Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2344
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: 384062
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:226354 original size:10 final size:10
Alignment explanation
Indices: 226335--226365 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
226325 AATCTCATTT
226335 TCACTGTTCA
1 TCACTGTTCA
*
226345 TCACTATTCA
1 TCACTGTTCA
226355 TCACTGTTCA
1 TCACTGTTCA
226365 T
1 T
226366 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:226387 original size:21 final size:22
Alignment explanation
Indices: 226353--226408 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
226343 CATCACTATT
226353 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
226375 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
226396 CATCACTGTTCAT
1 CATCACTGTTCAT
226409 AGGTCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:226509 original size:13 final size:13
Alignment explanation
Indices: 226491--226516 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
226481 ACATATTTGT
226491 GTGTATCGATACA
1 GTGTATCGATACA
226504 GTGTATCGATACA
1 GTGTATCGATACA
226517 TCATAAATAG
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:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:227058 original size:34 final size:35
Alignment explanation
Indices: 226995--227061 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
226985 CTAAGTGATT
226995 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
227031 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
227062 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:230180 original size:13 final size:13
Alignment explanation
Indices: 230162--230186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230152 TTTTCCAGAT
230162 TGTATCGATACAA
1 TGTATCGATACAA
230175 TGTATCGATACA
1 TGTATCGATACA
230187 TTGCTTCAGT
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:231846 original size:21 final size:21
Alignment explanation
Indices: 231813--231853 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
231803 CTAAGTAAAA
231813 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
231834 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
231854 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:231918 original size:20 final size:19
Alignment explanation
Indices: 231893--231963 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
231883 ACCCTGAAAA
231893 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
231913 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
231932 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
231953 GTATCGATACA
1 GTATCGATACA
231964 GGTCATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:232059 original size:10 final size:10
Alignment explanation
Indices: 232040--232070 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
232030 AATCTCATTT
232040 TCACTGTTCA
1 TCACTGTTCA
*
232050 TCACTATTCA
1 TCACTGTTCA
232060 TCACTGTTCA
1 TCACTGTTCA
232070 T
1 T
232071 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:232092 original size:21 final size:22
Alignment explanation
Indices: 232058--232113 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
232048 CATCACTATT
232058 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
232080 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
232101 CATCACTGTTCAT
1 CATCACTGTTCAT
232114 AGGTCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:232214 original size:13 final size:13
Alignment explanation
Indices: 232196--232221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
232186 ACATATTTGT
232196 GTGTATCGATACA
1 GTGTATCGATACA
232209 GTGTATCGATACA
1 GTGTATCGATACA
232222 TCATAAATAG
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:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:232763 original size:34 final size:35
Alignment explanation
Indices: 232700--232766 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
232690 CTAAGTGATT
232700 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
232736 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
232767 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:234556 original size:80 final size:79
Alignment explanation
Indices: 234361--234884 Score: 632
Period size: 80 Copynumber: 6.6 Consensus size: 79
234351 GATAAAAATG
* *
234361 GGGTTGGAGTATCCCCGCTGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTTGAGTAT-C
1 GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCC
*
234425 CCTTCAAAAATAATA
66 CCTT-AAAAATAACA
* * *
234440 GGGTTGGAGTATCCCCGATGGTGGAAAATCGGTGTTTTAGAAATAAAATTGGGGCTGGAGTATCC
1 GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCC
*
234505 CCTTAGAAATAAACA
66 CCTTAAAAAT-AACA
** **
234520 GGGTTTAAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAA-TCGGGGTAAGAGTATC
1 GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACT-GGGGTTGGAGTATC
*
234584 CCTTTAAAAATAAC-
65 CCCTTAAAAATAACA
* * *
234598 GAGTTGGAGTATCCTCGATGGTAGAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCC
** *
234663 CCTTGGAAATAAACG
66 CCTTAAAAAT-AACA
* *
234678 GGGTTGGAGTAGT-CCCGATGGTGGAAAATCAATGTTTTAGAAATAAAACTGGGGTTAGAGTATC
1 GGGTTGGAGTA-TCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATC
*
234742 CCTTTAAAAATAA-A
65 CCCTTAAAAATAACA
* * *
234756 TGGGGTTGGAGTATCCCCGATGGTGAAAAAT-TAGTGTTTTAGAAATAAAA-TCGAGGTTGGAGT
1 --GGGTTGGAGTATCCCCGATGGTGGAAAATCGA-TGTTTTAGAAATAAAACT-GGGGTTGGAGT
* * *
234819 ATCTCCTCAGAAATAACA
62 ATCCCCTTAAAAATAACA
* * *
234837 GGGTTGGAGTATCCCCGATGGT-GAAAATTTGGTATTTTAGAAATAAAA
1 GGGTTGGAGTATCCCCGATGGTGGAAAA-TCGATGTTTTAGAAATAAAA
234885 ACATCAATGA
Statistics
Matches: 384, Mismatches: 46, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
78 67 0.17
79 114 0.30
80 201 0.52
81 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCC
CCTTAAAAATAACA
Found at i:234674 original size:158 final size:157
Alignment explanation
Indices: 234361--234884 Score: 709
Period size: 158 Copynumber: 3.3 Consensus size: 157
234351 GATAAAAATG
* *
234361 GGGTTGGAGTATCCCCGCTGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTTGAGTATCC
1 GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTAGAGTATCC
* *
234426 CTTCAAAAATAATAGGGTTGGAGTATCCCCGATGGTGGAAAATCGGTGTTTTAGAAATAAAATTG
66 CTTTAAAAATAATAGGGTTGGAGTATCCCCGATGGT-GAAAATCGATGTTTTAGAAATAAAA-TG
*
234491 GGGCTGGAGTATCCCCTTAGAAATAAACA
129 GGGTTGGAGTATCCCCTTAGAAATAAACA
** *
234520 GGGTTTAAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAA-TCGGGGTAAGAGTATC
1 GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACT-GGGGTTAGAGTATC
* * *
234584 CCTTTAAAAATAA-CGAGTTGGAGTATCCTCGATGGTAGAAAATCGATGTTTTAGAAATAAAACT
65 CCTTTAAAAATAATAGGGTTGGAGTATCCCCGATGGT-GAAAATCGATGTTTTAGAAATAAAA-T
* *
234648 GGGGTTGGAGTATCCCCTTGGAAATAAACG
128 GGGGTTGGAGTATCCCCTTAGAAATAAACA
*
234678 GGGTTGGAGTAGT-CCCGATGGTGGAAAATCAATGTTTTAGAAATAAAACTGGGGTTAGAGTATC
1 GGGTTGGAGTA-TCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTAGAGTATC
* *
234742 CCTTTAAAAATAAATGGGGTTGGAGTATCCCCGATGGTGAAAAAT-TAGTGTTTTAGAAATAAAA
65 CCTTTAAAAAT-AATAGGGTTGGAGTATCCCCGATGGTG-AAAATCGA-TGTTTTAGAAATAAAA
* * *
234806 TCGAGGTTGGAGTATCTCCTCAGAAAT-AACA
127 T-GGGGTTGGAGTATCCCCTTAGAAATAAACA
* * *
234837 GGGTTGGAGTATCCCCGATGGT-GAAAATTTGGTATTTTAGAAATAAAA
1 GGGTTGGAGTATCCCCGATGGTGGAAAA-TCGATGTTTTAGAAATAAAA
234885 ACATCAATGA
Statistics
Matches: 323, Mismatches: 32, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
158 146 0.45
159 115 0.36
160 62 0.19
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (157 bp):
GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTGGGGTTAGAGTATCC
CTTTAAAAATAATAGGGTTGGAGTATCCCCGATGGTGAAAATCGATGTTTTAGAAATAAAATGGG
GTTGGAGTATCCCCTTAGAAATAAACA
Found at i:234762 original size:29 final size:31
Alignment explanation
Indices: 234713--234772 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
234703 AAATCAATGT
*
234713 TTTAGAAATAAAACTGGGGTTAGAGTATCCC
1 TTTAAAAATAAAACTGGGGTTAGAGTATCCC
*
234744 TTTAAAAAT-AAA-TGGGGTTGGAGTATCCC
1 TTTAAAAATAAAACTGGGGTTAGAGTATCCC
234773 CGATGGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 3 0.11
31 8 0.30
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (31 bp):
TTTAAAAATAAAACTGGGGTTAGAGTATCCC
Found at i:236491 original size:13 final size:13
Alignment explanation
Indices: 236473--236499 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
236463 ACATCTTGCT
236473 TTGTATCGATACA
1 TTGTATCGATACA
236486 TTGTATCGATACA
1 TTGTATCGATACA
236499 T
1 T
236500 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:236496 original size:33 final size:32
Alignment explanation
Indices: 236454--236518 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
236444 CACACCCAGA
*
236454 TGTATCGATACATCTTGCTTTGTATCGATACAT
1 TGTATCGATACATCTT-CATTGTATCGATACAT
*
236487 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATCTTCATTGTATCGATACAT
236519 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATCTTCATTGTATCGATACAT
Found at i:236529 original size:20 final size:19
Alignment explanation
Indices: 236483--236539 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
236473 TTGTATCGAT
*
236483 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
236502 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
236521 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
236540 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:244567 original size:21 final size:19
Alignment explanation
Indices: 244541--244628 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 19
244531 ATTTCAAAAT
244541 AAATTTTTATAAAGGGGGAGA
1 AAATTTTT-T-AAGGGGGAGA
244562 AAATTTTTATAAAGGGGGAGA
1 AAATTTTT-T-AAGGGGGAGA
* **
244583 TAATCGTTTAAGGGGGAGA
1 AAATTTTTTAAGGGGGAGA
* *
244602 TAATTATTTAAGGGGGA-A
1 AAATTTTTTAAGGGGGAGA
*
244620 AAGTTTTTT
1 AAATTTTTT
244629 TTTAAGGGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
18 7 0.12
19 25 0.42
20 1 0.02
21 26 0.44
ACGTcount: A:0.38, C:0.01, G:0.28, T:0.33
Consensus pattern (19 bp):
AAATTTTTTAAGGGGGAGA
Found at i:244616 original size:18 final size:19
Alignment explanation
Indices: 244573--244618 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
244563 AATTTTTATA
*
244573 AAGGGGGAGATAATCGTTT
1 AAGGGGGAGATAATCATTT
*
244592 AAGGGGGAGATAATTATTT
1 AAGGGGGAGATAATCATTT
244611 AAGGGGGA
1 AAGGGGGA
244619 AAAGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.39, T:0.24
Consensus pattern (19 bp):
AAGGGGGAGATAATCATTT
Found at i:245232 original size:13 final size:13
Alignment explanation
Indices: 245214--245240 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
245204 ACATCTTACT
245214 TTGTATCGATACA
1 TTGTATCGATACA
245227 TTGTATCGATACA
1 TTGTATCGATACA
245240 T
1 T
245241 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:245255 original size:32 final size:33
Alignment explanation
Indices: 245195--245259 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
245185 CACACTAAGA
* *
245195 TGTATTGATACATCTTACTTTGTATCGATACAT
1 TGTATCGATACATCTTACATTGTATCGATACAT
*
245228 TGTATCGATACATGTT-CATTGTATCGATACAT
1 TGTATCGATACATCTTACATTGTATCGATACAT
245260 GAAACTGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATCTTACATTGTATCGATACAT
Found at i:247317 original size:13 final size:13
Alignment explanation
Indices: 247299--247324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247289 CATTTTAGGC
247299 ATGTATCGATACA
1 ATGTATCGATACA
247312 ATGTATCGATACA
1 ATGTATCGATACA
247325 TTTATTATTT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:250703 original size:79 final size:78
Alignment explanation
Indices: 250569--250751 Score: 174
Period size: 79 Copynumber: 2.3 Consensus size: 78
250559 TTGTTTCAAT
* * * *
250569 GAAAGGTACGAAACT-AACTTAAAAAGGCTCAATTTTGATAGATTATACAAAACTAAACCTAACA
1 GAAA-GTACAAAACTAAACTTAAAAAGGCTCAATTTCGATAGA-TAGACAAAACTAAACATAACA
250633 AACTTAATTTC-AGTG
64 AACTTAATTTCGA-TG
* * * **
250648 GAAAGTACAAAACTAAACTTAAAAAGGCTTAATTTCGATAGA-AGGCATGATACTAAACATAATG
1 GAAAGTACAAAACTAAACTTAAAAAGGCTCAATTTCGATAGATAGACA--AAACTAAACATAACA
* **
250712 GACTTGGTTTCGATG
64 AACTTAATTTCGATG
* *
250727 GAAAATACAAAACTAAATTTAAAAA
1 GAAAGTACAAAACTAAACTTAAAAA
250752 AGTTCACTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
77 3 0.03
78 9 0.10
79 73 0.85
80 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (78 bp):
GAAAGTACAAAACTAAACTTAAAAAGGCTCAATTTCGATAGATAGACAAAACTAAACATAACAAA
CTTAATTTCGATG
Found at i:253899 original size:21 final size:21
Alignment explanation
Indices: 253875--253924 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
253865 GGAACCATTT
253875 GGTGATTTGACTAAATCTTAG
1 GGTGATTTGACTAAATCTTAG
253896 GGTGATTTGACTAAATCTTAG
1 GGTGATTTGACTAAATCTTAG
*
253917 GGGGATTT
1 GGTGATTT
253925 TAGTAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (21 bp):
GGTGATTTGACTAAATCTTAG
Found at i:254400 original size:74 final size:74
Alignment explanation
Indices: 254259--254401 Score: 189
Period size: 74 Copynumber: 1.9 Consensus size: 74
254249 ACCCATTAAT
* ** * *
254259 GTCATTTTAGTAATTCTCATGTTAAAATTGAGTCCTTAGGATCATGTTGGCATTTTCATATTGAT
1 GTCATTTTAATAATTCTCATGTTAAAACCGAGTCCTTAGAATCATGTTGGCATTTTCAAATTGAT
254324 GCATAGTCA
66 GCATAGTCA
* * **
254333 GTCATTTTAATAATTCTTATGTTAAAACCGAGTTCTTAGAATTGTGTTGGCATTTTCAAATCT-A
1 GTCATTTTAATAATTCTCATGTTAAAACCGAGTCCTTAGAATCATGTTGGCATTTTCAAAT-TGA
254397 TGCAT
65 TGCAT
254402 GGTTATTAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 58 0.98
75 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (74 bp):
GTCATTTTAATAATTCTCATGTTAAAACCGAGTCCTTAGAATCATGTTGGCATTTTCAAATTGAT
GCATAGTCA
Found at i:254653 original size:4 final size:4
Alignment explanation
Indices: 254644--254676 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
254634 GGCTTTAAGT
254644 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
254677 CACATCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:255804 original size:14 final size:15
Alignment explanation
Indices: 255785--255818 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
255775 GGGCTTTTGC
255785 AAAAAGCAAAAA-AA
1 AAAAAGCAAAAATAA
*
255799 AAAAAGGAAAAATAA
1 AAAAAGCAAAAATAA
255814 AAAAA
1 AAAAA
255819 AAGAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (15 bp):
AAAAAGCAAAAATAA
Found at i:255817 original size:16 final size:15
Alignment explanation
Indices: 255785--255827 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
255775 GGGCTTTTGC
*
255785 AAAAAGCAAAAAAAA
1 AAAAAGAAAAAAAAA
*
255800 AAAAGGAAAAATAAAA
1 AAAAAGAAAAA-AAAA
255816 AAAAAGAAAAAA
1 AAAAAGAAAAAA
255828 TGGAAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:255835 original size:17 final size:17
Alignment explanation
Indices: 255795--255828 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
255785 AAAAAGCAAA
*
255795 AAAAAAAAAGGAAAAAT
1 AAAAAAAAAGAAAAAAT
255812 AAAAAAAAAGAAAAAAT
1 AAAAAAAAAGAAAAAAT
255829 GGAAAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAT
Found at i:256883 original size:33 final size:33
Alignment explanation
Indices: 256839--256901 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
256829 TTAGGCATAA
* * * *
256839 TGTATCGATACATTTTACTATGTATCGATATAT
1 TGTATCAATACAATGTACCATGTATCGATATAT
*
256872 TGTATCAATACAATGTCCCATGTATCGATA
1 TGTATCAATACAATGTACCATGTATCGATA
256902 CAAACAGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCAATACAATGTACCATGTATCGATATAT
Found at i:257254 original size:21 final size:20
Alignment explanation
Indices: 257230--257269 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
257220 TTTAAAAGAA
257230 TAAAACTTGTTTACGATTTTT
1 TAAAACTT-TTTACGATTTTT
* *
257251 TAAACCTTTTTTCGATTTT
1 TAAAACTTTTTACGATTTT
257270 ATCCATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (20 bp):
TAAAACTTTTTACGATTTTT
Found at i:263458 original size:3 final size:3
Alignment explanation
Indices: 263450--263481 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
263440 CGAGTCAACT
*
263450 TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
263482 CTTGATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:265175 original size:20 final size:20
Alignment explanation
Indices: 265149--265202 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
265139 CTGCCAGTTT
* *
265149 CATGTATCGATACAATTGAG
1 CATGTATCGATACAACTGAA
*
265169 TATGTATCGATAC-ACTGAA
1 CATGTATCGATACAACTGAA
265188 CATGTATCGATACAA
1 CATGTATCGATACAA
265203 AGCATAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAACTGAA
Found at i:268964 original size:22 final size:23
Alignment explanation
Indices: 268939--268986 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
268929 AAAATTAAAA
268939 TTAAAAAATTAATTT-TATTTA-T
1 TTAAAAAATT-ATTTATATTTACT
* *
268961 TTAAGATATTATTTATATTTACT
1 TTAAAAAATTATTTATATTTACT
268984 TTA
1 TTA
268987 TAAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
22 14 0.64
23 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTAAAAAATTATTTATATTTACT
Found at i:269162 original size:17 final size:17
Alignment explanation
Indices: 269116--269164 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
269106 TACTTATTCC
* *
269116 TATCTTAAATAAATGTT
1 TATCTTAAATAAATATA
*
269133 TA-CTCAAATTAAATATA
1 TATCTTAAA-TAAATATA
269150 TATCTTAAATAAATA
1 TATCTTAAATAAATA
269165 AAACAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 5 0.19
17 16 0.62
18 5 0.19
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (17 bp):
TATCTTAAATAAATATA
Found at i:271611 original size:14 final size:14
Alignment explanation
Indices: 271592--271621 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
271582 CTCCTTTTTT
*
271592 AAATCTTTAACCTA
1 AAATCTCTAACCTA
271606 AAATCTCTAACCTA
1 AAATCTCTAACCTA
271620 AA
1 AA
271622 GTTAACCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATCTCTAACCTA
Found at i:281182 original size:13 final size:13
Alignment explanation
Indices: 281164--281188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
281154 CATTTTACTA
281164 TGTATCGATACAT
1 TGTATCGATACAT
281177 TGTATCGATACA
1 TGTATCGATACA
281189 ATATCCCATG
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:281187 original size:33 final size:33
Alignment explanation
Indices: 281144--281208 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
281134 TTGGGCATAA
* * * *
281144 TGTATTGATACATTTTACTATGTATCGATACAT
1 TGTATCGATACAATATACCATGTATCGATACAT
*
281177 TGTATCGATACAATATCCCATGTATCGATACA
1 TGTATCGATACAATATACCATGTATCGATACA
281209 AACAGTGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAATATACCATGTATCGATACAT
Found at i:281323 original size:52 final size:52
Alignment explanation
Indices: 281240--281356 Score: 164
Period size: 52 Copynumber: 2.2 Consensus size: 52
281230 GCCAGTTTCT
* * * *
281240 TGTATCGATACAGTTGAGTATGTATCGATACAATGAACATGAATC-GATATAA
1 TGTATCGATACAATTGAGTATGCATCAATACAATGAACATGAATCAG-TACAA
* *
281292 TGTATCGATGCAATTGAGTATGCATCAATACAATGAACATGTATCAGTACAA
1 TGTATCGATACAATTGAGTATGCATCAATACAATGAACATGAATCAGTACAA
281344 TGTATCGATACAA
1 TGTATCGATACAA
281357 AGCATAAAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 56 0.98
53 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACAATTGAGTATGCATCAATACAATGAACATGAATCAGTACAA
Found at i:281375 original size:52 final size:52
Alignment explanation
Indices: 281240--281375 Score: 134
Period size: 52 Copynumber: 2.6 Consensus size: 52
281230 GCCAGTTTCT
* * * *
281240 TGTATCGATACAGTTGAGTATGTATCGATACAATGAACATGAATCGATATAA
1 TGTATCGATACAATAGAGTAAGTATCGATACAATGAACATGAATCGATACAA
* * * * * *
281292 TGTATCGATGCAATTGAGTATGCATCAATACAATGAACATGTATC-AGTACAA
1 TGTATCGATACAATAGAGTAAGTATCGATACAATGAACATGAATCGA-TACAA
281344 TGTATCGATACAA-AGCA-TAAAGTATCGATACA
1 TGTATCGATACAATAG-AGT-AAGTATCGATACA
281376 TCTGGATGTG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
51 3 0.04
52 67 0.96
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACAATAGAGTAAGTATCGATACAATGAACATGAATCGATACAA
Found at i:282385 original size:20 final size:21
Alignment explanation
Indices: 282362--282413 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
282352 AAATTGCACA
**
282362 GTATCGATACATGACCA-AAT
1 GTATCGATACATGAAAAGAAT
*
282382 GTATCGATACTTGAAAAGAAT
1 GTATCGATACATGAAAAGAAT
282403 GTATCGATACA
1 GTATCGATACA
282414 GGTCATTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (21 bp):
GTATCGATACATGAAAAGAAT
Found at i:288422 original size:8 final size:8
Alignment explanation
Indices: 288409--288434 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
288399 ATATGATTAA
288409 ATTTTGTG
1 ATTTTGTG
288417 ATTTTGTG
1 ATTTTGTG
288425 ATTTTGTG
1 ATTTTGTG
288433 AT
1 AT
288435 GAATGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:288686 original size:13 final size:13
Alignment explanation
Indices: 288644--288691 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
288634 CAGTATTCTC
* *
288644 TGTATTGATACAT
1 TGTATCGATACAG
* *
288657 TATATCGATACAT
1 TGTATCGATACAG
*
288670 TGTATCGATATAG
1 TGTATCGATACAG
288683 TGTATCGAT
1 TGTATCGAT
288692 GCAAAGGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:289164 original size:20 final size:21
Alignment explanation
Indices: 289128--289179 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
289118 CCCTTAGGCA
289128 GCACCCACCAGGTCGCAACC-G
1 GCACCC-CCAGGTCGCAACCGG
*
289149 GCACCCCCATGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
289170 GCAGCCCCCA
1 GCA-CCCCCA
289180 CACTAGTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 10 0.36
22 6 0.21
ACGTcount: A:0.21, C:0.50, G:0.23, T:0.06
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:291170 original size:13 final size:13
Alignment explanation
Indices: 291152--291176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291142 AAATTGCACA
291152 GTATCGATACATT
1 GTATCGATACATT
291165 GTATCGATACAT
1 GTATCGATACAT
291177 GACCAAATGT
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):
GTATCGATACATT
Found at i:291189 original size:20 final size:21
Alignment explanation
Indices: 291164--291216 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
291154 ATCGATACAT
**
291164 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
291184 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
291205 TGTATCGATACA
1 TGTATCGATACA
291217 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:291274 original size:19 final size:19
Alignment explanation
Indices: 291250--291312 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
291240 TAGCCAAATT
291250 TGTATCGATACACACAATA
1 TGTATCGATACACACAATA
291269 TGTATCGAT----AC-AT-
1 TGTATCGATACACACAATA
291282 TGTATCGATACACACAATA
1 TGTATCGATACACACAATA
291301 TGTATCGATACA
1 TGTATCGATACA
291313 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 2 0.05
17 2 0.05
18 2 0.05
19 21 0.55
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (19 bp):
TGTATCGATACACACAATA
Found at i:291287 original size:13 final size:13
Alignment explanation
Indices: 291269--291326 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
291259 ACACACAATA
291269 TGTATCGATACAT
1 TGTATCGATACAT
291282 TGTATCGATACACACAAT
1 TGTATCGAT----AC-AT
291300 ATGTATCGATACAT
1 -TGTATCGATACAT
291314 TGTATCGATACAT
1 TGTATCGATACAT
291327 CCCAAAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 22 0.56
14 2 0.05
15 2 0.05
17 2 0.05
18 2 0.05
19 9 0.23
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:291290 original size:32 final size:32
Alignment explanation
Indices: 291249--291348 Score: 164
Period size: 32 Copynumber: 3.1 Consensus size: 32
291239 GTAGCCAAAT
291249 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAATATGTATCGATACA
291281 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAATATGTATCGATACA
* * *
291313 TTGTATCGATACATCCCAAAATGTATTGATACA
1 TTGTATCGATACA-CACAATATGTATCGATACA
291346 TTG
1 TTG
291349 GCTTGTAACG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 45 0.70
33 19 0.30
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACACACAATATGTATCGATACA
Found at i:292734 original size:19 final size:20
Alignment explanation
Indices: 292689--292740 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
292679 TTACAAGCCA
**
292689 ATGTATCGATACATTTTATG
1 ATGTATCGATACATACTATG
*
292709 ATGTATCGATACATACTGTG
1 ATGTATCGATACATACTATG
292729 -TGTATCGATACA
1 ATGTATCGATACA
292741 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATACTATG
Found at i:292820 original size:20 final size:21
Alignment explanation
Indices: 292773--292825 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
292763 GCCAATAACT
**
292773 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
292794 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
292814 TGTATCGATACA
1 TGTATCGATACA
292826 ATGCAATCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:292860 original size:20 final size:20
Alignment explanation
Indices: 292814--292864 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
292804 CATTTGGTCA
*
292814 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * * *
292834 TGCATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
292854 TGTATCGATAC
1 TGTATCGATAC
292865 TTTTCAGGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:293340 original size:15 final size:15
Alignment explanation
Indices: 293320--293348 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
293310 CCCCCTTTGT
293320 CAAATGCCAAATTTC
1 CAAATGCCAAATTTC
293335 CAAATGCCAAATTT
1 CAAATGCCAAATTT
293349 GTTTTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (15 bp):
CAAATGCCAAATTTC
Found at i:293359 original size:23 final size:23
Alignment explanation
Indices: 293331--293376 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
293321 AAATGCCAAA
293331 TTTCCAAATGCCAAATTTGTTTT
1 TTTCCAAATGCCAAATTTGTTTT
293354 TTTCCAAATGCCAAATTTGTTTT
1 TTTCCAAATGCCAAATTTGTTTT
293377 CAAAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (23 bp):
TTTCCAAATGCCAAATTTGTTTT
Found at i:301569 original size:33 final size:33
Alignment explanation
Indices: 301527--301593 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
301517 AAAATTTCCA
***
301527 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
* *
301560 AATGTATCGATGCATAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
301593 A
1 A
301594 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:301640 original size:19 final size:18
Alignment explanation
Indices: 301613--301680 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
301603 CAGTAGCTAA
*
301613 TTATATATCGATACAATAC
1 TTATGTATCGATACAA-AC
301632 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
301647 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
301664 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
301681 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:301653 original size:13 final size:13
Alignment explanation
Indices: 301635--301659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301625 ACAATACTTA
301635 TGTATCGATACAT
1 TGTATCGATACAT
301648 TGTATCGATACA
1 TGTATCGATACA
301660 AAACTTATGT
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:301659 original size:32 final size:32
Alignment explanation
Indices: 301618--301678 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
301608 GCTAATTATA
*
301618 TATCGATACAATACTTATGTATCGATACATTG
1 TATCGATACAAAACTTATGTATCGATACATTG
301650 TATCGATACAAAACTTATGTATCGATACA
1 TATCGATACAAAACTTATGTATCGATACA
301679 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTG
Found at i:301742 original size:21 final size:21
Alignment explanation
Indices: 301716--301794 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
301706 GTTAGGACCC
301716 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
** *
301737 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGTA-GAA
301758 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
301779 TGTATCGATACATTTG
1 TGTATCGATACATTTG
301795 GATAATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.06
21 44 0.88
22 3 0.06
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:302669 original size:26 final size:26
Alignment explanation
Indices: 302640--302729 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
302630 GTGTGGGCTT
302640 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** ** *
302666 TGAAAAATG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
302693 TTCGAAAGGGGTCCTGCTCTTTGGGGAC
1 -T-GAAAGGTGTCCTGCTCTTTGGGGAC
302721 TGAAAGGTG
1 TGAAAGGTG
302730 CCACCAACTT
Statistics
Matches: 45, Mismatches: 12, Indels: 14
0.63 0.17 0.20
Matches are distributed among these distances:
25 3 0.07
26 17 0.38
27 7 0.16
28 7 0.16
29 8 0.18
30 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:302842 original size:59 final size:59
Alignment explanation
Indices: 302532--303349 Score: 1137
Period size: 59 Copynumber: 14.0 Consensus size: 59
302522 GGGGGCTTTG
* * * *
302532 AAAGGCATCCTGCTCTTTGAGGACTCAAAGGTGCCACTAACTTGTGTGGGCTTT--AAG-
1 AAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * **
302589 --AGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-
1 AAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * * ** *
302642 AAAGGTGTCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGC-TT---CG-
1 AAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * *
302697 AAAGGGGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGA
* * * * *
302758 AAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
302817 AAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
302876 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
302935 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
302994 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
303053 AAAGGCGTCCCACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
303112 AAAGGCGTCTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
303171 AAAGGCGTCCCGCTCTTTTAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* ** *
303230 AAAGGCGTTCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGG
1 AAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GA
* * *
303291 GAAGGCGTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCATCTTGTGTGGGCTTTAAAAG
1 AAAGGCGTCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
303350 GTGTCCTGCT
Statistics
Matches: 706, Mismatches: 42, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
53 1 0.00
54 3 0.00
55 140 0.20
56 2 0.00
59 428 0.61
60 57 0.08
61 71 0.10
62 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (59 bp):
AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
Found at i:304380 original size:17 final size:17
Alignment explanation
Indices: 304360--304402 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
304350 TCTCTTTTTC
304360 TTTGTTTTGTTTTTTGT
1 TTTGTTTTGTTTTTTGT
*
304377 TTTGTTTTGTTTTTTTT
1 TTTGTTTTGTTTTTTGT
*
304394 TTTTTTTTG
1 TTTGTTTTG
304403 AAGAGAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (17 bp):
TTTGTTTTGTTTTTTGT
Found at i:304385 original size:22 final size:22
Alignment explanation
Indices: 304360--304402 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
304350 TCTCTTTTTC
304360 TTTGTTTTGTTTTTTGTTTTGT
1 TTTGTTTTGTTTTTTGTTTTGT
* *
304382 TTTGTTTTTTTTTTTTTTTTG
1 TTTGTTTTGTTTTTTGTTTTG
304403 AAGAGAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (22 bp):
TTTGTTTTGTTTTTTGTTTTGT
Found at i:309216 original size:21 final size:21
Alignment explanation
Indices: 309183--309223 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
309173 CTCAGTAAAA
309183 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
309204 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
309224 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:309288 original size:20 final size:19
Alignment explanation
Indices: 309263--309333 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
309253 ACCCTGAAAA
309263 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
309283 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
309302 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
309323 GTATCGATACA
1 GTATCGATACA
309334 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:309384 original size:53 final size:53
Alignment explanation
Indices: 309303--309439 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
309293 AGATTGCATA
*
309303 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACA-AAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
* * *
309357 GTATCGATACACATAATATGTATCGATACAGGTCATTGGCAGTAGCGAAAATT
1 GTATCGATACACAAAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
309410 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACAAAATATGTATCGATACA
309440 TTGGTAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
Found at i:309433 original size:19 final size:18
Alignment explanation
Indices: 309404--309439 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
309394 GGCAGTAGCG
309404 AAAATTGTATCGATACAC
1 AAAATTGTATCGATACAC
309422 AAAATATGTATCGATACA
1 AAAAT-TGTATCGATACA
309440 TTGGTAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAATTGTATCGATACAC
Found at i:309482 original size:10 final size:10
Alignment explanation
Indices: 309463--309493 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
309453 AATCTCATTT
*
309463 TCACTGTTCA
1 TCACTATTCA
309473 TCACTATTCA
1 TCACTATTCA
309483 TCACTATTCA
1 TCACTATTCA
309493 T
1 T
309494 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (10 bp):
TCACTATTCA
Found at i:309515 original size:21 final size:22
Alignment explanation
Indices: 309481--309535 Score: 94
Period size: 21 Copynumber: 2.5 Consensus size: 22
309471 CATCACTATT
309481 CATCACTATTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
309503 CATCACT-TTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
*
309524 CATCACTGTTCA
1 CATCACTATTCA
309536 CACTGTTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (22 bp):
CATCACTATTCATGTATCGATA
Found at i:311579 original size:32 final size:33
Alignment explanation
Indices: 311524--311585 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
311514 CAAGCCAATG
**
311524 TATCGATACAATTTTTTGTGTATCGATACATTA
1 TATCGATACAATACTTTGTGTATCGATACATTA
311557 TATCGATAC-ATACTTTGTGTATCGATACA
1 TATCGATACAATACTTTGTGTATCGATACA
311586 AGTTTGGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (33 bp):
TATCGATACAATACTTTGTGTATCGATACATTA
Found at i:311662 original size:20 final size:20
Alignment explanation
Indices: 311616--311689 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
311606 ATCCCAATGA
***
311616 TATGTATCGATACATCTTTTT
1 TATGTATCGATACAT-TGAAT
311637 TATGTATCGATACATTGCAA-
1 TATGTATCGATACATTG-AAT
*
311657 TATGTATCGATACTTTGAAT
1 TATGTATCGATACATTGAAT
*
311677 TGTGTATCGATAC
1 TATGTATCGATAC
311690 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (20 bp):
TATGTATCGATACATTGAAT
Found at i:316025 original size:13 final size:13
Alignment explanation
Indices: 316009--316033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315999 TTGGGCATAA
316009 TGTATCGATACAT
1 TGTATCGATACAT
316022 TGTATCGATACA
1 TGTATCGATACA
316034 ATGTCCCATG
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:316113 original size:20 final size:20
Alignment explanation
Indices: 316083--316137 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
316073 CTGCCAATTT
* *
316083 CATGCATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
* *
316103 TATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
*
316122 CATGTATCAATACAAT
1 CATGTATCGATACAAT
316138 ATACAAAGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:321298 original size:17 final size:18
Alignment explanation
Indices: 321268--321301 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
321258 CACAAAATAA
321268 TAAAAATATATTTAATTT
1 TAAAAATATATTTAATTT
*
321286 TAAAATTAT-TTTAATT
1 TAAAAATATATTTAATT
321302 ACTATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAAAATATATTTAATTT
Found at i:324127 original size:19 final size:19
Alignment explanation
Indices: 324105--324145 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
324095 AATTTTCAAT
* *
324105 AAAAATAATTATCTTTAAA
1 AAAAATAATAATATTTAAA
324124 AAAAATAATAATATTTAAA
1 AAAAATAATAATATTTAAA
324143 AAA
1 AAA
324146 TTACAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATAATAATATTTAAA
Found at i:324344 original size:41 final size:41
Alignment explanation
Indices: 324281--324363 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
324271 AGTGTAGAAG
* *
324281 GAGATTGCAAAGAAAAGACCAAAAGACGAGGATTGCATCAT
1 GAGATTGCAAACAAAAGACCAAAAGACGAGGATCGCATCAT
* * * *
324322 GAGATTGTAAACAAAGGGCCAAAAGATGAGGATCGCATCAT
1 GAGATTGCAAACAAAAGACCAAAAGACGAGGATCGCATCAT
324363 G
1 G
324364 CGAGTCTAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (41 bp):
GAGATTGCAAACAAAAGACCAAAAGACGAGGATCGCATCAT
Found at i:324475 original size:3 final size:3
Alignment explanation
Indices: 324467--324511 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
324457 ATTAATCCTC
324467 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
324512 GTTTCTCCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:330114 original size:156 final size:157
Alignment explanation
Indices: 329914--330272 Score: 363
Period size: 156 Copynumber: 2.3 Consensus size: 157
329904 ATTTTAGAAG
* * * * * *
329914 AAAAAC-AGGTTTAGAGTATCCCCTCGGA-ATGATAAGGTTAGAGTAACCCCGATGGTGAAAATT
1 AAAAACGAGG-TTAGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTAACCCC-AAGATGAAAATT
* *
329977 TT-ATATTTTAGAAA-AAAAATAGAGTTGGAGTAT-TCCCTCAAAAATGATAGGGTTGGAGTATC
64 TTAATATTTT-GAAAGAAAAACAGAGTTGAAGTATCT-CCTCAAAAATG-TAGGGTTGGAGTATC
*
330039 CTCAATGGTGAAAAATAGATATTTTGGAAAA-
126 CCCAATGGTGAAAAATAGATATTTTGGAAAAT
* * *
330070 AAAAACGAGGTTGGAGTATTCCCT-AGAGATGGTAGGGTTGGAGTATCCCCAAGATGAAAATTTT
1 AAAAACGAGGTTAGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTAACCCCAAGATGAAAATTTT
* * * *** * *
330134 AATATTTTGAAAGTAAAAACAGGGTTTAAGTATCTCTTGGGAAATGTGGGGTTGGAGTATCCCCG
66 AATATTTTGAAAG-AAAAACAGAGTTGAAGTATCTCCTCAAAAATGTAGGGTTGGAGTATCCCCA
* ** *
330199 ATGGTTAAAAATTTATATTTTTGAAAAT
130 ATGGTGAAAAATAGATATTTTGGAAAAT
* * * *
330227 AAAAATGGGGTTAGAGTATCCCCTCAGTGATGGTGGGGTTGGAGTA
1 AAAAACGAGGTTAGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTA
330273 TCCCTTCAGT
Statistics
Matches: 165, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
155 18 0.11
156 82 0.50
157 45 0.27
158 20 0.12
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (157 bp):
AAAAACGAGGTTAGAGTATCCCCTCAGAGATGGTAGGGTTGGAGTAACCCCAAGATGAAAATTTT
AATATTTTGAAAGAAAAACAGAGTTGAAGTATCTCCTCAAAAATGTAGGGTTGGAGTATCCCCAA
TGGTGAAAAATAGATATTTTGGAAAAT
Found at i:330245 original size:79 final size:80
Alignment explanation
Indices: 329870--330276 Score: 295
Period size: 78 Copynumber: 5.2 Consensus size: 80
329860 TCGAAATACG
* * * * * *
329870 GGGTTGGAGTACCCCCGATGATTATAAATTTAATATTTTAGAAGAAAAACA--GGTTTAGAGTAT
1 GGGTTGGAGTATCCCCGATGGTGAAAAATTT-ATATTTTAGAA-AAAAAAATGGGGTTAGAGTAT
*
329933 C-CCCTC-GGAATGATA
64 CTCCCTCAGAAATGATA
* * * * * * *
329948 AGGTTAGAGTAACCCCGATGGTGAAAATTTTATATTTTAG-AAAAAAAATAGAGTTGGAGTAT-T
1 GGGTTGGAGTATCCCCGATGGTGAAAAATTTATATTTTAGAAAAAAAAATGGGGTTAGAGTATCT
*
330011 CCCTCAAAAATGATA
66 CCCTCAGAAATGATA
* * ** * * * *
330026 GGGTTGGAGTATCCTCAATGGTGAAAAATAGATATTTTGGAAAAAAAAACGAGGTTGGAGTAT-T
1 GGGTTGGAGTATCCCCGATGGTGAAAAATTTATATTTTAGAAAAAAAAATGGGGTTAGAGTATCT
* *
330090 CCCT-AGAGATGGTA
66 CCCTCAGAAATGATA
* * * *
330104 GGGTTGGAGTATCCCC-AAGATGAAAATTTTAATATTTT-GAAAGTAAAAACA-GGGTTTA-AGT
1 GGGTTGGAGTATCCCCGATGGTGAAAAATTT-ATATTTTAGAAA--AAAAA-ATGGGGTTAGAGT
* ** *
330165 ATCT-CTTGGGAAATG-TG
62 ATCTCCCTCAGAAATGATA
* *
330182 GGGTTGGAGTATCCCCGATGGTTAAAAATTTATATTTTTGAAAATAAAAATGGGGTTAGAGTATC
1 GGGTTGGAGTATCCCCGATGGTGAAAAATTTATATTTTAGAAAA-AAAAATGGGGTTAGAGTATC
** * *
330247 -CCCTCAGTGATGGTG
65 TCCCTCAGAAATGATA
330262 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
330277 TTCAGTGATG
Statistics
Matches: 259, Mismatches: 52, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
75 6 0.02
76 1 0.00
77 38 0.15
78 132 0.51
79 64 0.25
80 18 0.07
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (80 bp):
GGGTTGGAGTATCCCCGATGGTGAAAAATTTATATTTTAGAAAAAAAAATGGGGTTAGAGTATCT
CCCTCAGAAATGATA
Found at i:330271 original size:28 final size:28
Alignment explanation
Indices: 330232--330304 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
330222 AAAATAAAAA
*
330232 TGGGGTTAGAGTATCCCCTCAGTGATGG
1 TGGGGTTGGAGTATCCCCTCAGTGATGG
*
330260 TGGGGTTGGAGTATCCCTTCAGTGATGG
1 TGGGGTTGGAGTATCCCCTCAGTGATGG
* *
330288 TGGAGTTGGAGCATCCC
1 TGGGGTTGGAGTATCCC
330305 TAAGATGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.16, C:0.18, G:0.37, T:0.29
Consensus pattern (28 bp):
TGGGGTTGGAGTATCCCCTCAGTGATGG
Found at i:332783 original size:51 final size:51
Alignment explanation
Indices: 332721--332858 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 51
332711 CATAGTCTGC
*
332721 ATGTATCGATACATTAAAGAATGTATCGATATATTTGGGTC-AAAACCCAAA
1 ATGTATCGATACAATAAA-AATGTATCGATATATTTGGGTCAAAAACCCAAA
* * * * *
332772 ATGTATCGATACAATGAATAATATATCAATATATTTGGGTCAAAAATCCATA
1 ATGTATCGATACAAT-AAAAATGTATCGATATATTTGGGTCAAAAACCCAAA
* * *
332824 ATGTATCGATAAAATAGAAATGTATCGATAAATTT
1 ATGTATCGATACAATAAAAATGTATCGATATATTT
332859 TCCTTCCAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
51 49 0.67
52 24 0.33
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACAATAAAAATGTATCGATATATTTGGGTCAAAAACCCAAA
Found at i:332937 original size:20 final size:21
Alignment explanation
Indices: 332914--332967 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
332904 ATATTTAGAT
*
332914 ATGTATTGATACATTCAC-TC
1 ATGTATCGATACATTCACTTC
** *
332934 ATGTATCGATATGTTCACTTT
1 ATGTATCGATACATTCACTTC
332955 ATGTATCGATACA
1 ATGTATCGATACA
332968 AATTGTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTTC
Found at i:334566 original size:45 final size:46
Alignment explanation
Indices: 334515--334608 Score: 145
Period size: 49 Copynumber: 2.0 Consensus size: 46
334505 ATTATGACTT
*
334515 GTTGTCATTTTGAAC-TTATTAACTTTTAATAAGTCATATAAACTC
1 GTTGTCACTTTGAACTTTATTAACTTTTAATAAGTCATATAAACTC
334560 GTTGTCACTTTGAACTTGATTATTAACTTTTAATAAGTCATATAAACTC
1 GTTGTCACTTTGAAC-T--TTATTAACTTTTAATAAGTCATATAAACTC
334609 CCACTAAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 14 0.32
49 30 0.68
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.44
Consensus pattern (46 bp):
GTTGTCACTTTGAACTTTATTAACTTTTAATAAGTCATATAAACTC
Found at i:342761 original size:2 final size:2
Alignment explanation
Indices: 342754--342779 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
342744 CGTTTTCTTG
342754 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
342780 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:344971 original size:22 final size:22
Alignment explanation
Indices: 344922--344971 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
344912 ATTCATCTAT
344922 TTAA-ATTTAAATTACTGTTTA
1 TTAATATTTAAATTACTGTTTA
* *
344943 -TACTATTTAAAATTA-TTTTTA
1 TTAATATTT-AAATTACTGTTTA
344964 TTAATATT
1 TTAATATT
344972 ATTATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
20 2 0.09
21 9 0.39
22 12 0.52
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATATTTAAATTACTGTTTA
Found at i:346605 original size:15 final size:15
Alignment explanation
Indices: 346585--346616 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
346575 CACATTAATT
346585 TTAAATTAATTTAAA
1 TTAAATTAATTTAAA
*
346600 TTAAATTATTTTAAA
1 TTAAATTAATTTAAA
346615 TT
1 TT
346617 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAATTAATTTAAA
Found at i:346659 original size:16 final size:15
Alignment explanation
Indices: 346635--346705 Score: 63
Period size: 16 Copynumber: 4.5 Consensus size: 15
346625 TTTAGATTCG
346635 ATCATTTTAATTTTAA
1 ATCA-TTTAATTTTAA
*
346651 ATCACTTTAAATTTAA
1 ATCA-TTTAATTTTAA
*
346667 ATCATTATGATTTTAA
1 ATCATT-TAATTTTAA
*
346683 ATTATTTCATATTTTAA
1 ATCATTT-A-ATTTTAA
346700 AT-ATTT
1 ATCATTT
346706 TTATTTTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
15 3 0.07
16 34 0.74
17 9 0.20
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (15 bp):
ATCATTTAATTTTAA
Found at i:346765 original size:16 final size:16
Alignment explanation
Indices: 346739--346792 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
346729 ACATCTAAAT
346739 TATTAAAATTCAAATCA
1 TATT-AAATTCAAATCA
*
346756 TATTAAATTCATATCA
1 TATTAAATTCAAATCA
* *
346772 T-TTTAATTTAAATCA
1 TATTAAATTCAAATCA
346787 -ATTAAA
1 TATTAAA
346793 ATTAATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 15 0.48
16 12 0.39
17 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAAATTCAAATCA
Found at i:346795 original size:16 final size:16
Alignment explanation
Indices: 346740--346795 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
346730 CATCTAAATT
346740 ATTAAAATTCAAATCA
1 ATTAAAATTCAAATCA
*
346756 TATT-AAATTCATATC-
1 -ATTAAAATTCAAATCA
** *
346771 ATTTTAATTTAAATCA
1 ATTAAAATTCAAATCA
346787 ATTAAAATT
1 ATTAAAATT
346796 AATATTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 3 0.10
15 8 0.26
16 17 0.55
17 3 0.10
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTAAAATTCAAATCA
Found at i:346818 original size:14 final size:14
Alignment explanation
Indices: 346786--346833 Score: 64
Period size: 12 Copynumber: 3.5 Consensus size: 14
346776 AATTTAAATC
*
346786 AATTAAAATTAAT-
1 AATTTAAATTAATA
346799 -ATTTAAATTAATA
1 AATTTAAATTAATA
346812 AATTTAAATTAATTA
1 AATTTAAATTAA-TA
346827 AATTTAA
1 AATTTAA
346834 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.35
14 11 0.35
15 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTTAAATTAATA
Found at i:346826 original size:30 final size:29
Alignment explanation
Indices: 346771--346911 Score: 98
Period size: 30 Copynumber: 4.9 Consensus size: 29
346761 AATTCATATC
* *
346771 ATTTT-AATTTAAATCAATTAAAATTAA-T
1 ATTTTAAATTT-AATAAATTTAAATTAATT
346799 A-TTTAAA-TTAATAAATTTAAATTAATT
1 ATTTTAAATTTAATAAATTTAAATTAATT
* * *
346826 AAATTTAATATTTAA-AATTTTTAAA-AAATT
1 -ATTTTAA-ATTTAATAA-ATTTAAATTAATT
* *
346856 ATTTTAAATTTAAATAATTTTTAATTAATT
1 ATTTTAAATTT-AATAAATTTAAATTAATT
*
346886 ATTTTAAA-TAAATTCAAATTTAAATT
1 ATTTTAAATTTAA-T-AAATTTAAATT
346912 TTTTTGAATT
Statistics
Matches: 91, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
26 14 0.15
27 6 0.07
28 10 0.11
29 21 0.23
30 30 0.33
31 10 0.11
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTTAAATTTAATAAATTTAAATTAATT
Found at i:346859 original size:14 final size:14
Alignment explanation
Indices: 346844--346899 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
346834 TATTTAAAAT
346844 TTTTAAA-AAATTA
1 TTTTAAATAAATTA
*
346857 TTTTAAATTTAAATAA
1 TTTTAAA--TAAATTA
* *
346873 TTTTTAATTAATTA
1 TTTTAAATAAATTA
346887 TTTTAAATAAATT
1 TTTTAAATAAATT
346900 CAAATTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
13 7 0.21
14 16 0.47
16 11 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTAAATAAATTA
Found at i:346875 original size:16 final size:16
Alignment explanation
Indices: 346795--346959 Score: 65
Period size: 16 Copynumber: 11.1 Consensus size: 16
346785 CAATTAAAAT
346795 TAATATTTAAA-TT-AA
1 TAAT-TTTAAATTTAAA
* *
346810 TAAATTTAAA-TTAAT
1 TAATTTTAAATTTAAA
*
346825 TAAATTTAATATTTAAA
1 TAATTTTAA-ATTTAAA
*
346842 -ATTTTTAAA---AAA
1 TAATTTTAAATTTAAA
*
346854 TTATTTTAAATTTAAA
1 TAATTTTAAATTTAAA
*
346870 TAATTTTTAA-TT-AA
1 TAATTTTAAATTTAAA
*
346884 TTATTTTAAA--T--A
1 TAATTTTAAATTTAAA
*
346896 -AA-TTCAAATTTAAA
1 TAATTTTAAATTTAAA
** *
346910 TTTTTTTGAATTTAAA
1 TAATTTTAAATTTAAA
*
346926 CT-ATTTTATATTTAAA
1 -TAATTTTAAATTTAAA
*
346942 TCATTTTTAAATTTAAA
1 T-AATTTTAAATTTAAA
346959 T
1 T
346960 TATTAATTTT
Statistics
Matches: 112, Mismatches: 22, Indels: 30
0.68 0.13 0.18
Matches are distributed among these distances:
10 5 0.04
11 1 0.01
12 5 0.04
13 8 0.07
14 19 0.17
15 17 0.15
16 39 0.35
17 18 0.16
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (16 bp):
TAATTTTAAATTTAAA
Found at i:346987 original size:5 final size:5
Alignment explanation
Indices: 346977--347003 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
346967 TTTTTTAATC
346977 AAATT AAATT AAATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AA
347004 TTTTAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:352437 original size:2 final size:2
Alignment explanation
Indices: 352432--352477 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
352422 AAAAGCATGC
352432 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
352474 AT AT
1 AT AT
352478 GTAAAATGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355352 original size:41 final size:41
Alignment explanation
Indices: 355264--355344 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
355254 TGTTTTAAAA
* * *
355264 AATCAAATGATATTATTGGTACAGATTGTTAGAGAACCACC
1 AATCAAATGATATTATCGGTACAGATCGTTAGAAAACCACC
*
355305 AATCAAATGATATTATCGGTACAGATCGTTGGAAAACCAC
1 AATCAAATGATATTATCGGTACAGATCGTTAGAAAACCAC
355345 ACCTCAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (41 bp):
AATCAAATGATATTATCGGTACAGATCGTTAGAAAACCACC
Found at i:356620 original size:13 final size:13
Alignment explanation
Indices: 356563--356623 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
356553 ATCTTTGTAA
356563 ATTTTAATA-TAT
1 ATTTTAATATTAT
*
356575 -TTTTAAAATATAT
1 ATTTTAATAT-TAT
*
356588 AATTTTAAT-TTAA
1 -ATTTTAATATTAT
356601 ATTTTAATATTAT
1 ATTTTAATATTAT
*
356614 TTTTTAATAT
1 ATTTTAATAT
356624 GAAAAATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
11 7 0.18
12 8 0.21
13 17 0.44
14 1 0.03
15 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATTAT
Found at i:357184 original size:18 final size:18
Alignment explanation
Indices: 357158--357222 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 18
357148 TACTATTAAA
*
357158 ATATAATATAAATATTTT
1 ATATTATATAAATATTTT
357176 ATATTATATAAAT-TTATT
1 ATATTATATAAATATT-TT
357194 -TATT-TATAAA-ATTTT
1 ATATTATATAAATATTTT
357209 ATA-TAT-TAAATATT
1 ATATTATATAAATATT
357223 AAATTATATG
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
15 7 0.17
16 14 0.34
17 6 0.15
18 14 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTATATAAATATTTT
Found at i:357205 original size:17 final size:19
Alignment explanation
Indices: 357158--357216 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
357148 TACTATTAAA
* *
357158 ATATAATATAAATAT-TTT
1 ATATTATATAAATTTATTT
357176 ATATTATATAAATTTATTT
1 ATATTATATAAATTTATTT
*
357195 AT-TTATA-AAATTT-TAT
1 ATATTATATAAATTTATTT
357211 ATATTA
1 ATATTA
357217 AATATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.11
17 9 0.25
18 18 0.50
19 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTATATAAATTTATTT
Found at i:357209 original size:14 final size:15
Alignment explanation
Indices: 357159--357230 Score: 56
Period size: 16 Copynumber: 4.6 Consensus size: 15
357149 ACTATTAAAA
*
357159 TATAATATAAATATTT
1 TATATTATAAA-ATTT
357175 TATATTATATAAATTT
1 TATATTATA-AAATTT
*
357191 ATTTATTTATAAAATTT
1 -TATA-TTATAAAATTT
* *
357208 TATA-TATTAAATAT
1 TATATTATAAAATTT
*
357222 TAAATTATA
1 TATATTATA
357231 TGTTATATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
14 11 0.24
15 3 0.07
16 15 0.33
17 11 0.24
18 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTATAAAATTT
Found at i:359439 original size:17 final size:17
Alignment explanation
Indices: 359417--359460 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
359407 TTTTTTGTAT
* *
359417 TATTTATTTAGGATATA
1 TATTTATTTAGAATAAA
359434 TATTTAATTT-GAATAAA
1 TATTT-ATTTAGAATAAA
359451 TATTTATTTA
1 TATTTATTTA
359461 AGACAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TATTTATTTAGAATAAA
Found at i:359524 original size:5 final size:5
Alignment explanation
Indices: 359514--359541 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
359504 TAATTTTAAG
359514 AATTA AATTA AATTA AATTA AATTA AAT
1 AATTA AATTA AATTA AATTA AATTA AAT
359542 AGATATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATTA
Found at i:359654 original size:33 final size:33
Alignment explanation
Indices: 359556--359654 Score: 80
Period size: 33 Copynumber: 3.0 Consensus size: 33
359546 ATGACTAGGT
*
359556 TATTTATATAATTAATTTAATATCTAA-AT-AA
1 TATTTATAGAATTAATTTAATATCTAATATAAA
* * * *
359587 TCTTGTTTAGATATTTATTTATAAAT-TAAATATAAA
1 TATT-TATAGA-ATTAATTTA-ATATCT-AATATAAA
359623 TATTTATA-AATTAATTTAATATCTAACTATAA
1 TATTTATAGAATTAATTTAATATCTAA-TATAA
359655 GAAAACTATC
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
31 3 0.06
32 9 0.18
33 23 0.45
34 6 0.12
35 5 0.10
36 5 0.10
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.48
Consensus pattern (33 bp):
TATTTATAGAATTAATTTAATATCTAATATAAA
Found at i:359826 original size:26 final size:26
Alignment explanation
Indices: 359797--359850 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
359787 CTAGTACATA
*
359797 AACTATTTACATGATTTGAATTTTTT
1 AACTATTTACATAATTTGAATTTTTT
359823 AACTATTTACATAATTTGAATTTTTT
1 AACTATTTACATAATTTGAATTTTTT
359849 AA
1 AA
359851 ACTTCAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (26 bp):
AACTATTTACATAATTTGAATTTTTT
Found at i:360352 original size:13 final size:13
Alignment explanation
Indices: 360336--360399 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
360326 TAAATATGAT
*
360336 ATAATTATATAAA
1 ATAAATATATAAA
360349 ATAAATATATATAA
1 ATAAATATATA-AA
*
360363 TATAAA-AAAT-AA
1 -ATAAATATATAAA
* *
360375 TTAAA-ATATAAT
1 ATAAATATATAAA
360387 ATAAATATATAAA
1 ATAAATATATAAA
360400 TATATTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 7 0.17
13 16 0.40
14 5 0.12
15 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAATATATAAA
Found at i:360383 original size:23 final size:22
Alignment explanation
Indices: 360334--360401 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
360324 TTTAAATATG
* *
360334 ATATAATTATATAAAATAAATAT
1 ATATAA-TATAAAAAATAAATAA
*
360357 ATATAATATAAAAAATAATTAAA
1 ATATAATATAAAAAATAAAT-AA
*
360380 ATATAATATAAATATATAAATA
1 ATATAATATAAA-AAATAAATA
360402 TATTAAAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 12 0.32
23 20 0.53
24 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATAATATAAAAAATAAATAA
Found at i:360385 original size:11 final size:12
Alignment explanation
Indices: 360342--360403 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 12
360332 TGATATAATT
360342 ATATAAAATA-A
1 ATATAAAATATA
360353 ATAT---ATATA
1 ATATAAAATATA
*
360362 ATATAAAAAATA
1 ATATAAAATATA
360374 AT-TAAAATATA
1 ATATAAAATATA
360385 ATATAAATATATAA
1 ATATAAA-ATAT-A
360399 ATATA
1 ATATA
360404 TTAAAATCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 3 0.07
9 5 0.12
11 14 0.33
12 10 0.24
13 4 0.10
14 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:360432 original size:2 final size:2
Alignment explanation
Indices: 360425--360455 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
360415 ATAAATTTTC
360425 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
360456 GATAGAGACA
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:361764 original size:17 final size:16
Alignment explanation
Indices: 361738--361771 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
361728 ATTTTGTTTT
*
361738 AATTTATTAATTTTAA
1 AATTTATTAAATTTAA
361754 AATTATATTAAATTTAA
1 AATT-TATTAAATTTAA
361771 A
1 A
361772 TAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTATTAAATTTAA
Found at i:365190 original size:232 final size:232
Alignment explanation
Indices: 364784--365247 Score: 802
Period size: 232 Copynumber: 2.0 Consensus size: 232
364774 TATTATTATT
* *
364784 TCTTTTACAATTACTTTTTCCATTTTACACACTCCAAACGAATTCCAAAAATTTTATTCACTGAC
1 TCTTTTACAATTACTTTTTCCATTTTACACACTCCAAACAAATTCAAAAAATTTTATTCACTGAC
* *
364849 ATTGGCATATGTGAAGTGTGCTTTTAAAAGGAAACCACATGGGTGCTTTCCATTTGTTTTCCATT
66 ATTGGCATATATGAAGTGTGCTTTTAAAAGGAAACCACATGAGTGCTTTCCATTTGTTTTCCATT
*
364914 CCTTTTACTTTAAGTATAATCACCCTTTGTTATTTTTTTGATAATGTATTTTTATTTATTTCAAC
131 CCTTTTACTTTAAGTATAATCACCCTTTGTTATTTTTTTGATAATATATTTTTATTTATTTCAAC
* *
364979 GGAATAATAAGTTTTATTAATAAATCAATTATAGGTA
196 GGAACAATAAGTTTTATTAATAAATAAATTATAGGTA
* * *
365016 TCTTTTACAATTACTTTTTTCATTTTACACACTCCAAATAAATTTAAAAAATTTTATTCACTGAC
1 TCTTTTACAATTACTTTTTCCATTTTACACACTCCAAACAAATTCAAAAAATTTTATTCACTGAC
*
365081 ATTGGCATATATGAAGTGTGCTTTTAAAAGGAAACCACATGAGTGCTTTCCATTTGTTTTCCCTT
66 ATTGGCATATATGAAGTGTGCTTTTAAAAGGAAACCACATGAGTGCTTTCCATTTGTTTTCCATT
* **
365146 CCTTTTATTTTAAGTATAATCACTTTTTGTTATTTTTTTGATAATATATTTTTATTTATTTCAAC
131 CCTTTTACTTTAAGTATAATCACCCTTTGTTATTTTTTTGATAATATATTTTTATTTATTTCAAC
365211 GGAACAATAAGTTTTATTAATAAATAAATTATAGGTA
196 GGAACAATAAGTTTTATTAATAAATAAATTATAGGTA
365248 ATTATCTAAA
Statistics
Matches: 218, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
232 218 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (232 bp):
TCTTTTACAATTACTTTTTCCATTTTACACACTCCAAACAAATTCAAAAAATTTTATTCACTGAC
ATTGGCATATATGAAGTGTGCTTTTAAAAGGAAACCACATGAGTGCTTTCCATTTGTTTTCCATT
CCTTTTACTTTAAGTATAATCACCCTTTGTTATTTTTTTGATAATATATTTTTATTTATTTCAAC
GGAACAATAAGTTTTATTAATAAATAAATTATAGGTA
Found at i:366720 original size:18 final size:20
Alignment explanation
Indices: 366697--366734 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
366687 ATTCCTTTTT
366697 ATTA-TTATTTC-TTTTACA
1 ATTATTTATTTCATTTTACA
*
366715 ATTATTTTTTTCATTTTACA
1 ATTATTTATTTCATTTTACA
366735 CACACCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTATTTATTTCATTTTACA
Found at i:368806 original size:232 final size:232
Alignment explanation
Indices: 368397--368902 Score: 967
Period size: 232 Copynumber: 2.2 Consensus size: 232
368387 TATTATTATT
*
368397 TCTTTTACAATTACTTTTTTTCATTTTACACACTCCAAATAAATTTAAAAATTTTTATTCACTGA
1 TCTTTTACAATTAC-TTTTTTCATTTTACACACTCCAAATAAATTTAAAAAATTTTATTCACTGA
368462 CATTAGCATATATAAAGTGTGCTTTTAAAAAGAAACCACATGAGTGCTTTCCATTTGTTTTCCCT
65 CATTAGCATATATAAAGTGTGCTTTTAAAAAGAAACCACATGAGTGCTTTCCATTTGTTTTCCCT
368527 TCCTTTTATTTTAAATATAATCACCCTTTGTTATTTTTTTGATAATGTATTTTTATTTATTTCAA
130 TCCTTTTATTTTAAATATAATCACCCTTTGTTATTTTTTTGATAATGTATTTTTATTTATTTCAA
*
368592 CGGAATAATAGGTTTTATTAATAAATCAATTATAGGTA
195 CGGAATAATAAGTTTTATTAATAAATCAATTATAGGTA
368630 TCTTTTACAATTACTTTTTTCATTTTACACACTCCAAATAAATTTAAAAAATTTTATTCACTGAC
1 TCTTTTACAATTACTTTTTTCATTTTACACACTCCAAATAAATTTAAAAAATTTTATTCACTGAC
368695 ATTAGCATATATAAAGTGTGCTTTTAAAAAGAAACCACATGAGTGCTTTCCATTTGTTTTCCCTT
66 ATTAGCATATATAAAGTGTGCTTTTAAAAAGAAACCACATGAGTGCTTTCCATTTGTTTTCCCTT
*
368760 CCTTTTATTTTAAATATAATCACCCTTTGTTATTTTTTTTATAATGTATTTTTATTTATTTCAAC
131 CCTTTTATTTTAAATATAATCACCCTTTGTTATTTTTTTGATAATGTATTTTTATTTATTTCAAC
368825 GGAATAATAAGTTTTATTAATAAATCAATTATAGGTA
196 GGAATAATAAGTTTTATTAATAAATCAATTATAGGTA
*
368862 TCTTTTATAATTACTTTTTTCATTTTACACACTCCAAATAA
1 TCTTTTACAATTACTTTTTTCATTTTACACACTCCAAATAA
368903 TGTCGTAACG
Statistics
Matches: 269, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
232 255 0.95
233 14 0.05
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (232 bp):
TCTTTTACAATTACTTTTTTCATTTTACACACTCCAAATAAATTTAAAAAATTTTATTCACTGAC
ATTAGCATATATAAAGTGTGCTTTTAAAAAGAAACCACATGAGTGCTTTCCATTTGTTTTCCCTT
CCTTTTATTTTAAATATAATCACCCTTTGTTATTTTTTTGATAATGTATTTTTATTTATTTCAAC
GGAATAATAAGTTTTATTAATAAATCAATTATAGGTA
Found at i:372057 original size:13 final size:13
Alignment explanation
Indices: 372039--372063 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
372029 CAAAGATCAG
372039 TGTATCGATACAA
1 TGTATCGATACAA
372052 TGTATCGATACA
1 TGTATCGATACA
372064 TTTGAGTAAT
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:372141 original size:33 final size:33
Alignment explanation
Indices: 372104--372170 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
372094 AGTAGCTTAA
372104 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
372137 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
372170 A
1 A
372171 AATCGTTGAA
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:372144 original size:13 final size:13
Alignment explanation
Indices: 372126--372150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
372116 CAAAAAAATA
372126 TGTATCGATACAT
1 TGTATCGATACAT
372139 TGTATCGATACA
1 TGTATCGATACA
372151 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:373161 original size:49 final size:49
Alignment explanation
Indices: 372986--373229 Score: 283
Period size: 49 Copynumber: 4.8 Consensus size: 49
372976 GTGATAAAGA
* * * *
372986 TGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCT-GATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG
* * * *
373040 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGG
*
373093 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
*
373142 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
373191 TGCCAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
373230 GAAGGGTTGC
Statistics
Matches: 170, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
49 88 0.52
51 1 0.01
52 39 0.23
53 6 0.04
54 1 0.01
55 34 0.20
56 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
Found at i:373410 original size:88 final size:87
Alignment explanation
Indices: 373269--373490 Score: 367
Period size: 88 Copynumber: 2.6 Consensus size: 87
373259 TGGAAAAGGG
* * *
373269 TGCCACTGATTTGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTG
1 TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
373332 ACTTGTGGGCTTTTAAAAAATA
66 ACTTGTGGGCTTTTAAAAAATA
*
373354 TGCCATTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACT
1 TGCCACTGACTTGTGGGCTTTTGAA-AGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACT
*
373419 GACTTGTGGGCTTTTGAAAAATA
65 GACTTGTGGGCTTTTAAAAAATA
373442 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGGTGCCACTAACTTGTGGGCT
373491 GAAAAGAGTG
Statistics
Matches: 127, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
85 16 0.13
86 4 0.03
87 1 0.01
88 104 0.82
89 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.34
Consensus pattern (87 bp):
TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
ACTTGTGGGCTTTTAAAAAATA
Found at i:373416 original size:58 final size:59
Alignment explanation
Indices: 373250--373700 Score: 336
Period size: 57 Copynumber: 7.7 Consensus size: 59
373240 CATCGACTTG
* * *
373250 TGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTT-GAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAAGGTTGCCACTGACT
* ** *
373307 TGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTAAAAAATATGCCATTGACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAAGGT-TGCCACTGACT
* *
373365 TGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAAGGTTGCCACTGACT
*** * *
373423 TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT-AAAAGGTTGCCACTGACT
* * * * ** * * *
373483 TGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
1 TGTGGGCTTTTGAAAAGGGTGCCACT-GACTTGTGGGCTTTTAAAAG-----G-TTGCCACTGAC
373544 T
59 T
* * * * ** * *
373545 TGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTT-TTAAAAGGTTGCCACTGACT
* * *** *
373604 TGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCATTGACT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT-TAAAAGGTTGCCACTGACT
*** *
373661 TGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTT
1 TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT
373701 GAAGGGTGAT
Statistics
Matches: 313, Mismatches: 58, Indels: 45
0.75 0.14 0.11
Matches are distributed among these distances:
55 22 0.07
56 11 0.04
57 79 0.25
58 70 0.22
59 42 0.13
60 48 0.15
61 1 0.00
62 15 0.05
64 15 0.05
65 10 0.03
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (59 bp):
TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAAGGTTGCCACTGACT
Found at i:373576 original size:29 final size:29
Alignment explanation
Indices: 373527--373699 Score: 170
Period size: 29 Copynumber: 5.9 Consensus size: 29
373517 TTACAAAAGA
* * *
373527 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* *
373557 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
373586 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
373615 -AAGGTTGCCACTGACTTGTGGGCTTTCGA
1 AAAAGATGCCACTGACTTGTGGGCTTT-GG
* * *
373644 AAAAAATGCCATTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
373673 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
373700 TGAAGGGTGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
27 21 0.17
28 2 0.02
29 51 0.42
30 47 0.39
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:373702 original size:30 final size:30
Alignment explanation
Indices: 373250--373703 Score: 366
Period size: 30 Copynumber: 15.5 Consensus size: 30
373240 CATCGACTTG
* * *
373250 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
373280 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
373307 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* ** *
373335 TGTGGGCTTTTAAAAAATATGCCATTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* * *
373365 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
373395 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
373423 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
373453 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
373483 TGTGGGC---TGAAAA-GAGTGCTA-TAGAGT
1 TGTGGGCTTTTGAAAAGGA-TGCCACT-GACT
* ** * * *
373510 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTGAAAAGGA-TGCCACTGACT
* * *
373545 TGTGGACTTTGGAAAA-GATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** * *
373574 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
373604 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* ** *
373631 TGTGGGCTTTCGAAAAAAATGCCATTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
373661 TGTGGGC-TTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
373690 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
373704 GGGTGATGAA
Statistics
Matches: 347, Mismatches: 55, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.01
27 60 0.17
28 58 0.17
29 54 0.16
30 145 0.42
31 5 0.01
34 5 0.01
35 18 0.05
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAAGGATGCCACTGACT
Done.