAAGAAAAA
Statistics
Matches: 326, Mismatches: 30, Indels: 50
0.80 0.07 0.12
Matches are distributed among these distances:
27 23 0.07
28 25 0.08
29 1 0.00
30 18 0.06
31 2 0.01
32 56 0.17
33 24 0.07
34 126 0.39
35 45 0.14
36 6 0.02
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:4003383 original size:160 final size:155
Alignment explanation
Indices: 4003200--4003587 Score: 532
Period size: 160 Copynumber: 2.4 Consensus size: 155
4003190 CTTAAAAGGG
4003200 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
*
4003265 AGA-GTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGCTTAGAAG
65 AGAGGTGCCACGGAGTCGTGGGCTTT-AAAGG-AAAA-GGTGCCACGGAGTTATGGACTTA-AAG
*
4003329 -GAAAAAGAGTGCCACAGAGTTGTGGGCTTTT
126 AGAAAAA-AGTGCCACAGAATTGTGGGC-TTT
*
4003360 AAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--
* *
4003425 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAA
63 --A-AAG-AGGTGCCACGGAGTCGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTATGGACTTAA
*
4003490 AGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
124 AGA-GAAAAAAGTGCCACAGAATTGTGGGCTTT
* * *
4003523 -AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAA-AAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA
4003586 GA
66 GA
4003588 AAAAATGCCA
Statistics
Matches: 208, Mismatches: 11, Indels: 24
0.86 0.05 0.10
Matches are distributed among these distances:
154 1 0.00
155 3 0.01
160 86 0.41
161 6 0.03
162 26 0.12
163 6 0.03
164 40 0.19
165 13 0.06
166 6 0.03
167 21 0.10
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (155 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA
GAGGTGCCACGGAGTCGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTATGGACTTAAAGAGAAA
AAAGTGCCACAGAATTGTGGGCTTT
Found at i:4003423 original size:194 final size:192
Alignment explanation
Indices: 4003168--4003585 Score: 539
Period size: 194 Copynumber: 2.1 Consensus size: 192
4003158 AGGAAGGGAG
*
4003168 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAG-TGCCACGGAGTTGTGGGCTTTGAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
4003231 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA-G-A-GTGCCACGGAGTCGTGGGCTTTAAA
64 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAGGTGCCACGGAGTCGTGGAC-TTAAA
* *
4003293 -AGGAAAAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCT
128 GAGGAAAAA-AGTGCCACGGAATTATGGGCTT------AAAAAGAGTGCCACAGAGTTGTGGGC-
4003357 TTTAAA-A
185 TTTAAAGA
*
4003364 AAAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
*
4003427 AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAG
66 AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGG--AAGGTGCCACGGAGTCGTGGACTTAAAG
* * * * *
4003492 ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGA
129 AGGAAAAAAGTGCCACGGAATTATGGGCTTAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA-GA
4003557 AAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAA-GTGCCACGGAGTTGTGGGCTTTGAA
4003586 GAAAAAATGC
Statistics
Matches: 200, Mismatches: 11, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
191 6 0.03
192 23 0.12
193 4 0.02
194 84 0.42
195 24 0.12
196 6 0.03
197 4 0.02
198 25 0.12
199 24 0.12
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (192 bp):
AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAGGTGCCACGGAGTCGTGGACTTAAAGAG
GAAAAAAGTGCCACGGAATTATGGGCTTAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAGA
Found at i:4003715 original size:21 final size:21
Alignment explanation
Indices: 4003674--4003715 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4003664 ATTGGGACCT
*
4003674 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
4003695 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
4003716 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:4004027 original size:55 final size:55
Alignment explanation
Indices: 4003938--4004159 Score: 282
Period size: 55 Copynumber: 3.9 Consensus size: 55
4003928 GAAGTGTCTA
* *
4003938 CAAAGCCCACACAAGTTTGTGGCATTTTTTAGTCCTCAAAGAGCAGGACGCCTTT
1 CAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCCTTT
*
4003993 CAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAACAGGACGCCTTT
1 CAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
4004048 TAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCTTTCTCCTTT
1 CAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA------CGCCTTT
* * * * *
4004109 CAAAGCCCACACAAGTTGGTGGCACTTCTCGGTCCTCAAATAGTAGGACGC
1 CAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGC
4004160 TCTCTCCTTT
Statistics
Matches: 144, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
55 98 0.68
61 46 0.32
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (55 bp):
CAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:4004244 original size:55 final size:56
Alignment explanation
Indices: 4004178--4004301 Score: 178
Period size: 55 Copynumber: 2.2 Consensus size: 56
4004168 TTCGCCCTTT
4004178 AGTCCTCAAAGAGAAAGACACCTTTCAAAGCCCACACGAGTGGGTGG-AATTTTCC
1 AGTCCTCAAAGAGAAAGACACCTTTCAAAGCCCACACGAGTGGGTGGCAATTTTCC
* * * * * *
4004233 AGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCATTTTTTC
1 AGTCCTCAAAGAGAAAGACACCTTTCAAAGCCCACACGAGTGGGTGGCAATTTTCC
*
4004289 AATCCTCAAAGAG
1 AGTCCTCAAAGAG
4004302 CAGGATGCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
55 43 0.70
56 18 0.30
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (56 bp):
AGTCCTCAAAGAGAAAGACACCTTTCAAAGCCCACACGAGTGGGTGGCAATTTTCC
Found at i:4004369 original size:61 final size:61
Alignment explanation
Indices: 4004253--4004564 Score: 351
Period size: 61 Copynumber: 5.1 Consensus size: 61
4004243 GAGTAGGACG
* ** *
4004253 CCTTTCAAAGCCCACACGAGTTGGTGGCATTTTTTCAATCCTCAAAGAGCAGGATGCTTTCT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCA-CCTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
* * *
4004315 CCTTTTAAAGACCACTCGAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
* * * *
4004376 CCTTTTAAAGACCACTCGAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGATGCTTTCT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
* ** * * * * * *
4004437 CATTGCAAAGCCCACACAAGTTGGTGGTACTTTTCAGTCCTCAAAGAACAAGACGCCTTT-T
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG-CTTTCT
* * * *
4004498 -CTTTTCAAAGCCCACACGAGTTGGTGGCACGTTTTAGTCTTCAAAGAGCAAGATGCCTTT-T
1 CCTTTT-AAAGCCCACACGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG-CTTTCT
4004559 CCTTTT
1 CCTTTT
4004565 CTCCTTTGTC
Statistics
Matches: 216, Mismatches: 31, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
60 2 0.01
61 179 0.83
62 35 0.16
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
Found at i:4004671 original size:42 final size:42
Alignment explanation
Indices: 4004555--4004691 Score: 145
Period size: 42 Copynumber: 3.2 Consensus size: 42
4004545 GCAAGATGCC
4004555 TTTTCCT-TTTCTCCTTTGTCCTCAAAGAGCAGCACACACTTCA
1 TTTTCCTCTTTCT--TTTGTCCTCAAAGAGCAGCACACACTTCA
*
4004598 -TTTCCTTCTTTTTGCTTTTGTCCTCAAAGAGCATG-ACACACTTTA
1 TTTTCC-TC--TTT-CTTTTGTCCTCAAAGAGCA-GCACACACTTCA
* * * *
4004643 TTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCG
1 TTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGCACACACTTCA
4004685 TTTTCCT
1 TTTTCCT
4004692 TTTTTCCTAT
Statistics
Matches: 81, Mismatches: 5, Indels: 17
0.79 0.05 0.17
Matches are distributed among these distances:
41 1 0.01
42 37 0.46
43 4 0.05
45 28 0.35
46 9 0.11
47 2 0.02
ACGTcount: A:0.18, C:0.28, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGCACACACTTCA
Found at i:4004769 original size:41 final size:40
Alignment explanation
Indices: 4004724--4004836 Score: 115
Period size: 41 Copynumber: 2.8 Consensus size: 40
4004714 CAGGACGTGC
*
4004724 TCTTTTTCACTTTGTCCTCAAGAAGTAGGACACT-TTCCTTT
1 TCTTTTTC-CTTTGTCCTCAAGAAGTAGGACACTATTCC-AT
* * * *
4004765 TCTTTTTTCCTTTGTCCTCAAGGAGCAAGAC-CTATTTCAT
1 TC-TTTTTCCTTTGTCCTCAAGAAGTAGGACACTATTCCAT
*
4004805 TCTCTTTTCCTTTGTCCTCAA-AAGTGGGACAC
1 TCT-TTTTCCTTTGTCCTCAAGAAGTAGGACAC
4004837 CCCCTCCATT
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
39 6 0.10
40 23 0.39
41 24 0.41
42 6 0.10
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (40 bp):
TCTTTTTCCTTTGTCCTCAAGAAGTAGGACACTATTCCAT
Found at i:4005488 original size:13 final size:13
Alignment explanation
Indices: 4005470--4005497 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4005460 ACATTTTGCA
4005470 TGTATCGATACAT
1 TGTATCGATACAT
4005483 TGTATCGATACAT
1 TGTATCGATACAT
4005496 TG
1 TG
4005498 CTTATTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4007948 original size:50 final size:51
Alignment explanation
Indices: 4007888--4008018 Score: 180
Period size: 51 Copynumber: 2.6 Consensus size: 51
4007878 GTTATTTCCG
* *
4007888 AGGGGATACTCCAACCCCGATTTTATTT-CTAAATACCAATTTTCCACAAT
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAAT
* * *
4007938 CGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAAT
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAAT
*
4007989 AAGGGATACTCCAACCCC-A--TTATTTCCAAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAA
4008019 GGGATACTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
48 11 0.15
50 27 0.38
51 34 0.47
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (51 bp):
AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAAT
Found at i:4008180 original size:157 final size:158
Alignment explanation
Indices: 4007939--4008245 Score: 366
Period size: 157 Copynumber: 1.9 Consensus size: 158
4007929 TTCCACAATC
* *
4007939 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATAAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAATTTTTCACAATAAGGGATACTCCAAC
** * * * *
4008004 CCCATTATTTCCAAAGGGATACTTTAACCCCGGCCTTATTTCT-AAATCATCGATTTTTCACAAT
66 CCCATTATTTCCAAAGGGATACTCCAACCCCGACCTTATTTCTGAAA-CACCAATTTTCCACAAT
4008068 CGGGGATACTCCAACCCCGTTATTTTCGA
130 CGGGGATACTCCAACCCCGTTATTTTCGA
* * * * * *
4008097 GGGGATACTCCAACCCCGATTTCATTTTCAAAATATCGATTTTT-ATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAATTTTTCACAATAAGGGATACTCCAAC
** * * * ** * *
4008161 CCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTGGAACACCAATTTTCCATAATC
66 CCCATTATTTCCAAAGGGATACTCCAACCCCGACCTTATTTCTGAAACACCAATTTTCCACAATC
* *
4008226 GGGGATACTCTATCCCCGTT
131 GGGGATACTCCAACCCCGTT
4008246 GTTATCTCCA
Statistics
Matches: 123, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
157 83 0.67
158 40 0.33
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (158 bp):
GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAATTTTTCACAATAAGGGATACTCCAAC
CCCATTATTTCCAAAGGGATACTCCAACCCCGACCTTATTTCTGAAACACCAATTTTCCACAATC
GGGGATACTCCAACCCCGTTATTTTCGA
Found at i:4008217 original size:78 final size:79
Alignment explanation
Indices: 4007939--4008245 Score: 330
Period size: 79 Copynumber: 3.9 Consensus size: 79
4007929 TTCCACAATC
* * *
4007939 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATAAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
* * *
4008004 CCCATTATTTCCAA
66 CCCGTTATTTTCGA
* ** *** * * * *
4008018 AGGGATACTTTAACCCCGGCCTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
4008083 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * * * *
4008097 GGGGATACTCCAACCCCGATTTCATTT-TCAAAATATCGATTTTT-ATAATCAGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTTCACAATCAGGGATACTCCAA
*
4008160 CCCTGTTATTTTCGA
65 CCCCGTTATTTTCGA
** * * * * *
4008175 GGGGATACTCCAACCCCGATTTTATTTCTGGAACACCAATTTTCCATAATCGGGGATACTCTATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
4008240 CCCGTT
66 CCCGTT
4008246 GTTATCTCCA
Statistics
Matches: 186, Mismatches: 39, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
78 67 0.36
79 119 0.64
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:4010466 original size:3 final size:3
Alignment explanation
Indices: 4010458--4010501 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4010448 AAGAATCACC
4010458 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4010502 AACAACTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4013026 original size:23 final size:25
Alignment explanation
Indices: 4012999--4013049 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
4012989 TCGTATAATA
*
4012999 TTTTTATT-TAT-ATTTTAATTATAT
1 TTTTTATTATATAATTAT-ATTATAT
4013023 TTTTTATTATATAATTATATTATAT
1 TTTTTATTATATAATTATATTATAT
4013048 TT
1 TT
4013050 AATTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 12 0.50
26 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTATTATATAATTATATTATAT
Found at i:4014551 original size:34 final size:32
Alignment explanation
Indices: 4014515--4014653 Score: 162
Period size: 32 Copynumber: 4.3 Consensus size: 32
4014505 TATATATTTT
*
4014515 TATATATTATAATTATATTTAA-AATATTATAATTTA
1 TATATATTTTAA-TATA-TTAATAAT-TTAT-A-TTA
*
4014551 TATAAATTTTAATATATTAATAATTTATATTA
1 TATATATTTTAATATATTAATAATTTATATTA
4014583 TATATATTTTAATATATTAATAATTTATATTA
1 TATATATTTTAATATATTAATAATTTATATTA
*
4014615 TATAAATTTTAATATATT-AT--TTTATATT-
1 TATATATTTTAATATATTAATAATTTATATTA
4014643 TATATTATTTT
1 TATA-TATTTT
4014654 TTTATGATAT
Statistics
Matches: 96, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
28 4 0.04
29 13 0.14
31 2 0.02
32 51 0.53
33 1 0.01
34 8 0.08
35 7 0.07
36 10 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATATATTTTAATATATTAATAATTTATATTA
Found at i:4014584 original size:32 final size:32
Alignment explanation
Indices: 4014548--4014633 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
4014538 ATATTATAAT
4014548 TTATATAAATTTTAATATATTAATAATTTATA
1 TTATATAAATTTTAATATATTAATAATTTATA
*
4014580 TTATATATATTTTAATATATTAATAATTTATA
1 TTATATAAATTTTAATATATTAATAATTTATA
4014612 TTATATAAATTTTAATATATTA
1 TTATATAAATTTTAATATATTA
4014634 TTTTATATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTATATAAATTTTAATATATTAATAATTTATA
Found at i:4014665 original size:18 final size:16
Alignment explanation
Indices: 4014556--4014653 Score: 64
Period size: 16 Copynumber: 6.3 Consensus size: 16
4014546 ATTTATATAA
*
4014556 ATTTTA-ATATATTAAT
1 ATTTTATATATA-TATT
*
4014572 AATTTATAT-TATATAT
1 ATTTTATATATATAT-T
*
4014588 ATTTTA-ATATATTAAT
1 ATTTTATATATA-TATT
* *
4014604 AATTTATAT-TATATA
1 ATTTTATATATATATT
*
4014619 AATTT-TA-ATATATT
1 ATTTTATATATATATT
*
4014633 ATTTTATATTTATATT
1 ATTTTATATATATATT
4014649 ATTTT
1 ATTTT
4014654 TTTATGATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
14 11 0.17
15 13 0.20
16 34 0.53
17 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATATATATATT
Found at i:4014673 original size:64 final size:64
Alignment explanation
Indices: 4014515--4014682 Score: 166
Period size: 64 Copynumber: 2.6 Consensus size: 64
4014505 TATATATTTT
* *
4014515 TATATATTATAATTATATTTAA-AATATTATAATTTATATAAATTTTAATATATTAATAATTTAT
1 TATATATTTTAA-TATA-TTAATAAT-TTA-AAATTATATAAATTTTAATATATTAAT-ATTTAT
4014579 ATTA
61 ATTA
*
4014583 TATATATTTTAATATATTAATAATTT-ATATTATATAAATTTTAATATATT-AT-TTTATATTTA
1 TATATATTTTAATATATTAATAATTTAAAATTATATAAATTTTAATATATTAATATTTATA-TTA
* * *
4014645 TATTATTTTTTTATGATATATCAT-ATTTAAAATTATAT
1 TA-TATATTTTAAT-ATAT-TAATAATTTAAAATTATAT
4014683 TTTAATTATT
Statistics
Matches: 87, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
61 6 0.07
62 5 0.06
63 11 0.13
64 30 0.34
65 11 0.13
66 6 0.07
67 7 0.08
68 11 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (64 bp):
TATATATTTTAATATATTAATAATTTAAAATTATATAAATTTTAATATATTAATATTTATATTA
Found at i:4015167 original size:2 final size:2
Alignment explanation
Indices: 4015160--4015201 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4015150 TTATTCATAA
4015160 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
4015202 TCTTGCTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4015493 original size:19 final size:19
Alignment explanation
Indices: 4015471--4015510 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4015461 ATAAGATTTG
* *
4015471 TTTAAAACTTATATTATTA
1 TTTAAAAATGATATTATTA
*
4015490 TTTAAAAATGATATTTTTA
1 TTTAAAAATGATATTATTA
4015509 TT
1 TT
4015511 CAAATTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTAAAAATGATATTATTA
Found at i:4018886 original size:2 final size:2
Alignment explanation
Indices: 4018881--4018909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4018871 AAAATTTATG
4018881 TA 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 TA T
4018910 TCTTTTTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4019161 original size:2 final size:2
Alignment explanation
Indices: 4019156--4019219 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
4019146 TACGTTTCAG
* *
4019156 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AG 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
*
4019198 AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
4019220 TAAATAATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4019175 original size:16 final size:16
Alignment explanation
Indices: 4019154--4019218 Score: 130
Period size: 16 Copynumber: 4.1 Consensus size: 16
4019144 TATACGTTTC
4019154 AGATATATATATATAT
1 AGATATATATATATAT
4019170 AGATATATATATATAT
1 AGATATATATATATAT
4019186 AGATATATATATATAT
1 AGATATATATATATAT
4019202 AGATATATATATATAT
1 AGATATATATATATAT
4019218 A
1 A
4019219 TTAAATAATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
AGATATATATATATAT
Found at i:4021880 original size:2 final size:2
Alignment explanation
Indices: 4021873--4021912 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4021863 AATTTTTATT
4021873 TA TA 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
4021913 GTATTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4022665 original size:48 final size:44
Alignment explanation
Indices: 4022626--4022709 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 44
4022616 AATATAATTA
* * *
4022626 ATAATTACTATTA-TT-TG-TATTTTATTTTATTTATTTATAAT
1 ATAATTAATATTATTTATGTTATATTATTTTATTTAATTATAAT
4022667 ATAATTAATATTATTTATGTTATATTATTTTATATTAAATTAT
1 ATAATTAATATTATTTATGTTATATTATTTTAT-TT-AATTAT
4022710 TAAACAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 12 0.34
42 2 0.06
43 2 0.06
44 12 0.34
45 2 0.06
46 5 0.14
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (44 bp):
ATAATTAATATTATTTATGTTATATTATTTTATTTAATTATAAT
Found at i:4023541 original size:12 final size:12
Alignment explanation
Indices: 4023509--4023547 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
4023499 CATTTTCGGC
*
4023509 TTAAATTGTAGT
1 TTAAATTTTAGT
*
4023521 TT-AACTTTAGT
1 TTAAATTTTAGT
4023532 TTAAATTTTAGT
1 TTAAATTTTAGT
4023544 TTAA
1 TTAA
4023548 TATCTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (12 bp):
TTAAATTTTAGT
Found at i:4025351 original size:33 final size:33
Alignment explanation
Indices: 4025307--4025369 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
4025297 TTGGACACAA
* *
4025307 TGTATCAATAC-ATTTCATCATGTTTCGATATAG
1 TGTATCAATACAATGTC-TCATGTATCGATATAG
*
4025340 TGTATCGATACAATGTCTCATGTATCGATA
1 TGTATCAATACAATGTCTCATGTATCGATA
4025370 CATTTCACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 22 0.85
34 4 0.15
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCAATACAATGTCTCATGTATCGATATAG
Found at i:4025445 original size:19 final size:20
Alignment explanation
Indices: 4025400--4025455 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
4025390 TTGTCAATTT
* *
4025400 CATGTATCAATTCAATTGAG
1 CATGTATCAATACAATGGAG
*
4025420 TATGTATCAATACAA-GGAG
1 CATGTATCAATACAATGGAG
**
4025439 CATGTATTGATACAATG
1 CATGTATCAATACAATG
4025456 TATCAATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGTATCAATACAATGGAG
Found at i:4033057 original size:20 final size:20
Alignment explanation
Indices: 4033032--4033087 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
4033022 ATTGGACACA
*
4033032 ATGTATCGATACATTTTATC
1 ATGTATCGATACATTTTACC
* * *
4033052 ATGTATCGATACAATGTCCC
1 ATGTATCGATACATTTTACC
*
4033072 ATGTGTCGATACATTT
1 ATGTATCGATACATTT
4033088 CACTTAGGGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTACC
Found at i:4034937 original size:44 final size:44
Alignment explanation
Indices: 4034874--4034961 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
4034864 TCTTTAAAGT
4034874 TAAAACTCTTTTTAATGAAATTTTAAAATTAGATCCAAAAAATG
1 TAAAACTCTTTTTAATGAAATTTTAAAATTAGATCCAAAAAATG
4034918 TAAAACTCTTTTTAATGAAATTTTAAAATTAGATCCAAAAAATG
1 TAAAACTCTTTTTAATGAAATTTTAAAATTAGATCCAAAAAATG
4034962 CCATTACTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (44 bp):
TAAAACTCTTTTTAATGAAATTTTAAAATTAGATCCAAAAAATG
Found at i:4038917 original size:15 final size:15
Alignment explanation
Indices: 4038893--4038936 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4038883 ATATACCATC
4038893 AATAAATTTAAATAT
1 AATAAATTTAAATAT
* *
4038908 TATAATTTTAAATAT
1 AATAAATTTAAATAT
*
4038923 AATAAAATTAAATA
1 AATAAATTTAAATA
4038937 ACACAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATAAATTTAAATAT
Found at i:4038995 original size:11 final size:11
Alignment explanation
Indices: 4038962--4039000 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
4038952 ATATACAAGC
*
4038962 TAAAACATAACA
1 TAAAA-ATAATA
4038974 TAAAAACTAATA
1 TAAAAA-TAATA
4038986 TAAAAATAATA
1 TAAAAATAATA
4038997 TAAA
1 TAAA
4039001 TATACGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:4046069 original size:21 final size:20
Alignment explanation
Indices: 4046045--4046084 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4046035 TATTATATTC
* *
4046045 TTAATTTGTATTTTTTTTTTA
1 TTAACTTGT-TTTTATTTTTA
4046066 TTAACTTGTTTTTATTTTT
1 TTAACTTGTTTTTATTTTT
4046085 CTCTATGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (20 bp):
TTAACTTGTTTTTATTTTTA
Found at i:4060647 original size:18 final size:17
Alignment explanation
Indices: 4060617--4060661 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
4060607 AATATAAATA
* *
4060617 TAAAATATTATTTTTTT
1 TAAAATATAATTTTGTT
4060634 TAAATATATAATTTTGTT
1 TAAA-ATATAATTTTGTT
*
4060652 TAAAAAATAA
1 TAAAATATAA
4060662 AGATATTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAAAATATAATTTTGTT
Found at i:4061271 original size:2 final size:2
Alignment explanation
Indices: 4061266--4061290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4061256 AAAAAGGAAG
4061266 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
4061291 CATTGCATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4063066 original size:31 final size:31
Alignment explanation
Indices: 4063031--4063090 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
4063021 GATAATGTAA
* *
4063031 TAAAAG-TCGTTGAGATTTTGATATTTAGAGC
1 TAAAAGCT-GTTGAGACTTTGATAGTTAGAGC
4063062 TAAAAGCTGTTGAGACTTTGATAGTTAGA
1 TAAAAGCTGTTGAGACTTTGATAGTTAGA
4063091 TTGGAGGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (31 bp):
TAAAAGCTGTTGAGACTTTGATAGTTAGAGC
Found at i:4064075 original size:2 final size:2
Alignment explanation
Indices: 4064068--4064103 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4064058 AAAAAGCTGA
4064068 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
4064104 TGTAAACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4066087 original size:33 final size:33
Alignment explanation
Indices: 4065993--4066087 Score: 95
Period size: 33 Copynumber: 2.8 Consensus size: 33
4065983 GATGGAGAAT
* * *
4065993 TAATTTATTTAAATTTTTTTATGTTTAAAATATTA
1 TAATTTATTT-AATTATTTTATATTT-AAATAATA
* *
4066028 TAAAGTTATTTAA-AATTTTATATTTAAATAATA
1 T-AATTTATTTAATTATTTTATATTTAAATAATA
4066061 TAATTTATCTTAATTATTTTAT-TTTAA
1 TAATTTAT-TTAATTATTTTATATTTAA
4066088 CTTTAATTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
32 6 0.12
33 17 0.34
34 16 0.32
35 3 0.06
36 8 0.16
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (33 bp):
TAATTTATTTAATTATTTTATATTTAAATAATA
Found at i:4067709 original size:41 final size:40
Alignment explanation
Indices: 4067621--4067716 Score: 120
Period size: 41 Copynumber: 2.4 Consensus size: 40
4067611 GGGATCAGGT
* * * * *
4067621 TTTATGCTTTTAAAATATGTAATTTTCACTTTAGGATAAG
1 TTTATACTTTTAAAATATATAATTATCACTTTAAGATAAA
4067661 TTCTATACTTTTAAAATATATAATTATCACTTTAAGATAAA
1 TT-TATACTTTTAAAATATATAATTATCACTTTAAGATAAA
*
4067702 TCTTATACTCTTAAA
1 T-TTATACTTTTAAA
4067717 TATTTAACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.04
41 45 0.94
42 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (40 bp):
TTTATACTTTTAAAATATATAATTATCACTTTAAGATAAA
Found at i:4067925 original size:19 final size:19
Alignment explanation
Indices: 4067897--4067939 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4067887 CATACTCAAA
* *
4067897 TTATTTTTTGACTTTTTC-T
1 TTATTCTTTG-CTTTCTCAT
4067916 TTATTCTTTGCTTTCTCAT
1 TTATTCTTTGCTTTCTCAT
4067935 TTATT
1 TTATT
4067940 TCTACCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.70
Consensus pattern (19 bp):
TTATTCTTTGCTTTCTCAT
Found at i:4071910 original size:15 final size:15
Alignment explanation
Indices: 4071867--4071910 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4071857 TAAACCTAAT
4071867 TGACCTGAACCTAAAA
1 TGACCTGAACC-AAAA
*
4071883 TG-CCTTAACCCAAAA
1 TGACCTGAA-CCAAAA
4071898 TGACCTGAACCAA
1 TGACCTGAACCAA
4071911 TTAACCTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.18
Consensus pattern (15 bp):
TGACCTGAACCAAAA
Found at i:4072208 original size:16 final size:16
Alignment explanation
Indices: 4072173--4072213 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
4072163 ATTATTTTTG
4072173 AAAATATTTGTGTACA
1 AAAATATTTGTGTACA
*
4072189 AAAAGTATTTGTGTATA
1 AAAA-TATTTGTGTACA
4072206 AAAATATT
1 AAAATATT
4072214 ACAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (16 bp):
AAAATATTTGTGTACA
Found at i:4074441 original size:21 final size:21
Alignment explanation
Indices: 4074417--4074460 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4074407 TTTTTGCCAA
* *
4074417 AATGTATCGATACATGCCCTT
1 AATGTATCAATACAAGCCCTT
*
4074438 AATGTATCAATACAAGGCCTT
1 AATGTATCAATACAAGCCCTT
4074459 AA
1 AA
4074461 CGGTCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (21 bp):
AATGTATCAATACAAGCCCTT
Found at i:4074516 original size:20 final size:21
Alignment explanation
Indices: 4074491--4074544 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
4074481 TCACAATTTT
4074491 TATCGATACATTGT-TCATTG
1 TATCGATACATTGTCTCATTG
4074511 TATCGATACATT-TCTCATTG
1 TATCGATACATTGTCTCATTG
4074531 TATCGATACATTGT
1 TATCGATACATTGT
4074545 ATCGATACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (21 bp):
TATCGATACATTGTCTCATTG
Found at i:4074544 original size:13 final size:13
Alignment explanation
Indices: 4074526--4074555 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4074516 ATACATTTCT
4074526 CATTGTATCGATA
1 CATTGTATCGATA
4074539 CATTGTATCGATA
1 CATTGTATCGATA
4074552 CATT
1 CATT
4074556 CTAGGTTTAC
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:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:4074596 original size:20 final size:20
Alignment explanation
Indices: 4074571--4074625 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4074561 TTTACCCAGA
*
4074571 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
4074591 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
*
4074611 TGTATCGATATATTG
1 TGTATCGATACATTG
4074626 TATCGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:4074627 original size:13 final size:13
Alignment explanation
Indices: 4074608--4074638 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4074598 ATACATTGCT
4074608 CATTGTATCGATA
1 CATTGTATCGATA
*
4074621 TATTGTATCGATA
1 CATTGTATCGATA
4074634 CATTG
1 CATTG
4074639 CTCATATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:4077265 original size:78 final size:78
Alignment explanation
Indices: 4076960--4077293 Score: 323
Period size: 79 Copynumber: 4.2 Consensus size: 78
4076950 TTTCATCTCG
* * * *
4076960 GGGATACTCCAATCCCATTATTTCCGAAGGGATACTCCAACCCTGATTTTATTTCTAAAATACCA
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGATTTTATTTCTAAAACACC-
4077025 AATTTTCACAAT-A
65 AATTTTCACAATCA
** * *** *
4077038 GGGAATACTCCAACCCCGTTATTTCTAAGGGGATACTTCAACCCTGGCCTTATTTCTAAATCATC
1 GGG-ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGATTTTATTTCTAAAACA-C
* * **
4077103 GATTTTTCACAATTG
64 CAATTTTCACAATCA
* * * * * *
4077118 GGGATACTTCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCGATTTCATTT-TCAAAATACC
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGATTTTATTTCT-AAAACACC
* * *
4077182 GATTTTTATAATCA
65 AATTTTCACAATCA
* **
4077196 GGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACTCC-GATTTTATTTCTGGAACACC
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAAC-CCTGATTTTATTTCTAAAACACC
* *
4077260 AATTTTCCATAATCG
65 AATTTT-CACAATCA
*
4077275 GGGATACTCCAGCCCCGTT
1 GGGATACTCCAACCCCGTT
4077294 GTTATCTCCA
Statistics
Matches: 202, Mismatches: 47, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
78 69 0.34
79 129 0.64
80 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGATTTTATTTCTAAAACACCA
ATTTTCACAATCA
Found at i:4077265 original size:157 final size:158
Alignment explanation
Indices: 4076957--4077293 Score: 380
Period size: 157 Copynumber: 2.1 Consensus size: 158
4076947 ATTTTTCATC
* * * *
4076957 TCGGGGATACTCCAATCCCATTATTTCCGAAGGGATACTCCAACCCTGATTTTATTTCTAAAATA
1 TCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTCATTTCTAAAATA
* * *
4077022 CCAAATTTTCACAATAGGGAATACTCCAACCCCGTTATTTCTAAGGGGATACTTCAACCCTGGCC
66 CCAAATTTTCACAATAGGGAATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCTGACC
* * *
4077087 TTATTTCTAAATCATCGATTTTTCACAA
131 TTATTTCTAAATCACCAATTTTCCACAA
* * *
4077115 TTGGGGATACTTCAACCCCGTTATTTTCG-AGGGAATACTCCAACCCCGATTTCATTT-TCAAAA
1 TCGGGGATACTCCAACCCCGTTATTTCCGAAGGG-ATACTCCAACCCCGATTTCATTTCT-AAAA
* * * * *
4077178 TACC-GATTTTTATAATCAGGG-ATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACTCC-
64 TACCAAATTTTCACAAT-AGGGAATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAAC-CCT
** * *
4077240 GATTTTATTTCTGGAA-CACCAATTTTCCATAA
127 GACCTTATTTCT-AAATCACCAATTTTCCACAA
*
4077272 TCGGGGATACTCCAGCCCCGTT
1 TCGGGGATACTCCAACCCCGTT
4077294 GTTATCTCCA
Statistics
Matches: 149, Mismatches: 25, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
157 88 0.59
158 61 0.41
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (158 bp):
TCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTCATTTCTAAAATA
CCAAATTTTCACAATAGGGAATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCTGACC
TTATTTCTAAATCACCAATTTTCCACAA
Found at i:4078406 original size:33 final size:33
Alignment explanation
Indices: 4078351--4078415 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
4078341 TACCACTGTT
*
4078351 TGTATCGATACATGGCACATTGTATTGATACAA
1 TGTATCGATACATGGCACATTGTATCGATACAA
4078384 TGTATCGATACATGATG-A-ATTGTATCGATACA
1 TGTATCGATACATG--GCACATTGTATCGATACA
4078416 TTGCTTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGGCACATTGTATCGATACAA
Found at i:4079280 original size:86 final size:86
Alignment explanation
Indices: 4079135--4079307 Score: 292
Period size: 86 Copynumber: 2.0 Consensus size: 86
4079125 ATTAATCCTT
*
4079135 GGGCTTTCAATTGGTATCAAAGCCTAACCTCCTTTCAACGGATTCACACTTGGGAGAGACGATCT
1 GGGCTTTCAATTGGTATCAAAGCCTAACCTCCTTTCAACGGATTCACACCTGGGAGAGACGATCT
4079200 TCTTCAGCTCAAGAATGAAAA
66 TCTTCAGCTCAAGAATGAAAA
* * * *
4079221 GGGCTTTCAATTGGTATCAGAGCCTAACTTCCTTTTAATGGATTCACACCTGGGAGAGACGATCT
1 GGGCTTTCAATTGGTATCAAAGCCTAACCTCCTTTCAACGGATTCACACCTGGGAGAGACGATCT
*
4079286 TCTTCAGCTCAAGAATGGAAA
66 TCTTCAGCTCAAGAATGAAAA
4079307 G
1 G
4079308 TGCAGCAATG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (86 bp):
GGGCTTTCAATTGGTATCAAAGCCTAACCTCCTTTCAACGGATTCACACCTGGGAGAGACGATCT
TCTTCAGCTCAAGAATGAAAA
Found at i:4080097 original size:3 final size:3
Alignment explanation
Indices: 4080083--4080113 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4080073 CATCAAAGAC
*
4080083 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
4080114 GTGACTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:4088671 original size:2 final size:2
Alignment explanation
Indices: 4088664--4088694 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4088654 GCATAATTTA
4088664 AT 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 AT A
4088695 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4089762 original size:2 final size:2
Alignment explanation
Indices: 4089755--4089779 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4089745 TAGTTTGAAT
4089755 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 T
4089780 TTTCAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4094890 original size:30 final size:30
Alignment explanation
Indices: 4094854--4094935 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
4094844 TTAATTTTTG
*
4094854 TATTAATATATATTAATTTATATCGA-TTT
1 TATTAATATATATTAATTTATATAGACTTT
* * * *
4094883 ATATTAATCTTTATTGATATATATAGACTTT
1 -TATTAATATATATTAATTTATATAGACTTT
* *
4094914 TATTAATATGTATCAATTTATA
1 TATTAATATATATTAATTTATA
4094936 CTAATTGGTA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 38 0.93
31 3 0.07
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (30 bp):
TATTAATATATATTAATTTATATAGACTTT
Found at i:4094905 original size:20 final size:20
Alignment explanation
Indices: 4094854--4094906 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4094844 TTAATTTTTG
*
4094854 TATTAATATATATTAATTTA
1 TATTGATATATATTAATTTA
* *
4094874 TATCGATTTATATTAATCTT-
1 TATTGATATATATTAAT-TTA
4094894 TATTGATATATAT
1 TATTGATATATAT
4094907 AGACTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (20 bp):
TATTGATATATATTAATTTA
Found at i:4095758 original size:19 final size:20
Alignment explanation
Indices: 4095731--4095770 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4095721 ACATATCTTA
*
4095731 TTTATATTTTAAAT-TATTT
1 TTTACATTTTAAATATATTT
4095750 TTTACATTTTAAATATATTT
1 TTTACATTTTAAATATATTT
4095770 T
1 T
4095771 AAAAGTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTACATTTTAAATATATTT
Found at i:4107303 original size:20 final size:21
Alignment explanation
Indices: 4107255--4107308 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
4107245 TTTTACAATT
* *
4107255 TGTATCGATATAAACAATAAA
1 TGTATCGATACATACAATAAA
* *
4107276 TATATCGATACATA-AATGAA
1 TGTATCGATACATACAATAAA
4107296 TGTATCGATACAT
1 TGTATCGATACAT
4107309 TTTCTTTGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATACAATAAA
Found at i:4111153 original size:22 final size:21
Alignment explanation
Indices: 4111125--4111248 Score: 122
Period size: 22 Copynumber: 5.7 Consensus size: 21
4111115 TGAATTTAAT
4111125 ATATGTACATACTATTATAGTC
1 ATATGTACATA-TATTATAGTC
*
4111147 ATATGTACATACTTTTATAGTC
1 ATATGTACATA-TATTATAGTC
* * * *
4111169 TTATGTATATATTTTATAGTT
1 ATATGTACATATATTATAGTC
* *
4111190 ATATATACATAATGTTATAGTC
1 ATATGTACAT-ATATTATAGTC
* *
4111212 ATATATACATATTGTTATAGTC
1 ATATGTACATA-TATTATAGTC
*
4111234 ATATGTATATATATT
1 ATATGTACATATATT
4111249 CATGCTTATT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
21 20 0.23
22 68 0.77
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (21 bp):
ATATGTACATATATTATAGTC
Found at i:4111188 original size:43 final size:44
Alignment explanation
Indices: 4111125--4111240 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 44
4111115 TGAATTTAAT
* * * * *
4111125 ATATGTACATACTATTATAGTCATATGTACATACTTTTATAGTC
1 ATATATACATATTGTTATAGTCATATGTACATAATGTTATAGTC
* * * * *
4111169 TTATGTATATATT-TTATAGTTATATATACATAATGTTATAGTC
1 ATATATACATATTGTTATAGTCATATGTACATAATGTTATAGTC
4111212 ATATATACATATTGTTATAGTCATATGTA
1 ATATATACATATTGTTATAGTCATATGTA
4111241 TATATATTCA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 36 0.61
44 23 0.39
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (44 bp):
ATATATACATATTGTTATAGTCATATGTACATAATGTTATAGTC
Found at i:4111230 original size:65 final size:65
Alignment explanation
Indices: 4111124--4111245 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 65
4111114 TTGAATTTAA
* * * *
4111124 TATATGTACATACTATTATAGTCATATGTACATACTTTTATAGTCTTATGTATATATTTTATAGT
1 TATATATACATAATATTATAGTCATATATACATACTTTTATAGTCATATGTATATATTTTATAGT
*
4111189 TATATATACATAATGTTATAGTCATATATACATA-TTGTTATAGTCATATGTATATAT
1 TATATATACATAATATTATAGTCATATATACATACTT-TTATAGTCATATGTATATAT
4111246 ATTCATGCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 2 0.04
65 49 0.96
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (65 bp):
TATATATACATAATATTATAGTCATATATACATACTTTTATAGTCATATGTATATATTTTATAGT
Found at i:4112836 original size:31 final size:28
Alignment explanation
Indices: 4112801--4112858 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
4112791 AAAATTGGTA
* *
4112801 TTTTGGAAATAAAATCGGGGTTGGAGTATC
1 TTTTTGAAA-AAAA-CGGGGTTGGAATATC
*
4112831 TTTTTGAAAATAACGGGGTTGGAATATC
1 TTTTTGAAAAAAACGGGGTTGGAATATC
4112859 CCCGATTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.56
29 3 0.12
30 8 0.32
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (28 bp):
TTTTTGAAAAAAACGGGGTTGGAATATC
Found at i:4112871 original size:79 final size:79
Alignment explanation
Indices: 4112771--4112992 Score: 248
Period size: 79 Copynumber: 2.8 Consensus size: 79
4112761 ACAATGGAGC
* * * ****
4112771 TGGAGTATCCTCGATTATGGAAAATTGGTATTTTGGAAATAAAATCGGGGTTGGAGTATCTTTTT
1 TGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGT
4112836 GAAAATAACGGGGT
66 GAAAATAACGGGGT
* * * * ** ***
4112850 TGGAATATCCCCGATTGTGGAAAATCGATGCTTTACAAATAAGGCCGGGGTTGGAGTATCCCCGT
1 TGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGT
4112915 GAAAATAACGGGGT
66 GAAAATAACGGGGT
*** *
4112929 TGGAGTATCCCCGATTGT-GAGAAATTGGTGTTTTGGAAATAAAATCAAAGTTTGAGTATCCCCG
1 TGGAGTATCCCCGATTGTGGA-AAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCG
4112993 ATTGTGAAAA
Statistics
Matches: 113, Mismatches: 29, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
78 2 0.02
79 111 0.98
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (79 bp):
TGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGT
GAAAATAACGGGGT
Found at i:4113037 original size:51 final size:51
Alignment explanation
Indices: 4112923--4113042 Score: 159
Period size: 51 Copynumber: 2.4 Consensus size: 51
4112913 GTGAAAATAA
* * * *
4112923 CGGGGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAAT
*** * *
4112974 CAAAGTTTGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAGAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAAT
4113025 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
4113043 TCAGAAAAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAAT
Found at i:4113141 original size:108 final size:108
Alignment explanation
Indices: 4112982--4113257 Score: 285
Period size: 108 Copynumber: 2.6 Consensus size: 108
4112972 ATCAAAGTTT
* * *
4112982 GAGTATCCCCGATTGTG-AAAAATTAGTATTTTAGAAATAAGATCGGGGTTGGAGTATCCCCTCA
1 GAGTATCCCCGATTATGAAAAAATCAATATTTTAGAAATAAGATCGGGGTTGGAGTATCCCCTCA
* * *
4113046 GAAAAAATG-GGATTGGAGTAT-CCTTAGTGACATAACGGGGTGG
66 GAAAAAACGAGG-TTGGAGTATCCCTGA-TGAAATAACGGGGTGG
* * *
4113089 GAGTACCCCCGATTATGAAAAAATCAATATTTTAGATACA-AAG-TTGGGGTTGGAGTATCCCTT
1 GAGTATCCCCGATTATGAAAAAATCAATATTTTAGA-A-ATAAGATCGGGGTTGGAGTATCCCCT
* *
4113152 CAGAAATAACGAGGTTGGAGTATCCCTGATGAAATAACGGGGTTG
64 CAGAAAAAACGAGGTTGGAGTATCCCTGATGAAATAACGGGGTGG
* * * *** * * * *
4113197 GAGTTTTCCCAATTATG-AAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 GAGTATCCCCGATTATGAAAAAATCAATATTTTAGAAATAAGATCGGGGTTGGAGTATCCCC
4113258 GATTGCAGTA
Statistics
Matches: 138, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
105 1 0.01
106 3 0.02
107 44 0.32
108 79 0.57
109 10 0.07
110 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (108 bp):
GAGTATCCCCGATTATGAAAAAATCAATATTTTAGAAATAAGATCGGGGTTGGAGTATCCCCTCA
GAAAAAACGAGGTTGGAGTATCCCTGATGAAATAACGGGGTGG
Found at i:4113176 original size:28 final size:28
Alignment explanation
Indices: 4113136--4113200 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
4113126 ACAAAGTTGG
4113136 GGTTGGAGTATCCCTTCA-GAAATAACGA
1 GGTTGGAGTATCCC-TCATGAAATAACGA
* *
4113164 GGTTGGAGTATCCCTGATGAAATAACGG
1 GGTTGGAGTATCCCTCATGAAATAACGA
4113192 GGTTGGAGT
1 GGTTGGAGT
4113201 TTTCCCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 2 0.06
28 32 0.94
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCTCATGAAATAACGA
Found at i:4113336 original size:51 final size:51
Alignment explanation
Indices: 4113193--4113336 Score: 173
Period size: 51 Copynumber: 2.8 Consensus size: 51
4113183 AAATAACGGG
* * * * * *
4113193 GTTGGAGTTTTCCCAATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCAGA
* * * * *
4113244 GTTGGAGTATCCCCGATTGCAG-TAAATCGATGCTTTAGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATT-AAGAAAAATTGATGTTTTGGAAATAAAATCAGA
4113295 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAAT
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAAT
4113337 GGAACTGGGA
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
50 2 0.03
51 72 0.96
52 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCAGA
Found at i:4115662 original size:20 final size:20
Alignment explanation
Indices: 4115637--4115743 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
4115627 AAAATGCCTG
*
4115637 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
*
4115657 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
4115677 AATGTATCGATACAAT----
1 AATGTATCGATACAATGAGA
* *
4115693 -A--TATCGAAACAATGAGC
1 AATGTATCGATACAATGAGA
*
4115710 AATGTATCGATACAAT-ACAA
1 AATGTATCGATACAATGA-GA
4115730 AATGTATCGATACA
1 AATGTATCGATACA
4115744 TCTGGGTAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
13 11 0.15
15 1 0.01
18 1 0.01
19 2 0.03
20 57 0.79
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:4115705 original size:33 final size:33
Alignment explanation
Indices: 4115661--4115726 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
4115651 TTGTAAAATG
*
4115661 TATCGATACAATGAGCAATGTATCGATACAATA
1 TATCGAAACAATGAGCAATGTATCGATACAATA
4115694 TATCGAAACAATGAGCAATGTATCGATACAATA
1 TATCGAAACAATGAGCAATGTATCGATACAATA
4115727 CAAAATGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (33 bp):
TATCGAAACAATGAGCAATGTATCGATACAATA
Found at i:4115777 original size:13 final size:13
Alignment explanation
Indices: 4115759--4115788 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4115749 GTAAACCCAG
*
4115759 AATGTATCGATAC
1 AATGTATCAATAC
4115772 AATGTATCAATAC
1 AATGTATCAATAC
4115785 AATG
1 AATG
4115789 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:4115795 original size:20 final size:20
Alignment explanation
Indices: 4115770--4115826 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
4115760 ATGTATCGAT
*
4115770 ACAATGTATCAATACAATGA
1 ACAATGTATCGATACAATGA
*
4115790 ACAATGTATCGGTACAATGA
1 ACAATGTATCGATACAATGA
4115810 ACAATGTATCGATACAA
1 ACAATGTATCGATACAA
4115827 ATTGTGAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.25
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:4117213 original size:21 final size:23
Alignment explanation
Indices: 4117185--4117236 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4117175 TGTAGTGATT
4117185 CTTT-GTGAAA-AGGTTAG-TTC
1 CTTTAGTGAAAGAGGTTAGTTTC
*
4117205 CTTTAGTGAAAGGGGTTAGTTTC
1 CTTTAGTGAAAGAGGTTAGTTTC
4117228 C-TTAGTGAA
1 CTTTAGTGAA
4117237 GAGATTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 14 0.50
23 4 0.14
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (23 bp):
CTTTAGTGAAAGAGGTTAGTTTC
Found at i:4117282 original size:22 final size:22
Alignment explanation
Indices: 4117254--4117452 Score: 102
Period size: 22 Copynumber: 9.1 Consensus size: 22
4117244 ATTCTCTCAG
*
4117254 TTATAGTTATATGTACATACTA
1 TTATAGTGATATGTACATACTA
* * *
4117276 TTATAGTCATATATACAT-TTA
1 TTATAGTGATATGTACATACTA
* * *
4117297 GTTATTGTGATATGTACAGACCA
1 -TTATAGTGATATGTACATACTA
* ** *
4117320 TTATTGTGATACATACATTA-TG
1 TTATAGTGATATGTACA-TACTA
* **
4117342 TTACT-GTAATATGTATGTACTA
1 TTA-TAGTGATATGTACATACTA
* * *
4117364 TTAGATTCATATGTACA-AC-A
1 TTATAGTGATATGTACATACTA
* * *
4117384 TGATAGTGATATGTACACACTG
1 TTATAGTGATATGTACATACTA
* * * *
4117406 CTATATTGATATGTATATAGTA
1 TTATAGTGATATGTACATACTA
* *
4117428 GTATTGTGATATGTACATACTA
1 TTATAGTGATATGTACATACTA
4117450 TTA
1 TTA
4117453 ATGTAATGTT
Statistics
Matches: 126, Mismatches: 43, Indels: 16
0.68 0.23 0.09
Matches are distributed among these distances:
20 14 0.11
21 8 0.06
22 101 0.80
23 3 0.02
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (22 bp):
TTATAGTGATATGTACATACTA
Found at i:4118651 original size:26 final size:26
Alignment explanation
Indices: 4118621--4118674 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
4118611 AATAAGTAAC
**
4118621 TTTTAATTACATGTTAACTTTAAGCT
1 TTTTAATTACATCCTAACTTTAAGCT
4118647 TTTTAATTACATCCTAACTTTAAGCT
1 TTTTAATTACATCCTAACTTTAAGCT
4118673 TT
1 TT
4118675 GTTTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.50
Consensus pattern (26 bp):
TTTTAATTACATCCTAACTTTAAGCT
Found at i:4119289 original size:67 final size:67
Alignment explanation
Indices: 4119163--4119289 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 67
4119153 TTTGATATGA
* * * **
4119163 AAGTTCCCTATGACCCTAATAGACACTAAAATTACCAACATACCCCTTAAAGTGTACATTCAACA
1 AAGTTCCCTATGACCCTAATAGACACCAAAATGACAAACATACCCCTTAAAGTACACATTCAACA
4119228 TG
66 TG
* * *
4119230 AAGTTCCTTATGACCCTAATAGACTCCAAAATGATAAACATA-CCCTCTAAAGTACACATT
1 AAGTTCCCTATGACCCTAATAGACACCAAAATGACAAACATACCCCT-TAAAGTACACATT
4119290 GTAGAGAACT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 4 0.08
67 47 0.92
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (67 bp):
AAGTTCCCTATGACCCTAATAGACACCAAAATGACAAACATACCCCTTAAAGTACACATTCAACA
TG
Found at i:4123459 original size:20 final size:20
Alignment explanation
Indices: 4123434--4123488 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
4123424 AAAATGCCTG
*
4123434 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGCAA
*
4123454 AATGTATCGATACAATGCAA
1 AATGTATCGATACATTGCAA
4123474 AATGTATCGATACAT
1 AATGTATCGATACAT
4123489 CTGGGTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:4124142 original size:61 final size:61
Alignment explanation
Indices: 4124065--4124253 Score: 236
Period size: 61 Copynumber: 3.1 Consensus size: 61
4124055 TACAAAGTAG
** * *
4124065 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGAGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
4124126 GAAAA-GAAAAGATGTCCTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGTGCGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * ** * *
4124187 AAAAGGAGAAGGCGTCCCACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTATGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
4124248 AAAAGG
1 AAAAGG
4124254 CATCCTGCTC
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
60 4 0.04
61 100 0.93
62 4 0.04
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (61 bp):
AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:4124396 original size:55 final size:55
Alignment explanation
Indices: 4124292--4124704 Score: 515
Period size: 55 Copynumber: 7.4 Consensus size: 55
4124282 AAAGAAGAGA
* * * * * * *
4124292 GCATCCTACTCCTTGAGGACTAGGAAGTGCCACCAACTAGTGTCGGCTTTGAAAT
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* * * * *
4124347 GCGTCCTGCCCTTTCAGAACTAGAAAATGCCACTAACTTGTGTGGGCTTTGAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* *
4124402 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAG
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTG-AA--AG
4124460 AAAGCATCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 ---GCATCCTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* * * * *
4124518 GCATCCTACTCCTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* * * *
4124573 GCATCTTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
*
4124628 GCATCCTGCTCTTTGAGGA-TTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAG
*
4124683 GCGTCCTGCTCTTTGAGGACTA
1 GCATCCTGCTCTTTGAGGACTA
4124705 AAGGGTGAAA
Statistics
Matches: 312, Mismatches: 36, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
54 6 0.02
55 248 0.79
56 4 0.01
58 4 0.01
60 2 0.01
61 48 0.15
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (55 bp):
GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:4124571 original size:27 final size:27
Alignment explanation
Indices: 4124486--4124571 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
4124476 TGAGGACTGA
4124486 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
* * * ** * *
4124513 GAAA-GGCATCCTACTCCT-TGAGGATTGG
1 AAAATGCCA-CCAACTTGTGTG-GGCTT-T
4124541 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
4124568 AAAA
1 AAAA
4124572 GGCATCTTGC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 5 0.12
27 17 0.43
28 13 0.32
29 5 0.12
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (27 bp):
AAAATGCCACCAACTTGTGTGGGCTTT
Found at i:4124793 original size:55 final size:55
Alignment explanation
Indices: 4124722--4124962 Score: 383
Period size: 55 Copynumber: 4.4 Consensus size: 55
4124712 AAAGGAGAGA
* ** *
4124722 GCATCTTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* *
4124777 GCATCCTGCTTTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
*
4124832 GCATCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* **
4124887 GCATCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
*
4124942 GCGTCCTGCTCTTTGAGGACT
1 GCATCCTGCTCTTTGAGGACT
4124963 AAAGGGTGAA
Statistics
Matches: 171, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 171 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (55 bp):
GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:4124843 original size:149 final size:149
Alignment explanation
Indices: 4124573--4124855 Score: 485
Period size: 149 Copynumber: 1.9 Consensus size: 149
4124563 GCTTTAAAAG
*
4124573 GCATCTTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCT
1 GCATCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCT
* * * *
4124638 CTTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGAC
66 CTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGAC
4124703 TAAAGGGTGAAAGGAGAGA
131 TAAAGGGTGAAAGGAGAGA
* * *
4124722 GCATCTTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCT
1 GCATCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCT
*
4124787 TTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGAC
66 CTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGAC
4124852 TAAA
131 TAAA
4124856 AAATGCCACC
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
149 125 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (149 bp):
GCATCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCT
CTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGAC
TAAAGGGTGAAAGGAGAGA
Found at i:4124880 original size:204 final size:205
Alignment explanation
Indices: 4124530--4124913 Score: 644
Period size: 204 Copynumber: 1.9 Consensus size: 205
4124520 ATCCTACTCC
* *
4124530 TTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCTTGCTTTTTGAGGACTG
1 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTTTTTGAGGACTG
* * * * *
4124595 GAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCTCTTTGAGGATTGAAAAGTGCCA
66 AAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAAAATGCCA
*
4124660 CCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGGTGAAAGGAGAGAGC
131 CCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTGAAAGGGTGAAAGGAGAGAGC
4124724 ATCTTGCTCT
196 ATCTTGCTCT
* * *
4124734 TTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTTTTTGAGGACTG
1 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTTTTTGAGGACTG
*
4124799 AAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAAAATGCCA
66 AAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAAAATGCCA
*
4124864 CCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTTTTTGAGGACTGAAAGG
131 CCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTGAAAGG
4124914 TGCCACCAAC
Statistics
Matches: 166, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
204 161 0.97
205 5 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (205 bp):
TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTTTTTGAGGACTG
AAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAAAATGCCA
CCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTGAAAGGGTGAAAGGAGAGAGC
ATCTTGCTCT
Found at i:4124919 original size:259 final size:259
Alignment explanation
Indices: 4124451--4125009 Score: 922
Period size: 259 Copynumber: 2.2 Consensus size: 259
4124441 GTGTGGGCTT
* * ** *
4124451 TGAAAGGAGAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA
1 TGAAAGGAGAGAGCATCTTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAA
* * *
4124516 AGGCATCCTACTCCTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCTTG
66 AGGCATCCTACTCCTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTG
* **
4124581 CTTTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCTCTTTGAGG
131 CTCTTTGAGGACTAAAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCTCTTTGAGG
*
4124646 ATTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGG
196 ACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGG
4124710 TGAAAGGAGAGAGCATCTTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAA
1 TGAAAGGAGAGAGCATCTTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAA
* **
4124775 AGGCATCCTGCTTTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTG
66 AGGCATCCTACTCCTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTG
* *
4124840 CTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTTTTTGAGG
131 CTCTTTGAGGACTAAAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCTCTTTGAGG
*
4124905 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGG
196 ACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGG
* *
4124969 TGAAAGGAAAGAGCGT-TCTGCTCTTTGAGGACTGGGAAGTG
1 TGAAAGGAGAGAGCATCT-TGCTCTTTGAGGACTGGGAAGTG
4125010 AAAGGAGAAA
Statistics
Matches: 279, Mismatches: 20, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
258 1 0.00
259 278 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (259 bp):
TGAAAGGAGAGAGCATCTTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAA
AGGCATCCTACTCCTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTG
CTCTTTGAGGACTAAAAAATGCCACCAACTTGTATGGGCTTTGAAAGGCATCCTGCTCTTTGAGG
ACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGG
Found at i:4125013 original size:34 final size:36
Alignment explanation
Indices: 4124936--4125014 Score: 85
Period size: 39 Copynumber: 2.2 Consensus size: 36
4124926 GTGTGGGCTT
4124936 TGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGAAAG
1 TGAAAGGCGTCCTGCTCTTTGAGGACT--A-GGTGAAAG
*
4124975 -GAAAGAGCGTTCTGCTCTTTGAGGACT-GG-G-AAG
1 TGAAAG-GCGTCCTGCTCTTTGAGGACTAGGTGAAAG
4125008 TGAAAGG
1 TGAAAGG
4125015 AGAAAGTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
33 4 0.11
34 6 0.16
35 2 0.05
38 5 0.14
39 20 0.54
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (36 bp):
TGAAAGGCGTCCTGCTCTTTGAGGACTAGGTGAAAG
Found at i:4126001 original size:1 final size:1
Alignment explanation
Indices: 4125982--4126060 Score: 68
Period size: 1 Copynumber: 79.0 Consensus size: 1
4125972 CTTTTCTCTC
* * * * * * * *
4125982 TTTTTCTTTGTTTTGTTTTTTTTTATTTTTTTTATTTTTTTTGTTTTTTTTTATTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
**
4126047 TTGGTTTTTTTTTT
1 TTTTTTTTTTTTTT
4126061 CTAAAAAGAA
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.04, C:0.01, G:0.08, T:0.87
Consensus pattern (1 bp):
T
Done.