Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 24
Found at i:1226167 original size:20 final size:19
Alignment explanation
Indices: 1226144--1226182 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1226134 CTTTTCGTCT
1226144 CTTA-AAAATTATTTTCTTTC
1 CTTAGAAAA-TATTTT-TTTC
1226164 CTTAGAAAATATTTTTTTC
1 CTTAGAAAATATTTTTTTC
1226183 TTCCTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.54
Consensus pattern (19 bp):
CTTAGAAAATATTTTTTTC
Found at i:1226172 original size:22 final size:22
Alignment explanation
Indices: 1226147--1226188 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1226137 TTCGTCTCTT
1226147 AAAA-ATTATTTTCTTTCCTTAG
1 AAAATATTATTTTC-TTCCTTAG
*
1226169 AAAATATTTTTTTCTTCCTT
1 AAAATATTATTTTCTTCCTT
1226189 GTTTTCCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.29, C:0.14, G:0.02, T:0.55
Consensus pattern (22 bp):
AAAATATTATTTTCTTCCTTAG
Found at i:1227891 original size:52 final size:52
Alignment explanation
Indices: 1227813--1227912 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 52
1227803 TGAATTTTAT
*
1227813 TCATCCAAAAAGAACCTACCTATACAAGCCAATTTACAAA-AACAAAATACA
1 TCATCCAAAAAGAACCTACCTATACAAGCCAAATTACAAAGAACAAAATACA
* * *
1227864 TCATCCAGCAAAGAACCT-CCTTGTACAAGTCAAATTACAAAGAACAAAA
1 TCATCCA-AAAAGAACCTACC-TATACAAGCCAAATTACAAAGAACAAAA
1227913 CACCTCACCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 9 0.21
52 26 0.62
53 7 0.17
ACGTcount: A:0.50, C:0.25, G:0.07, T:0.18
Consensus pattern (52 bp):
TCATCCAAAAAGAACCTACCTATACAAGCCAAATTACAAAGAACAAAATACA
Found at i:1240572 original size:3 final size:3
Alignment explanation
Indices: 1240564--1240599 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1240554 TAAATAAATA
1240564 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1240600 TATGGATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1242773 original size:6 final size:6
Alignment explanation
Indices: 1242748--1242794 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
1242738 ACTAATGTAA
*
1242748 AAATGC AAAGATGC AAATGC AGATGC AAATGC AAATGC AAATGC AAA
1 AAATGC -AA-ATGC AAATGC AAATGC AAATGC AAATGC AAATGC AAA
1242795 AATGCAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 29 0.78
7 4 0.11
8 4 0.11
ACGTcount: A:0.51, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
AAATGC
Found at i:1245300 original size:17 final size:17
Alignment explanation
Indices: 1245268--1245317 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1245258 TAAGAGTTAA
* *
1245268 TTTAATAAACGAACTAG
1 TTTAATGAATGAACTAG
*
1245285 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
1245302 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
1245318 CTTCCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:1250403 original size:26 final size:27
Alignment explanation
Indices: 1250373--1250430 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
1250363 CTCTTTAAAC
*
1250373 TTTTTTCTTTCTT-TTG-CTTTTTTAT
1 TTTTTTATTTCTTCTTGACTTTTTTAT
* *
1250398 TATTTTTATTTGTTCTTGATTTTTTTAT
1 T-TTTTTATTTCTTCTTGACTTTTTTAT
1250426 TTTTT
1 TTTTT
1250431 ACTAACCCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 1 0.04
26 10 0.37
27 7 0.26
28 9 0.33
ACGTcount: A:0.09, C:0.07, G:0.05, T:0.79
Consensus pattern (27 bp):
TTTTTTATTTCTTCTTGACTTTTTTAT
Found at i:1251664 original size:17 final size:17
Alignment explanation
Indices: 1251642--1251680 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1251632 TTAATAAAAA
* *
1251642 AACTAGTTTGATGAATG
1 AACTAGGTTAATGAATG
*
1251659 AACTAGGTTAATTAATG
1 AACTAGGTTAATGAATG
1251676 AACTA
1 AACTA
1251681 CTTCCCTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (17 bp):
AACTAGGTTAATGAATG
Found at i:1252626 original size:30 final size:32
Alignment explanation
Indices: 1252556--1252630 Score: 118
Period size: 31 Copynumber: 2.4 Consensus size: 32
1252546 GGACCAAAAT
*
1252556 AAAAATAATAGAAACTTAAAGGACTAAAATAGC
1 AAAAAAAATA-AAACTTAAAGGACTAAAATAGC
1252589 AAAAAAAATAAAA-TTAAAGGACTAAAATAGC
1 AAAAAAAATAAAACTTAAAGGACTAAAATAGC
1252620 -AAAAAAATAAA
1 AAAAAAAATAAA
1252631 TTTGAAGGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 11 0.27
31 18 0.44
32 3 0.07
33 9 0.22
ACGTcount: A:0.68, C:0.07, G:0.09, T:0.16
Consensus pattern (32 bp):
AAAAAAAATAAAACTTAAAGGACTAAAATAGC
Found at i:1253969 original size:3 final size:3
Alignment explanation
Indices: 1253963--1253997 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1253953 GTAACTTGTA
1253963 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1253998 TAAATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1255399 original size:20 final size:21
Alignment explanation
Indices: 1255374--1255425 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1255364 TTTTCCCAAT
*
1255374 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1255394 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1255415 TCGCAATGCGA
1 TCGCAATGCGA
1255426 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1255548 original size:20 final size:20
Alignment explanation
Indices: 1255414--1255547 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
1255404 AATTGGGAAA
1255414 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1255434 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1255454 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1255474 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1255495 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1255515 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
1255535 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1255548 TTACATAGCG
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 84 0.83
21 13 0.13
22 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1256141 original size:19 final size:19
Alignment explanation
Indices: 1256105--1256146 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1256095 ACGAGAGAAT
*
1256105 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
1256124 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
1256143 CGCA
1 CGCA
1256147 TTGTGGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:1256202 original size:19 final size:19
Alignment explanation
Indices: 1256153--1256324 Score: 202
Period size: 19 Copynumber: 9.5 Consensus size: 19
1256143 CGCATTGTGG
1256153 TTTTCATTTCGCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
*
1256172 --TTC---TCTCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
1256186 TTTTCATTTCGCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
1256205 TTTTCATTTCGCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
1256224 TTTTCATTTCGCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
1256243 TTTTCATTTCGCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
*
1256262 --TTC---TCTCGTTGCGA
1 TTTTCATTTCGCGTTGCGA
** *
1256276 TAGTCATTTCGCATTGCGA
1 TTTTCATTTCGCGTTGCGA
* *
1256295 TTCTCATTATCTCGTTGCGA
1 TTTTCATT-TCGCGTTGCGA
1256315 TTTTCATTTC
1 TTTTCATTTC
1256325 AACCAAAAGA
Statistics
Matches: 131, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
14 20 0.15
16 5 0.04
17 6 0.05
19 84 0.64
20 16 0.12
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.47
Consensus pattern (19 bp):
TTTTCATTTCGCGTTGCGA
Found at i:1256283 original size:33 final size:33
Alignment explanation
Indices: 1256194--1256299 Score: 131
Period size: 33 Copynumber: 3.1 Consensus size: 33
1256184 GATTTTCATT
1256194 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTC
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGA--TTC
1256229 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
1 ---TCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
* ** *
1256265 TCTCGTTGCGATAGTCATTTCGCATTGCGATTC
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
1256298 TC
1 TC
1256300 ATTATCTCGT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
33 31 0.48
36 3 0.05
38 30 0.47
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
Found at i:1258493 original size:21 final size:21
Alignment explanation
Indices: 1258469--1258619 Score: 51
Period size: 21 Copynumber: 7.2 Consensus size: 21
1258459 TCATTCATCG
1258469 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * *
1258490 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCTCA-CCGTTCA
* * * *
1258511 AGAGTCCACTC-CTATCATTGA
1 AGAGTCCCCTCTC-ACCGTTCA
* * *
1258532 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCTCA--CCGTTCA
*
1258553 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * * *
1258574 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCTCACCGTTCA
* *
1258595 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCTCACCGTTCA
1258616 AGAG
1 AGAG
1258620 CCCGATTCAC
Statistics
Matches: 89, Mismatches: 32, Indels: 19
0.64 0.23 0.14
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 79 0.89
22 4 0.04
23 1 0.01
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:1258493 original size:42 final size:41
Alignment explanation
Indices: 1258417--1258580 Score: 166
Period size: 42 Copynumber: 3.9 Consensus size: 41
1258407 GACTCGCCTG
* * * * *
1258417 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCC-ACCGTTCAAGAGGCCCCTA
* * *
1258459 TCATTCATCGAGAGTCCCCTCTCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTC-CACCGTTCAAGAGGCCCCTA
* * * * * *
1258501 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCC-ACCGTTCAAGAGGCCCCTA
1258543 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATTCCTCGAGAGTCCCCT-CCACCGTTCAAGAGGCC
1258581 ACTGTCATCG
Statistics
Matches: 96, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
41 1 0.01
42 92 0.96
43 3 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (41 bp):
TCATTCCTCGAGAGTCCCCTCCACCGTTCAAGAGGCCCCTA
Found at i:1258598 original size:84 final size:84
Alignment explanation
Indices: 1258414--1258589 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
1258404 CCCGACTCGC
*
1258414 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCATCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCATCGAGAGTCCCCT
*
1258479 CTCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
1258498 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCATCGAGAGTCCCCT
1258563 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1258582 CTGTCATC
1 CTGTCATC
1258590 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCATCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1258605 original size:42 final size:41
Alignment explanation
Indices: 1258469--1258619 Score: 142
Period size: 42 Copynumber: 3.6 Consensus size: 41
1258459 TCATTCATCG
* * * *
1258469 AGAGTCCCCTCTCACCGTTCAAGAGGCCACTGTCATCCCTCA
1 AGAGT-CCCTCCCACCATTCAAGAGGCCACTGTCATCCTTGA
* * * * * *
1258511 AGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCG-
1 AGAGTCC-CTCCCACCATTCAAGAGGCCACTGTCA-TCCTTGA
* *
1258553 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTGA
1 AGAGT-CCCTCCCACCATTCAAGAGGCCACTGTCATCCTTGA
1258595 AGAGGTCCCTCCCACCATTCAAGAG
1 AGA-GTCCCTCCCACCATTCAAGAG
1258620 CCCGATTCAC
Statistics
Matches: 85, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
41 6 0.07
42 72 0.85
43 7 0.08
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (41 bp):
AGAGTCCCTCCCACCATTCAAGAGGCCACTGTCATCCTTGA
Found at i:1258619 original size:84 final size:84
Alignment explanation
Indices: 1258414--1258619 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
1258404 CCCGACTCGC
* * * *
1258414 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCATCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCATCGAGAGTCCCCT
*
1258479 CTCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
1258498 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCATCGAGAGTCCCCT
1258563 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
1258582 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
1258620 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCATCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1260674 original size:20 final size:20
Alignment explanation
Indices: 1260632--1260697 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
1260622 TAGTTTACTT
* * **
1260632 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
1260652 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1260672 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1260692 TCGCAA
1 TCGCAA
1260698 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1260706 original size:19 final size:20
Alignment explanation
Indices: 1260651--1260718 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
1260641 GAAACTTAAA
* *
1260651 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
1260671 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* **
1260691 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
1260710 ATCGCAACG
1 ATCGCAACG
1260719 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:1260785 original size:14 final size:14
Alignment explanation
Indices: 1260766--1260823 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1260756 TTTCATTTCG
1260766 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1260780 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1260796 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1260812 CGTTGCGATTTT
1 CGTTGCGATTTT
1260824 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1260830 original size:33 final size:33
Alignment explanation
Indices: 1260749--1260839 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1260739 ACAAATCGCA
*
1260749 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1260782 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1260814 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1260840 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1260846 original size:19 final size:20
Alignment explanation
Indices: 1260824--1260867 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1260814 TTGCGATTTT
1260824 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
1260843 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
1260863 CATTT
1 CATTT
1260868 TCGTGTTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:1261380 original size:18 final size:18
Alignment explanation
Indices: 1261354--1261398 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1261344 GTCGATCAGA
*
1261354 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1261372 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1261390 TGATGGCTC
1 TGATGGCTC
1261399 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1262745 original size:20 final size:20
Alignment explanation
Indices: 1262720--1262793 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1262710 AATAGTTTCT
*
1262720 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
1262740 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
1262760 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
1262780 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1262794 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:1263053 original size:22 final size:22
Alignment explanation
Indices: 1263026--1263069 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1263016 GATGGAGATA
1263026 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1263048 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1263070 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1263343 original size:20 final size:20
Alignment explanation
Indices: 1263237--1263371 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1263227 CGCTTTGAAA
*
1263237 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1263258 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1263278 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1263298 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1263319 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1263339 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1263359 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1263372 TTTTCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1263343 original size:61 final size:61
Alignment explanation
Indices: 1263237--1263374 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
1263227 CGCTTTGAAA
* * * *
1263237 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
1263298 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
1263359 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1263375 TCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1263390 original size:61 final size:61
Alignment explanation
Indices: 1263237--1263392 Score: 181
Period size: 61 Copynumber: 2.6 Consensus size: 61
1263227 CGCTTTGAAA
* * * * *
1263237 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
1263298 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
1263359 ATCGCATTGCGATTTT-TCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTTGT--AATATCGCGTTGCGAT
1263393 TTACTTATTC
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
60 1 0.01
61 77 0.96
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1263482 original size:21 final size:21
Alignment explanation
Indices: 1263442--1263482 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1263432 ACTGTAGACC
**
1263442 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1263463 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1263483 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1267529 original size:15 final size:15
Alignment explanation
Indices: 1267494--1267522 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1267484 ATGTACAGAA
1267494 AATAATTTTAAATTG
1 AATAATTTTAAATTG
1267509 AATAATTTTAAATT
1 AATAATTTTAAATT
1267523 ACTTAATAAT
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
AATAATTTTAAATTG
Found at i:1267750 original size:13 final size:13
Alignment explanation
Indices: 1267734--1267772 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
1267724 GAATCATATA
1267734 TTTAAATATAATT
1 TTTAAATATAATT
*
1267747 TTTAAATTGATTATT
1 TTTAAA-T-ATAATT
1267762 TTTAAATATAA
1 TTTAAATATAA
1267773 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (13 bp):
TTTAAATATAATT
Found at i:1267796 original size:15 final size:16
Alignment explanation
Indices: 1267762--1267801 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1267752 ATTGATTATT
* *
1267762 TTTAAATATAAATTAA
1 TTTAAAAATAAATCAA
1267778 TTTAAAAAT-AATCAA
1 TTTAAAAATAAATCAA
1267793 TTTAAAAAT
1 TTTAAAAAT
1267802 TATATATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTAAAAATAAATCAA
Found at i:1269496 original size:25 final size:25
Alignment explanation
Indices: 1269468--1269515 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1269458 TTCTAGATTA
1269468 ATTA-AAACCACCCATCTTTCTTCTT
1 ATTAGAAA-CACCCATCTTTCTTCTT
* *
1269493 ATTAGGAACACTCATCTTTCTTC
1 ATTAGAAACACCCATCTTTCTTC
1269516 GAGTCCTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTAGAAACACCCATCTTTCTTCTT
Found at i:1270315 original size:17 final size:17
Alignment explanation
Indices: 1270293--1270342 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1270283 AAATTCTTCT
1270293 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
1270310 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
1270324 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
1270341 AA
1 AA
1270343 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:1270680 original size:20 final size:20
Alignment explanation
Indices: 1270655--1270696 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1270645 TATAATATAT
*
1270655 ATATATGGATGGATGGATGG
1 ATATATGAATGGATGGATGG
* *
1270675 ATATATTAATGGGTGGATGG
1 ATATATGAATGGATGGATGG
1270695 AT
1 AT
1270697 GCTGCGGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (20 bp):
ATATATGAATGGATGGATGG
Found at i:1270686 original size:24 final size:26
Alignment explanation
Indices: 1270649--1270697 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
1270639 ATATAATATA
1270649 ATATATATATATGGATGGATGGATGG
1 ATATATATATATGGATGGATGGATGG
*
1270675 ATATAT-TA-ATGGGTGGATGGATG
1 ATATATATATATGGATGGATGGATG
1270698 CTGCGGGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 2 0.09
26 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (26 bp):
ATATATATATATGGATGGATGGATGG
Found at i:1277532 original size:30 final size:30
Alignment explanation
Indices: 1277491--1277550 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1277481 CAATTCAAGG
1277491 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTTTTTGGACTT-AATTGAATTTA
1277522 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATAGTTTTTGGACTTAATTGAATTTA
1277551 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATAGTTTTTGGACTTAATTGAATTTA
Found at i:1277656 original size:20 final size:20
Alignment explanation
Indices: 1277631--1277704 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1277621 GGGTGTCAAA
1277631 GTGCATCCATGCATCCTTCT
1 GTGCATCCATGCATCCTTCT
* ***
1277651 GTGCATCAATGCATCAAGGCT
1 GTGCATCCATGCATC-CTTCT
*
1277672 GTGCATCGATGCATCCTGT-T
1 GTGCATCCATGCATCCT-TCT
1277692 GTGCATCCATGCA
1 GTGCATCCATGCA
1277705 CGAAGGTTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (20 bp):
GTGCATCCATGCATCCTTCT
Found at i:1281262 original size:22 final size:20
Alignment explanation
Indices: 1281231--1281282 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
1281221 ATTCAACCAA
*
1281231 TATCGGTACCCAAGCAATGTGG
1 TATCGATACCCAAGCAA-G-GG
* *
1281253 TATCGATACCCTAGTAAGGG
1 TATCGATACCCAAGCAAGGG
1281273 TATCGATACC
1 TATCGATACC
1281283 AGTAAGCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 12 0.44
21 1 0.04
22 14 0.52
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (20 bp):
TATCGATACCCAAGCAAGGG
Found at i:1281372 original size:20 final size:20
Alignment explanation
Indices: 1281304--1281377 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
1281294 AATCTAATTT
*
1281304 GGGTATCGATACC-TAGAAG-
1 GGGTATCGATACCAT-GATGA
* * *
1281323 GGGTATCGGTACCATAACTTA
1 GGGTATCGATACCATGA-TGA
*
1281344 GGTTATCGATACCATGATGA
1 GGGTATCGATACCATGATGA
1281364 GGGTATCGATACCA
1 GGGTATCGATACCA
1281378 GGTTATTTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.30
20 16 0.37
21 14 0.33
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATGATGA
Found at i:1281449 original size:22 final size:21
Alignment explanation
Indices: 1281416--1281473 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
1281406 ATACATGAAG
*
1281416 GGGGTATTGATACCTTAA-TA
1 GGGGTATCGATACCTTAAGTA
*
1281436 GGGTAGTATCGATACCATAAGTA
1 GGG--GTATCGATACCTTAAGTA
1281459 GGGGTATCGATACCT
1 GGGGTATCGATACCT
1281474 AAGAGCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
22 13 0.41
23 5 0.16
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (21 bp):
GGGGTATCGATACCTTAAGTA
Found at i:1281467 original size:21 final size:21
Alignment explanation
Indices: 1281401--1281476 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
1281391 CTAATTTTGA
1281401 TATCGATA-CATGAAG--GGGG
1 TATCGATACCAT-AAGTAGGGG
* *
1281420 TATTGATACCTTAA-TAGGGTAG
1 TATCGATACCATAAGTAGGG--G
1281442 TATCGATACCATAAGTAGGGG
1 TATCGATACCATAAGTAGGGG
1281463 TATCGATACC-TAAG
1 TATCGATACCATAAG
1281477 AGCAAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
19 9 0.19
20 9 0.19
21 11 0.23
22 13 0.28
23 5 0.11
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (21 bp):
TATCGATACCATAAGTAGGGG
Found at i:1281885 original size:59 final size:59
Alignment explanation
Indices: 1281796--1282126 Score: 520
Period size: 59 Copynumber: 5.6 Consensus size: 59
1281786 TACCAAATGA
*
1281796 CACTTTGTGTGCTAAAAATGGTAATGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
1 CACTTTGTGTGCT-AAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* * *
1281856 CACTTGGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTAGGAAATTCCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* *
1281915 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAAATTCCAGATATGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
*
1281974 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* * *
1282033 CACTTTGTGTACTAAAA-GAGTAAGAAAAACATACTAAGTGTATGAATTTCCAGATAGGG
1 CACTTTGTGTGCTAAAATG-GTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* * *
1282092 CATTTTGTGTGCTAAAATGATAAGGAAGTCATACT
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACT
1282127 GTCTGTATGA
Statistics
Matches: 249, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
58 1 0.00
59 235 0.94
60 13 0.05
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (59 bp):
CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
Found at i:1288425 original size:22 final size:21
Alignment explanation
Indices: 1288391--1288451 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
1288381 ATACATGACG
*
1288391 GGGGTATTC-ATACCCTAA-TA
1 GGGGTA-TCGATACCATAAGTA
1288411 GGGTAGTATCGATACCATAAGTA
1 GGG--GTATCGATACCATAAGTA
1288434 GGGGTATCGATACC-TAAG
1 GGGGTATCGATACCATAAG
1288452 AGCCAGAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 7 0.19
21 13 0.36
22 11 0.31
23 5 0.14
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (21 bp):
GGGGTATCGATACCATAAGTA
Found at i:1289171 original size:59 final size:59
Alignment explanation
Indices: 1288771--1289158 Score: 607
Period size: 59 Copynumber: 6.6 Consensus size: 59
1288761 TACCAAATGA
*
1288771 CACTTTGTGTGCTAAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGG
1 CACTTTGTGTGCT-AAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* * *
1288831 CACTTTGTGTGCTTAAACGGTAAGGAAATCATACTAAGTGTATGAATTACCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* *
1288890 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAAATTCCATATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* * *
1288949 CACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTATATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
*
1289008 CACTTTGCGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* * *
1289067 CACTTTGTGTCCTAAAA-GAGTAAGGAAAACATACTAAGTGTATGAATTTCCAAATAGGG
1 CACTTTGTGTGCTAAAATG-GTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
* * *
1289126 CACTTTGTTTGCTAAAATGATAAGGAAGTCATA
1 CACTTTGTGTGCTAAAATGGTAAGGAAATCATA
1289159 ATGTTTGTAT
Statistics
Matches: 301, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
58 1 0.00
59 286 0.95
60 14 0.05
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (59 bp):
CACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGG
Found at i:1289418 original size:24 final size:24
Alignment explanation
Indices: 1289386--1289433 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1289376 AAATGCAGCT
*
1289386 GAGTAAGGAGATCTTTTGGACATC
1 GAGTAAGGAGATATTTTGGACATC
*
1289410 GAGTAAGGAGATATTTTGGGCATC
1 GAGTAAGGAGATATTTTGGACATC
1289434 CAGTCAGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.29
Consensus pattern (24 bp):
GAGTAAGGAGATATTTTGGACATC
Found at i:1290291 original size:32 final size:32
Alignment explanation
Indices: 1290213--1290298 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
1290203 AGAATATCGC
* * *
1290213 ATTTAAATAATACACAGTAGTGTCAATGACAT
1 ATTTAGATAATACATAGCAGTGTCAATGACAT
* * *
1290245 ATTCAGATAATACATAGCAGTGTCAGTGTCAT
1 ATTTAGATAATACATAGCAGTGTCAATGACAT
*
1290277 ATTTAGATAATACATATCAGTG
1 ATTTAGATAATACATAGCAGTG
1290299 AGTCCTGTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (32 bp):
ATTTAGATAATACATAGCAGTGTCAATGACAT
Found at i:1290316 original size:35 final size:32
Alignment explanation
Indices: 1290212--1290318 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 32
1290202 TAGAATATCG
* * * * *
1290212 CATTTAAATAATACACAGTAGTGTCAATGACA
1 CATTTAGATAATACATAGCAGTGTCAGTGTCA
* *
1290244 TATTCAGATAATACATAGCAGTGTCAGTGTCA
1 CATTTAGATAATACATAGCAGTGTCAGTGTCA
* * *
1290276 TATTTAGATAATACATATCAGTGAGTCCTGTGTCA
1 CATTTAGATAATACATAGCAGT--GT-CAGTGTCA
1290311 CATTTAGA
1 CATTTAGA
1290319 GAATGCACAA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
32 45 0.74
34 2 0.03
35 14 0.23
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
CATTTAGATAATACATAGCAGTGTCAGTGTCA
Found at i:1293846 original size:20 final size:20
Alignment explanation
Indices: 1293804--1293873 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1293794 AAAGTGTTTT
*
1293804 TATGAATAGTA-CTGTACTA
1 TATGAATAGTACCAGTACTA
*
1293823 TATGAATAGTACCAGTACTG
1 TATGAATAGTACCAGTACTA
1293843 TATGAATAGTACC-GATACTA
1 TATGAATAGTACCAG-TACTA
* *
1293863 TGTGAACAGTA
1 TATGAATAGTA
1293874 ATGAACAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 12 0.27
20 32 0.73
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (20 bp):
TATGAATAGTACCAGTACTA
Found at i:1297670 original size:20 final size:20
Alignment explanation
Indices: 1297645--1297694 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1297635 ATAGTACTGT
1297645 ACTGTATGAATAATACCGAC
1 ACTGTATGAATAATACCGAC
** *
1297665 ACTGTATGAATCTTACCGAT
1 ACTGTATGAATAATACCGAC
1297685 ACTGTATGAA
1 ACTGTATGAA
1297695 CAGTAATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
ACTGTATGAATAATACCGAC
Found at i:1298179 original size:33 final size:32
Alignment explanation
Indices: 1298124--1298186 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
1298114 AAGGGGTTTT
*
1298124 GGTTCTAGCTGATCCCGAGAAAAGCTAGGGAAA
1 GGTTCTAGCTGATCACGAGAAAA-CTAGGGAAA
* * *
1298157 GGTTCTAGTTTATCACGTGAAAACTAGGGA
1 GGTTCTAGCTGATCACGAGAAAACTAGGGA
1298187 GTTTGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 7 0.27
33 19 0.73
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGTTCTAGCTGATCACGAGAAAACTAGGGAAA
Found at i:1302992 original size:79 final size:79
Alignment explanation
Indices: 1302821--1303213 Score: 581
Period size: 79 Copynumber: 5.0 Consensus size: 79
1302811 TAACATACTT
* ** * * * ** * *
1302821 TTATGTTGATAATACACCCATATGCATTTCAACTTTGGCATCCTTTCATTGCTAATAATGCACCC
1 TTATGCTGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCA-TGCCACTAATGCACCC
1302886 ATATGCATTATTTTG
65 ATATGCATTATTTTG
* *
1302901 TTATGCTGATAATGTACCCATATACATATCTGCTAAGGCATCCTTTCATGCCACTAATACACCCA
1 TTATGCTGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCA
1302966 TATGCATTATTTTG
66 TATGCATTATTTTG
*
1302980 TTATGCTAATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCA
1 TTATGCTGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCA
*
1303045 TATGCATTATTCTG
66 TATGCATTATTTTG
* * *
1303059 TTATGCCGATAATGTACCCATATATATATCAGCTAAGGCATCCTTTCATACCACTAATGCACCCA
1 TTATGCTGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCA
*
1303124 TATGCATTATTATG
66 TATGCATTATTTTG
* *
1303138 TTATG-TCGATAATGTACCCATATATATATCAGCTAAGGCATCATTTCATGCCACTAATGCACCC
1 TTATGCT-GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCC
1303202 ATATGCATTATT
65 ATATGCATTATT
1303214 CTTTTATTCA
Statistics
Matches: 288, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
79 249 0.86
80 39 0.14
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (79 bp):
TTATGCTGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCA
TATGCATTATTTTG
Found at i:1303038 original size:45 final size:45
Alignment explanation
Indices: 1302989--1303205 Score: 124
Period size: 45 Copynumber: 5.3 Consensus size: 45
1302979 GTTATGCTAA
*
1302989 TAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAC
1 TAATGCACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAC
*
1303034 TAATGCACCCATATGCAT-T-A--T------T-CTGTT-ATGCCGA-
1 TAATGCACCCATATACATATCAGCTAAGGCATCCT-TTCATGCC-AC
* * *
1303068 TAATGTACCCATATATATATCAGCTAAGGCATCCTTTCATACCAC
1 TAATGCACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAC
* * * *
1303113 TAATGCACCCATATGCAT-T-A--T----TAT--GTT-ATGTCGA-
1 TAATGCACCCATATACATATCAGCTAAGGCATCCTTTCATG-CCAC
* * *
1303147 TAATGTACCCATATATATATCAGCTAAGGCATCATTTCATGCCAC
1 TAATGCACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAC
1303192 TAATGCACCCATAT
1 TAATGCACCCATAT
1303206 GCATTATTCT
Statistics
Matches: 124, Mismatches: 20, Indels: 56
0.62 0.10 0.28
Matches are distributed among these distances:
34 39 0.31
35 10 0.08
36 2 0.02
37 2 0.02
38 2 0.02
41 2 0.02
42 2 0.02
43 2 0.02
44 10 0.08
45 53 0.43
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (45 bp):
TAATGCACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAC
Found at i:1303636 original size:22 final size:21
Alignment explanation
Indices: 1303587--1303643 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
1303577 CTGGCCCTTC
*
1303587 GGTATCGATACCCCTACTTAT
1 GGTATCGATACCCCTACTTAG
1303608 GGTATCGATACTACCCTA-TTAG
1 GGTATCGATAC--CCCTACTTAG
1303630 GGTATCGATACCCC
1 GGTATCGATACCCC
1303644 CTTAATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 11 0.33
22 14 0.42
23 5 0.15
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (21 bp):
GGTATCGATACCCCTACTTAG
Found at i:1303806 original size:96 final size:93
Alignment explanation
Indices: 1303587--1303812 Score: 247
Period size: 95 Copynumber: 2.4 Consensus size: 93
1303577 CTGGCCCTTC
* * * *
1303587 GGTATCGATACCCCTACTTATGGTATCGATACTACCCTATTAGGGTATCGATACCCCCTTAATTT
1 GGTATCGATACCCTTAC-CATGGTATCGATAC--CCCTATTAGGGTATCAATACCCCCTTAATGT
* *
1303652 ATCAATACCAAAATTAGCTTCGATGTAGACT
63 ATCAATACCAAAATTAGATTCGATGTAGAAT
* * * * *
1303683 GGTATCGGTACCCTCACCATGGTATCGACACCCCTATACTATGGTATCAATACCCTCTCTAA-GT
1 GGTATCGATACCCTTACCATGGTATCGATACCCCTAT--TAGGGTATCAATACCCCCT-TAATGT
* * **
1303747 ATCGATACCCAAATTAGATTCGATGTTTTAAT
63 ATCAATACCAAAATTAGATTCGATG-TAGAAT
1303779 GGTATCGATACCCTTACCATGGTATCGATACCCC
1 GGTATCGATACCCTTACCATGGTATCGATACCCC
1303813 ATTGCTTGGG
Statistics
Matches: 108, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
93 6 0.06
95 51 0.47
96 51 0.47
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (93 bp):
GGTATCGATACCCTTACCATGGTATCGATACCCCTATTAGGGTATCAATACCCCCTTAATGTATC
AATACCAAAATTAGATTCGATGTAGAAT
Found at i:1314167 original size:25 final size:25
Alignment explanation
Indices: 1314133--1314182 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1314123 CCATCATTCT
1314133 ACTTCACATCGTGTAACTACGAACG
1 ACTTCACATCGTGTAACTACGAACG
*
1314158 ACTTCCCATCGTGTAACTACGAACG
1 ACTTCACATCGTGTAACTACGAACG
1314183 GCTCTAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (25 bp):
ACTTCACATCGTGTAACTACGAACG
Found at i:1315711 original size:25 final size:25
Alignment explanation
Indices: 1315683--1315730 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
1315673 AATCATTAAC
1315683 AGCAATCTTCTAGAACCACTATGCA
1 AGCAATCTTCTAGAACCACTATGCA
1315708 AGCAATCTTCTAGAACCACTATG
1 AGCAATCTTCTAGAACCACTATG
1315731 ATGCATGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (25 bp):
AGCAATCTTCTAGAACCACTATGCA
Found at i:1322734 original size:5 final size:5
Alignment explanation
Indices: 1322645--1322733 Score: 151
Period size: 5 Copynumber: 17.8 Consensus size: 5
1322635 GAAAGCATTA
*
1322645 TAATA TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG
* *
1322695 TAATG TAATG TAATA TAATG TAATG TAATG TAATA TAAT
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAAT
1322734 AATTTTCGTA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 80 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (5 bp):
TAATG
Found at i:1324587 original size:10 final size:9
Alignment explanation
Indices: 1324546--1324635 Score: 56
Period size: 10 Copynumber: 9.2 Consensus size: 9
1324536 TTCCACGAAG
1324546 AAGAAAAAA
1 AAGAAAAAA
1324555 AAGAAGAAAGA
1 AAGAA-AAA-A
*
1324566 AAGTTAAAAA
1 AAG-AAAAAA
1324576 AAGAAAAGAA
1 AAGAAAA-AA
**
1324586 AA-AATCCGAA
1 AAGAA--AAAA
1324596 AAGAAAAAA
1 AAGAAAAAA
*
1324605 ATGAAAAAA
1 AAGAAAAAA
*
1324614 AGGGAAAAAA
1 A-AGAAAAAA
1324624 GAAGAAAAAA
1 -AAGAAAAAA
1324634 AA
1 AA
1324636 ATGAAAAACG
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
9 23 0.37
10 29 0.46
11 10 0.16
12 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:1326358 original size:5 final size:5
Alignment explanation
Indices: 1326348--1326409 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
1326338 ATATTCGAAT
* *
1326348 TAAAA TAAAA TAAAA TAAAA T-AAA TAAAA TAATA TAAAA CAGATAA TAAATA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA-A-AA TAAA-A
*
1326400 AAAAA TAAAA
1 TAAAA TAAAA
1326410 AATAATAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 4 0.09
5 34 0.72
6 6 0.13
7 3 0.06
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:1326372 original size:14 final size:14
Alignment explanation
Indices: 1326348--1326385 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1326338 ATATTCGAAT
1326348 TAAAATAAAATAAAA
1 TAAAAT-AAATAAAA
1326363 TAAAATAAATAAAA
1 TAAAATAAATAAAA
*
1326377 TAATATAAA
1 TAAAATAAA
1326386 ACAGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAATAAATAAAA
Found at i:1326372 original size:19 final size:19
Alignment explanation
Indices: 1326350--1326386 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1326340 ATTCGAATTA
1326350 AAATAAAATAAAATAAAAT
1 AAATAAAATAAAATAAAAT
*
1326369 AAATAAAATAATATAAAA
1 AAATAAAATAAAATAAAA
1326387 CAGATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAT
Found at i:1326393 original size:19 final size:19
Alignment explanation
Indices: 1326350--1326393 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1326340 ATTCGAATTA
*
1326350 AAATAAAATAAAATAAAAT
1 AAATAAAATAAAATAAAAC
*
1326369 AAATAAAATAATATAAAAC
1 AAATAAAATAAAATAAAAC
*
1326388 AGATAA
1 AAATAA
1326394 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAC
Found at i:1326463 original size:27 final size:27
Alignment explanation
Indices: 1326443--1326496 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1326433 ATATTTTTTC
1326443 AAAAATATTTT-AAAACTATATATTAT
1 AAAAATATTTTCAAAACTATATATTAT
*
1326469 AAAAATGTTTTCAAAACTATATATTAT
1 AAAAATATTTTCAAAACTATATATTAT
1326496 A
1 A
1326497 TAGTTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (27 bp):
AAAAATATTTTCAAAACTATATATTAT
Found at i:1326463 original size:36 final size:37
Alignment explanation
Indices: 1326423--1326586 Score: 131
Period size: 36 Copynumber: 4.7 Consensus size: 37
1326413 AATAATATAT
*
1326423 TATATATAATATATTTTTTCAAAAATATTTT-AAAAC
1 TATATATAATATATTTTTTCAAAAATGTTTTCAAAAC
*
1326459 --TATAT-AT-TA-----T-AAAAATGTTTTCAAAA-C
1 TATATATAATATATTTTTTCAAAAATGTTTT-CAAAAC
* * *
1326486 TATATATTATATAGTTTTC-AAAAATGTTTTCAAAAC
1 TATATATAATATATTTTTTCAAAAATGTTTTCAAAAC
* *
1326522 TATATATTATATATATTTTC-AAAATGTTTTCAAAAAC
1 TATATATAATATATTTTTTCAAAAATGTTTTC-AAAAC
1326559 TATATATTATATATATTTTTTCAAAAAT
1 TATATA-TA-ATATATTTTTTCAAAAAT
1326587 TTATTTTTTA
Statistics
Matches: 103, Mismatches: 8, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
26 10 0.10
27 2 0.02
28 3 0.03
29 5 0.05
30 2 0.02
31 2 0.02
32 2 0.02
33 2 0.02
34 5 0.05
35 3 0.03
36 39 0.38
37 11 0.11
38 1 0.01
39 11 0.11
40 5 0.05
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
TATATATAATATATTTTTTCAAAAATGTTTTCAAAAC
Found at i:1326509 original size:25 final size:26
Alignment explanation
Indices: 1326444--1326508 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 26
1326434 TATTTTTTCA
*
1326444 AAAATATTTT-AAAACTATATATTAT
1 AAAATGTTTTCAAAACTATATATTAT
1326469 AAAAATGTTTTCAAAACTATATATTAT
1 -AAAATGTTTTCAAAACTATATATTAT
*
1326496 -ATA-GTTTTCAAAA
1 AAAATGTTTTCAAAA
1326509 ATGTTTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 10 0.28
25 2 0.06
26 9 0.25
27 15 0.42
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (26 bp):
AAAATGTTTTCAAAACTATATATTAT
Found at i:1326558 original size:37 final size:36
Alignment explanation
Indices: 1326459--1326577 Score: 186
Period size: 36 Copynumber: 3.3 Consensus size: 36
1326449 ATTTTAAAAC
* *
1326459 TATATATTATAAAAATGTTTTCAAAACTATATATTA
1 TATATATTTTCAAAATGTTTTCAAAACTATATATTA
*
1326495 TATA-GTTTTCAAAAATGTTTTCAAAACTATATATTA
1 TATATATTTTC-AAAATGTTTTCAAAACTATATATTA
1326531 TATATATTTTCAAAATGTTTTCAAAAACTATATATTA
1 TATATATTTTCAAAATGTTTTC-AAAACTATATATTA
1326568 TATATATTTT
1 TATATATTTT
1326578 TTCAAAAATT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 3 0.04
36 44 0.58
37 29 0.38
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATATTTTCAAAATGTTTTCAAAACTATATATTA
Found at i:1327206 original size:14 final size:14
Alignment explanation
Indices: 1327187--1327217 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1327177 TCTTCGTTGC
1327187 TACAATACAGCTGA
1 TACAATACAGCTGA
*
1327201 TACAATACAGTTGA
1 TACAATACAGCTGA
1327215 TAC
1 TAC
1327218 GCCCTCGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (14 bp):
TACAATACAGCTGA
Found at i:1327671 original size:260 final size:260
Alignment explanation
Indices: 1327222--1327849 Score: 943
Period size: 260 Copynumber: 2.4 Consensus size: 260
1327212 TGATACGCCC
* * *
1327222 TCGAGATGAATGAAATTGAACTCGAAAGTCTTCATTGACAGATAACCCTTCTCGCCTTGAGCTAT
1 TCGAGATGAATGGAATCGAACTCGAAAGTTTTCATTGACAGATAACCCTTCTCGCCTTGAGCTAT
* * * * *
1327287 GTTGTAAATTTGTTATGCCCTTGAGTTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAA
66 GATGTAAATTTATTATGCCCTTGAGCTGAATGAAATCGAACTCAAAAGTTTTTGTTGACAGATAA
* *
1327352 CCCTCATCGCCTTGAGTTATGCTATACTAGATTGAGAGATTGCCCCATATCTTCTTCTTGACTTA
131 CCCTCATCGCCTTGAGTTATGATATACTAGATTGAGAGATTGCCCCAGATCTTCTTCTTGACTTA
* *
1327417 AACACCTTGGTTTAAACTTTAACCGGAAAGTAATTCCTCGCTGCTACCATACTGTTGATATGTCA
196 AACACCTTGGTTTAAACTTTAACCGGAAAGTAATTCCTCACTGCTACCATACGGTTGATATGTCA
* * *
1327482 TCGAGTTGAATGGAATCGAACTCGAAAGTTTTCATTAACAAATAACCCTTCTCGCCTTGAGCTAT
1 TCGAGATGAATGGAATCGAACTCGAAAGTTTTCATTGACAGATAACCCTTCTCGCCTTGAGCTAT
* *
1327547 GCTATAAATTTATTATGCCCTTGAGCTGAATGAAATCGAACTCAAAAGTTTTTGTTGACAGATAA
66 GATGTAAATTTATTATGCCCTTGAGCTGAATGAAATCGAACTCAAAAGTTTTTGTTGACAGATAA
* * * * *
1327612 CCCTCCTCTCCTTGAGTTATGATGTACTAGATTGAGAGATTGCTCCAGGTCTTCTTCTTGACTTA
131 CCCTCATCGCCTTGAGTTATGATATACTAGATTGAGAGATTGCCCCAGATCTTCTTCTTGACTTA
* * * *
1327677 AAGACCTTGGTTTAAACTTTAACTGGAAAGTAGTTCCTCACTGCTACCATGCGGTTGATATGTCA
196 AACACCTTGGTTTAAACTTTAACCGGAAAGTAATTCCTCACTGCTACCATACGGTTGATATGTCA
* * ** * *
1327742 TCGAGCTGAATGGAATCGAACTCGACAGTTTTTTGTTGACAGACAACCCTTCTCGCCTTAAGCTA
1 TCGAGATGAATGGAATCGAACTCGAAAG-TTTTCATTGACAGATAACCCTTCTCGCCTTGAGCTA
1327807 TGATGTAAATTTGA-TATGCCCTTGAGCTGAATGAAATCGAACT
65 TGATGTAAATTT-ATTATGCCCTTGAGCTGAATGAAATCGAACT
1327850 TGAAATTCTT
Statistics
Matches: 331, Mismatches: 35, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
260 261 0.79
261 69 0.21
262 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (260 bp):
TCGAGATGAATGGAATCGAACTCGAAAGTTTTCATTGACAGATAACCCTTCTCGCCTTGAGCTAT
GATGTAAATTTATTATGCCCTTGAGCTGAATGAAATCGAACTCAAAAGTTTTTGTTGACAGATAA
CCCTCATCGCCTTGAGTTATGATATACTAGATTGAGAGATTGCCCCAGATCTTCTTCTTGACTTA
AACACCTTGGTTTAAACTTTAACCGGAAAGTAATTCCTCACTGCTACCATACGGTTGATATGTCA
Found at i:1334551 original size:5 final size:5
Alignment explanation
Indices: 1334541--1334631 Score: 78
Period size: 5 Copynumber: 17.4 Consensus size: 5
1334531 TGGACCGAAT
* * *
1334541 TAAAA TAAAA TAAAA TAAAA T-AAG CAAAA TAAAA TAAAA TAAAACA TATAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAA-A TAAAA
*
1334592 T-AAA TAAAA TAATA TAAATA TAATAA TAATAA TAATAA TA
1 TAAAA TAAAA TAAAA TAAA-A TAA-AA TAA-AA TAA-AA TA
1334632 TATTATATAT
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
4 5 0.07
5 40 0.56
6 24 0.33
7 3 0.04
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:1334591 original size:14 final size:15
Alignment explanation
Indices: 1334541--1334628 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 15
1334531 TGGACCGAAT
*
1334541 TAAAATAAAATAAAA
1 TAAAATAATATAAAA
**
1334556 TAAAATAA-GCAAAA
1 TAAAATAATATAAAA
*
1334570 TAAAATAAAATAAAACA
1 TAAAATAATAT-AAA-A
*
1334587 TATAATAA-ATAAAA
1 TAAAATAATATAAAA
*
1334601 TAATATAAATATAATAA
1 TAAAAT-AATATAA-AA
1334618 TAATAATAATA
1 TAA-AATAATA
1334629 ATATATTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
14 17 0.29
15 13 0.22
16 9 0.16
17 17 0.29
18 2 0.03
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (15 bp):
TAAAATAATATAAAA
Found at i:1334624 original size:9 final size:9
Alignment explanation
Indices: 1334544--1334631 Score: 52
Period size: 9 Copynumber: 10.4 Consensus size: 9
1334534 ACCGAATTAA
1334544 AATAA-AAT
1 AATAATAAT
1334552 AA-AATAA-
1 AATAATAAT
*
1334559 AATAAGCAA-
1 AATAA-TAAT
1334568 AATAA-AAT
1 AATAATAAT
1334576 AA-AATAA-
1 AATAATAAT
*
1334583 AACATATAAT
1 AATA-ATAAT
1334593 AAATAA-AAT
1 -AATAATAAT
1334602 AAT-ATAA-
1 AATAATAAT
1334609 ATATAATAAT
1 A-ATAATAAT
1334619 AATAATAAT
1 AATAATAAT
1334628 AATA
1 AATA
1334632 TATTATATAT
Statistics
Matches: 65, Mismatches: 2, Indels: 25
0.71 0.02 0.27
Matches are distributed among these distances:
7 12 0.18
8 18 0.28
9 30 0.46
10 2 0.03
11 3 0.05
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (9 bp):
AATAATAAT
Found at i:1334714 original size:2 final size:2
Alignment explanation
Indices: 1334702--1334751 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1334692 ATTTTAAAAC
1334702 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1334743 TA TA TA TA T
1 TA TA TA TA T
1334752 TTAAAATGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1334774 original size:37 final size:37
Alignment explanation
Indices: 1334629--1335099 Score: 359
Period size: 37 Copynumber: 12.6 Consensus size: 37
1334619 AATAATAATA
* *
1334629 ATATAT-TATATATATTTTCAAAAATATTTCCCAAAACT
1 ATATATATATATATATTTTC-AAAATGTTT-TCAAAACT
* *
1334667 ATATA-ATATATATTTTTTCAAAAATATTTT-AAAACT
1 ATATATATATATATATTTTC-AAAATGTTTTCAAAACT
* * * * *
1334703 ATAT-TATATATATA-TAT--ATAT-ATAT-ATATA-T
1 ATATATATATATATATTTTCAAAATGTTTTCA-AAACT
1334734 ATATATATATATATATATTT-AAAATGTTTTCAAAACT
1 ATATATATATATATAT-TTTCAAAATGTTTTCAAAACT
*
1334771 ATATAT-TATATA-ATTTTCAAAAATATTTT-AAAACT
1 ATATATATATATATATTTTC-AAAATGTTTTCAAAACT
* *
1334806 ATATATTATATATATTTTTTAAAAATGTTTTCAAAACT
1 ATATA-TATATATATATTTTCAAAATGTTTTCAAAACT
* * *
1334844 ATATAT-CATACA-GTTTTCAAAAATGTTTTCAAAACT
1 ATATATATATATATATTTTC-AAAATGTTTTCAAAACT
1334880 ATATAT-TATATATATTTTCAAAATGTTTTCAAAAACT
1 ATATATATATATATATTTTCAAAATGTTTTC-AAAACT
* *
1334917 ATATAT-TCTATATATTTTCAAAATGTTTTCAAAAACA
1 ATATATATATATATATTTTCAAAATGTTTTC-AAAACT
**** *
1334954 ATATAT-TATATATATTTTCAAAAAAAATTCAAAAATTATAT
1 ATATATATATATATATTTTCAAAATGTTTTC--AAA--A-CT
1334995 ATTATATATTATATATATTTTTTCAAAATGTTTTCAAAAACT
1 A-TATATA-TATATATA--TTTTCAAAATGTTTTC-AAAACT
* * * *
1335037 ATATATTATATATCTATATTCAAAATGTTTTTAAAAATT
1 ATATA-TATATATATATTTTCAAAATG-TTTTCAAAACT
*
1335076 ATATATTATATATATTTTTTCAAA
1 ATATA-TATATATATATTTTCAAA
1335100 GACCGATTTT
Statistics
Matches: 358, Mismatches: 45, Indels: 59
0.77 0.10 0.13
Matches are distributed among these distances:
31 8 0.02
32 15 0.04
34 5 0.01
35 22 0.06
36 80 0.22
37 95 0.27
38 46 0.13
39 36 0.10
40 5 0.01
41 12 0.03
42 9 0.03
43 1 0.00
44 8 0.02
45 4 0.01
46 12 0.03
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
ATATATATATATATATTTTCAAAATGTTTTCAAAACT
Found at i:1334799 original size:103 final size:102
Alignment explanation
Indices: 1334629--1334820 Score: 282
Period size: 103 Copynumber: 1.9 Consensus size: 102
1334619 AATAATAATA
*
1334629 ATATATTATATATATTTTCAAAAATATTTCCCAAAACTATATAATATATATTTTTTCAAAAATAT
1 ATATATTATATATATTTT-AAAAATATTTCCCAAAACTATATAATATATATATTTTCAAAAATAT
1334694 TTTAAAACTATATTATATATATATATATATATATATATAT
65 TTTAAAACTATA-TAT-TATATATATATATATATATATAT
* * *
1334734 ATATATATATATATATATTT-AAAATGTTT-TCAAAACTATATATTATATA-ATTTTCAAAAATA
1 ATATAT-TATATATAT-TTTAAAAATATTTCCCAAAACTATATAATATATATATTTTCAAAAATA
1334796 TTTTAAAACTATATATTATATATAT
64 TTTTAAAACTATATATTATATATAT
1334821 TTTTTAAAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
101 9 0.11
102 3 0.04
103 25 0.31
104 18 0.22
105 14 0.17
106 9 0.11
107 3 0.04
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.47
Consensus pattern (102 bp):
ATATATTATATATATTTTAAAAATATTTCCCAAAACTATATAATATATATATTTTCAAAAATATT
TTAAAACTATATATTATATATATATATATATATATAT
Found at i:1334935 original size:74 final size:73
Alignment explanation
Indices: 1334629--1335093 Score: 391
Period size: 73 Copynumber: 6.2 Consensus size: 73
1334619 AATAATAATA
* * * * *
1334629 ATATATTATATATATTTTCAAAAATATTTCCCAAAACTATATAATATATATTTTTTCAAAAATAT
1 ATATATTATATATATTTTCAAAAATGTTT-TCAAAACTATATATTATATATATTTTC-AAAATGT
1334694 TTT-AAAAC-
64 TTTCAAAACT
* * * * * *
1334702 -TATATTATATATA-TAT-ATATAT-ATAT-ATATA-TATATATATATATATATATTT-AAAATG
1 ATATATTATATATATTTTCAAAAATGTTTTCA-AAACTATATAT-TATATATAT-TTTCAAAATG
1334760 TTTTCAAAACT
63 TTTTCAAAACT
* *
1334771 ATATATTATATA-ATTTTCAAAAATATTTT-AAAACTATATATTATATATATTTTTTAAAAATGT
1 ATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATA--TTTTCAAAATGT
1334834 TTTCAAAACT
64 TTTCAAAACT
* * *
1334844 ATATATCATACA-GTTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTT
1 ATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTT
1334908 TCAAAAACT
66 TC-AAAACT
* * ****
1334917 ATATATTCTATATATTTTC-AAAATGTTTTCAAAAACAATATATTATATATATTTTCAAAAAAAA
1 ATATATTATATATATTTTCAAAAATGTTTTC-AAAACTATATATTATATATATTTTCAAAATGTT
*
1334981 TTCAAAAATTATATATT
65 TTC----A--A-A-ACT
*
1334998 ATATATTATATATATTTTTTC-AAAATGTTTTCAAAAACTATATATTATATATCTATATTCAAAA
1 ATATATTATATATA--TTTTCAAAAATGTTTTC-AAAACTATATATTATATA--TATTTTCAAAA
* *
1335062 TGTTTTTAAAAATT
61 TG-TTTTCAAAACT
1335076 ATATATTATATATATTTT
1 ATATATTATATATATTTT
1335094 TTCAAAGACC
Statistics
Matches: 324, Mismatches: 39, Indels: 55
0.78 0.09 0.13
Matches are distributed among these distances:
67 16 0.05
68 15 0.05
69 5 0.02
70 17 0.05
71 16 0.05
72 41 0.13
73 69 0.21
74 56 0.17
76 4 0.01
77 2 0.01
78 17 0.05
79 2 0.01
80 2 0.01
81 15 0.05
82 1 0.00
83 34 0.10
85 10 0.03
86 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (73 bp):
ATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTT
TCAAAACT
Found at i:1335098 original size:39 final size:39
Alignment explanation
Indices: 1334995--1335099 Score: 165
Period size: 39 Copynumber: 2.7 Consensus size: 39
1334985 AAAATTATAT
1334995 ATTATATATTATATATATTTTTTCAAAATGTTTTCAAAA
1 ATTATATATTATATATATTTTTTCAAAATGTTTTCAAAA
* * * * *
1335034 ACTATATATTATATATCTATATTCAAAATGTTTTTAAAA
1 ATTATATATTATATATATTTTTTCAAAATGTTTTCAAAA
1335073 ATTATATATTATATATATTTTTTCAAA
1 ATTATATATTATATATATTTTTTCAAA
1335100 GACCGATTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (39 bp):
ATTATATATTATATATATTTTTTCAAAATGTTTTCAAAA
Found at i:1340581 original size:141 final size:141
Alignment explanation
Indices: 1340330--1340610 Score: 447
Period size: 141 Copynumber: 2.0 Consensus size: 141
1340320 TCGGATACTC
* *
1340330 CATATATTATATTAATTAGGGTAAACTACATGTTTAGTAACTAAACTATTTATTTTGATCAGTTT
1 CATATATTATATTAATTAGGATAAACTACACGTTTAGTAACTAAACTATTTATTTTGATCAGTTT
*
1340395 TAATAATTAAACTTTTAATTTTTTCAAAAATATACCTAAAATTTAGTTTTTATT-TCATTTTAGT
66 TAATAATTAAACTTTTAATTTTTTCAAAAATATACATAAAATTTAGTTTTTATTGT-ATTTTAGT
**
1340459 ACTTACCGTTAT
130 ACCCACCGTTAT
1340471 CATATATTATATTAATTAGGATAAACTACACGTTTAGTAACTAAACTATTTATTTTGATCAGTTT
1 CATATATTATATTAATTAGGATAAACTACACGTTTAGTAACTAAACTATTTATTTTGATCAGTTT
* * * * * *
1340536 TAGTACTTAAACTTTTAATTTTTTCAAAAGTATACATGAAGTTTAGTTTTTGTTGTATTTTAGTA
66 TAATAATTAAACTTTTAATTTTTTCAAAAATATACATAAAATTTAGTTTTTATTGTATTTTAGTA
1340601 CCCACCGTTA
131 CCCACCGTTA
1340611 AAAACTTAAT
Statistics
Matches: 128, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
141 127 0.99
142 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (141 bp):
CATATATTATATTAATTAGGATAAACTACACGTTTAGTAACTAAACTATTTATTTTGATCAGTTT
TAATAATTAAACTTTTAATTTTTTCAAAAATATACATAAAATTTAGTTTTTATTGTATTTTAGTA
CCCACCGTTAT
Found at i:1341636 original size:2 final size:2
Alignment explanation
Indices: 1341629--1341662 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1341619 CTTTCAACAA
1341629 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
1341663 TGAAGTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1343183 original size:43 final size:41
Alignment explanation
Indices: 1343136--1343483 Score: 215
Period size: 43 Copynumber: 8.1 Consensus size: 41
1343126 GGGTTTAAAC
* * *
1343136 TATAAAAGTAAAAAGTATGATTGAAAAAATTAGAGACCCCAAT
1 TATAAAGGTAAAAAGTA-GATTGAAAAAATTAG-GGCCTCAAT
* *
1343179 TATAAAGGTAAAAAGT-GATT-AAAAAAATAGGTGCATCAAT
1 TATAAAGGTAAAAAGTAGATTGAAAAAATTAGG-GCCTCAAT
* * *
1343219 TTTAAAGGTAAAAAATGAGATTGAAAAAAATTATGGGCCTAAAT
1 TATAAAGGTAAAAAGT-AGATTG-AAAAAATTA-GGGCCTCAAT
* *
1343263 TAT-ATGAGTAAAAAATAGGATTGAAAAAATTAGGGGCCTCAAT
1 TATAAAG-GTAAAAAGTA-GATTGAAAAAATTA-GGGCCTCAAT
** * *
1343306 TATAAAGGTAAAAAGTGAGATTGAAAAAAACATGAG-CTTAAT
1 TATAAAGGTAAAAAGT-AGATTGAAAAAATTA-GGGCCTCAAT
* * * * * *
1343348 TATAAAGATACAAGGT-GATAT-TAAAAATTGAGGATCATCAAT
1 TATAAAGGTAAAAAGTAGAT-TGAAAAAATT-AGG-GCCTCAAT
* * *
1343390 TATAAATGTAAAAAAAATGAGATTGAAAAAAATTAAGGGCCTCCAT
1 TATAAAGGT--AAAAAGT-AGATTG-AAAAAATT-AGGGCCTCAAT
* * *
1343436 TATAAAGATAAAAAGTAGGATT-ACAAAAATGAAGGACCTCAAT
1 TATAAAGGTAAAAAGTA-GATTGA-AAAAAT-TAGGGCCTCAAT
1343479 TATAA
1 TATAA
1343484 GGATAAGAAA
Statistics
Matches: 235, Mismatches: 47, Indels: 46
0.72 0.14 0.14
Matches are distributed among these distances:
39 1 0.00
40 37 0.16
41 6 0.03
42 34 0.14
43 82 0.35
44 47 0.20
45 3 0.01
46 15 0.06
47 10 0.04
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (41 bp):
TATAAAGGTAAAAAGTAGATTGAAAAAATTAGGGCCTCAAT
Found at i:1343374 original size:127 final size:125
Alignment explanation
Indices: 1343131--1343451 Score: 290
Period size: 127 Copynumber: 2.5 Consensus size: 125
1343121 ATTAGGGGTT
* * * * * *
1343131 TAAACTATAAAAGTAAAAAGTATGATTGAAAAAATTAGAGACCCCAATTATAAAGGTAAAAAGTG
1 TAAATTAT-AAAGTAAAAAATAGGATTGAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTG
* * * * *
1343196 ATTAAAAAAATAGGTGCATCAATTTTAAAGGTAAAAAATGAGATTGAAAAAAATT-ATGG-GCC
65 ATTAAAAAAACAGGAGCATCAATTATAAAGATAAAAAATGAGATT--AAAAAATTGA-GGAGCA
*
1343258 TAAATTATATGAGTAAAAAATAGGATTGAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTG
1 TAAATTATA-AAGTAAAAAATAGGATTGAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGT-
* * * ** * *
1343323 AGATTGAAAAAAACATGAGC-TTAATTATAAAGATACAAGGTGATATT-AAAAATTGAGGATCA
64 -GATT-AAAAAAACAGGAGCATCAATTATAAAGATAAAAAATGAGATTAAAAAATTGAGGAGCA
* * * * *
1343385 TCAATTATAAATGTAAAAAAAATGAGATTGAAAAAAATTAAGGGCCTCCATTATAAAGATAAAAA
1 TAAATTATAAA-GTAAAAAATA-G-GATTG-AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAA
1343450 GT
62 GT
1343452 AGGATTACAA
Statistics
Matches: 159, Mismatches: 25, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
126 11 0.07
127 74 0.47
128 1 0.01
129 29 0.18
130 44 0.28
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (125 bp):
TAAATTATAAAGTAAAAAATAGGATTGAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGA
TTAAAAAAACAGGAGCATCAATTATAAAGATAAAAAATGAGATTAAAAAATTGAGGAGCA
Found at i:1343625 original size:2 final size:2
Alignment explanation
Indices: 1343618--1343662 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1343608 TAGCAAATAA
1343618 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
1343660 AT A
1 AT A
1343663 ATTTTAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1343819 original size:28 final size:28
Alignment explanation
Indices: 1343771--1343829 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1343761 ATATAATTTA
*
1343771 AAAAATAATAATAATTTAATAATCAAAAT
1 AAAAATAATAATAATTAAATAA-CAAAAT
*
1343800 AAAAA-AATAATAGA-TAAATAACTAAAT
1 AAAAATAATAATA-ATTAAATAACAAAAT
1343827 AAA
1 AAA
1343830 TAATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 13 0.48
29 6 0.22
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.25
Consensus pattern (28 bp):
AAAAATAATAATAATTAAATAACAAAAT
Found at i:1345150 original size:18 final size:19
Alignment explanation
Indices: 1345113--1345152 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1345103 AACAGAATGT
1345113 AAGATTATCAGTGAGAATAA
1 AAGATTATCAGT-AGAATAA
1345133 AAGATTATCAGT-GAATAA
1 AAGATTATCAGTAGAATAA
1345151 AA
1 AA
1345153 TTATTGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (19 bp):
AAGATTATCAGTAGAATAA
Found at i:1345234 original size:30 final size:29
Alignment explanation
Indices: 1345200--1345265 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 29
1345190 GCAAGAATGT
*
1345200 AAGATTACCATATTTGGTTAAAGGAATAAA
1 AAGATTACCATATTTGGTTAAAAGAAT-AA
1345230 AAGATTACCATATTTGGTTAAAAGAATAA
1 AAGATTACCATATTTGGTTAAAAGAATAA
1345259 AAGATTA
1 AAGATTA
1345266 TTGAAATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (29 bp):
AAGATTACCATATTTGGTTAAAAGAATAA
Found at i:1346308 original size:2 final size:2
Alignment explanation
Indices: 1346303--1346350 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1346293 GCGCGCGCGC
1346303 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
1346345 AT AT AT
1 AT AT AT
1346351 TGTAGATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1347908 original size:3 final size:3
Alignment explanation
Indices: 1347902--1347932 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1347892 ATATATATAT
1347902 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1347933 AGTAGCGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1347911 original size:6 final size:6
Alignment explanation
Indices: 1347866--1347932 Score: 71
Period size: 6 Copynumber: 10.5 Consensus size: 6
1347856 TTATTATTAT
* * *
1347866 TAATAA TAATAA TATTAT TATTATA TATATATA TATATAA TAATAA TAATAA
1 TAATAA TAATAA TAATAA TAATA-A TA-ATA-A TA-ATAA TAATAA TAATAA
1347918 TAATAA TAATAA TAA
1 TAATAA TAATAA TAA
1347933 AGTAGCGGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
6 40 0.73
7 5 0.09
8 10 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
TAATAA
Found at i:1347916 original size:9 final size:9
Alignment explanation
Indices: 1347866--1347932 Score: 71
Period size: 9 Copynumber: 7.0 Consensus size: 9
1347856 TTATTATTAT
1347866 TAATAATAA
1 TAATAATAA
* *
1347875 TAATATTAT
1 TAATAATAA
*
1347884 TATTATATATA
1 TAATA-ATA-A
1347895 TATATATATAA
1 TA-ATA-ATAA
1347906 TAATAATAA
1 TAATAATAA
1347915 TAATAATAA
1 TAATAATAA
1347924 TAATAATAA
1 TAATAATAA
1347933 AGTAGCGGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
9 33 0.67
10 5 0.10
11 5 0.10
12 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATAATAA
Found at i:1351569 original size:20 final size:20
Alignment explanation
Indices: 1351544--1351585 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1351534 ACGACACTTG
*
1351544 GGACCTTCTCAACTATTGCA
1 GGACCTTCTCAACCATTGCA
*
1351564 GGACCTTCTCGACCATTGCA
1 GGACCTTCTCAACCATTGCA
1351584 GG
1 GG
1351586 TTTAACTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.26
Consensus pattern (20 bp):
GGACCTTCTCAACCATTGCA
Found at i:1354139 original size:20 final size:20
Alignment explanation
Indices: 1354101--1354139 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1354091 ATCGGCCCTC
*
1354101 AAATTTTATTTTTTAATTTG
1 AAATTTTATTTTATAATTTG
*
1354121 AAATTTTATTTTATGATTT
1 AAATTTTATTTTATAATTT
1354140 TTTTAAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
AAATTTTATTTTATAATTTG
Found at i:1374613 original size:15 final size:15
Alignment explanation
Indices: 1374595--1374639 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1374585 TAATTTTTTC
1374595 ATAATTATAATTATA
1 ATAATTATAATTATA
1374610 ATAATTATTAA-TATA
1 ATAATTA-TAATTATA
*
1374625 ATATATTATTATTAT
1 ATA-ATTATAATTAT
1374640 TATTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAATTATAATTATA
Found at i:1374637 original size:19 final size:19
Alignment explanation
Indices: 1374613--1374668 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
1374603 AATTATAATA
1374613 ATTATTAATATAATATATT
1 ATTATTAATATAATATATT
* * *
1374632 ATTATTATTATTATTTATT
1 ATTATTAATATAATATATT
* *
1374651 A-AATAAATA-AATATATT
1 ATTATTAATATAATATATT
1374668 A
1 A
1374669 CAAATTACAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 7 0.24
18 5 0.17
19 17 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATTAATATAATATATT
Found at i:1386989 original size:45 final size:45
Alignment explanation
Indices: 1386797--1387862 Score: 1738
Period size: 45 Copynumber: 23.6 Consensus size: 45
1386787 ACTATTTCCC
* *
1386797 TCATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGG
* *
1386843 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTCCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGG
* *
1386889 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTACGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGG
* * *
1386935 TCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAACTTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* * *
1386980 TCATTTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCAGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*
1387025 TCATCTGTAAGCCCTTCAGTACATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* *
1387070 TCATCTGTAAGCCCTTCAGTGCATGACGTTTTCAAAATCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*
1387115 TCATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* *
1387160 TCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*
1387205 TCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*
1387250 TCATCTGTAAGCCGTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* *
1387295 TCATCTGTAAGCCCTTCAGTGCATAATGTTTTCAAAACCTTTGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1387340 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1387385 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*
1387430 CCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1387475 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*** *
1387520 TCATCTGTAATTTCTTCAGTGCATGATGTTATCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*
1387565 TCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*
1387610 TCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* * *
1387655 TCATCTGTAAGCCCTTCAGTGCAAGATGTTATCAAAACCTTCAGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1387700 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* *
1387745 TCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAACCTTCGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* *
1387790 TCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAGCC-TCAGGG
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC-GGG
* * *
1387835 TCATCTGTAAGACCTACAGTGCAAGATG
1 TCATCTGTAAGCCCTTCAGTGCATGATG
1387863 ATAAGACTTC
Statistics
Matches: 963, Mismatches: 56, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
44 2 0.00
45 840 0.87
46 121 0.13
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
Found at i:1388049 original size:3 final size:3
Alignment explanation
Indices: 1388043--1388093 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
1388033 TATAATAATA
* * *
1388043 ATT ATT ATT AAT ATA ATAT ATT AGT ATT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT A-TT ATT
1388090 ATT A
1 ATT A
1388094 AATAAATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1389527 original size:21 final size:19
Alignment explanation
Indices: 1389503--1389558 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
1389493 TATTTAATTT
1389503 TATTTTAATTATTGTTTAACA
1 TATTTTAATTATTGTTT-A-A
1389524 TATTTTAATTTTATATGTTTAA
1 TATTTTAA--TTAT-TGTTTAA
*
1389546 TATTTAAATTATT
1 TATTTTAATTATT
1389559 ATTATTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.03
20 4 0.13
21 8 0.26
22 8 0.26
23 5 0.16
24 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (19 bp):
TATTTTAATTATTGTTTAA
Found at i:1389702 original size:37 final size:37
Alignment explanation
Indices: 1389668--1389738 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1389658 TAATATATTT
*
1389668 TAAATAAAT-AAATATTTTACTATTATAAAGTATATA
1 TAAATAAATAAAATATTTTAATATTATAAAGTATATA
* * *
1389704 TATATACATAAAATATTTTAATATTATAAATTATA
1 TAAATAAATAAAATATTTTAATATTATAAAGTATA
1389739 AATATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (37 bp):
TAAATAAATAAAATATTTTAATATTATAAAGTATATA
Found at i:1389904 original size:19 final size:20
Alignment explanation
Indices: 1389853--1389905 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
1389843 TAAATATTTT
*
1389853 ATTTAAAAATATAGATATTA
1 ATTTAAAAATATAGATATGA
1389873 ATTTGAAATAATAT-GATTATGA
1 ATTT-AAA-AATATAGA-TATGA
1389895 A-TTAAAAATAT
1 ATTTAAAAATAT
1389906 TTGTGAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 5 0.17
20 7 0.24
21 7 0.24
22 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (20 bp):
ATTTAAAAATATAGATATGA
Found at i:1394008 original size:22 final size:23
Alignment explanation
Indices: 1393963--1394008 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
1393953 GGAGTGTGAA
1393963 AGTAACCCCAAATGGACACACAAT
1 AGTAACCCCAAATGGA-ACACAAT
1393987 AGTAACCCCAAATGG-ACACAAT
1 AGTAACCCCAAATGGAACACAAT
1394009 TCTGTGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.32
24 15 0.68
ACGTcount: A:0.46, C:0.28, G:0.13, T:0.13
Consensus pattern (23 bp):
AGTAACCCCAAATGGAACACAAT
Found at i:1399419 original size:2 final size:2
Alignment explanation
Indices: 1399414--1399442 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1399404 ATATATATAT
1399414 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1399443 TGATACATTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1401965 original size:21 final size:21
Alignment explanation
Indices: 1401939--1401991 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1401929 AGTTTTAAGA
*
1401939 ATCGATACTTTTCATATGTGT
1 ATCGATACTTTTCATATATGT
1401960 ATCGATACTTTTCATATATGT
1 ATCGATACTTTTCATATATGT
1401981 ATCGATACTTT
1 ATCGATACTTT
1401992 ATAGGTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.47
Consensus pattern (21 bp):
ATCGATACTTTTCATATATGT
Found at i:1414530 original size:20 final size:21
Alignment explanation
Indices: 1414483--1414530 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 21
1414473 TGAGTTACTA
1414483 TATATATTTTACAATGTTGTAT
1 TATA-ATTTTACAATGTTGTAT
1414505 TA-AATTTT-CAATGTT-TATT
1 TATAATTTTACAATGTTGTA-T
1414524 TATAATT
1 TATAATT
1414531 CAATCTGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.08
19 10 0.42
20 9 0.38
21 1 0.04
22 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (21 bp):
TATAATTTTACAATGTTGTAT
Found at i:1419314 original size:194 final size:194
Alignment explanation
Indices: 1418985--1419603 Score: 996
Period size: 194 Copynumber: 3.2 Consensus size: 194
1418975 GCTTTACTGG
* * * *
1418985 TTTTGTCATATTTTAACTTGTTATATTGTCATGTATCGATACATGTTTATAAAATATCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTT
* *
1419050 TATAGGCACCATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATAATATGATACATATAATTA
66 TATAGGCTCCATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATAATATGATACATATACTTA
*
1419115 TTAAAGTATCGATACCTTCAACATACCCGGTAGCTTTTTACTGGTTTTGTCATATTGAAACCGA
131 TTAAAGTATCGATACCTTCAACATATCCGGTAGCTTTTTACTGGTTTTGTCATATTGAAACCGA
*
1419179 TTTTGTCATATTTTTACCTGTTATATTATTATGTATCGATACATGTTTATAAAGTATCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTT
* *
1419244 TATAGGCTTCATTATTGCAATTCTTTTAAATTCCTAAAGTATCAATAATATGATACATATACTTA
66 TATAGGCTCCATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATAATATGATACATATACTTA
* *
1419309 TTAAAGTATCGATACCTTCAACATATCTGGTAGCTTTTTACTGGTTTTGTCATATTGAAATC-A
131 TTAAAGTATCGATACCTTCAACATATCCGGTAGCTTTTTACTGGTTTTGTCATATTGAAACCGA
*
1419372 GTTTTGTCATATTTTTACCTATTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACT
1 -TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACT
*
1419437 TTATAGG-TGCCATTATTGCAATTCTTTTAAATTCCTAAAGTATTGATAATATGATACATATACT
65 TTATAGGCT-CCATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATAATATGATACATATACT
* ** *
1419501 TATTAAAGTGTCGATACCTTCAACATATCCGGTAGCGCTTTACCGG--TTGTCATATTGAAACCG
129 TATTAAAGTATCGATACCTTCAACATATCCGGTAGCTTTTTACTGGTTTTGTCATATTGAAACCG
*
1419564 G
194 A
* *
1419565 TTTTGTTATATTTTTACCTGTTATATT-TTATGTGTCGAT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGAT
1419604 GCTTATTTGC
Statistics
Matches: 395, Mismatches: 27, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
191 11 0.03
192 40 0.10
193 2 0.01
194 342 0.87
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (194 bp):
TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTT
TATAGGCTCCATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATAATATGATACATATACTTA
TTAAAGTATCGATACCTTCAACATATCCGGTAGCTTTTTACTGGTTTTGTCATATTGAAACCGA
Found at i:1420865 original size:16 final size:17
Alignment explanation
Indices: 1420840--1420872 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1420830 AATTAAATGA
1420840 TTTATAATTATA-ACTT
1 TTTATAATTATATACTT
*
1420856 TTTATTATTATATACTT
1 TTTATAATTATATACTT
1420873 CCTTTCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATAATTATATACTT
Found at i:1424416 original size:18 final size:18
Alignment explanation
Indices: 1424374--1424416 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1424364 TTTAAATGTT
1424374 TTATTTTGATAAATTATA
1 TTATTTTGATAAATTATA
* ** *
1424392 TTGTTTTGATTTATTATG
1 TTATTTTGATAAATTATA
1424410 TTATTTT
1 TTATTTT
1424417 TATACTTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
TTATTTTGATAAATTATA
Found at i:1427478 original size:30 final size:30
Alignment explanation
Indices: 1427433--1427496 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1427423 AAGGAACATA
* *
1427433 TGGATAGTTGCCGAGGATATTTATGACCTC
1 TGGATAGTTACCGAGGATATTTATAACCTC
* * * *
1427463 TGGATAGTTATCGAGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATATTTATAACCTC
1427493 TGGA
1 TGGA
1427497 CAGGTCCTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATATTTATAACCTC
Found at i:1429802 original size:15 final size:15
Alignment explanation
Indices: 1429779--1429810 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1429769 AAAAGTTTAA
1429779 AATTATGTAAATGAT
1 AATTATGTAAATGAT
*
1429794 AATTGTGTAAATGAT
1 AATTATGTAAATGAT
1429809 AA
1 AA
1429811 AAAAATTTAA
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:0.16, T:0.38
Consensus pattern (15 bp):
AATTATGTAAATGAT
Found at i:1430559 original size:66 final size:66
Alignment explanation
Indices: 1430453--1430576 Score: 203
Period size: 66 Copynumber: 1.9 Consensus size: 66
1430443 GAGTGATCAC
* * *
1430453 TGAATACTGTACAGATCTCTCGATGAGACTCGTGTACCTTTGTGGTGCATGAGGTGGACTGATAA
1 TGAATACTGTACAGATCACTCGATAAAACTCGTGTACCTTTGTGGTGCATGAGGTGGACTGATAA
1430518 T
66 T
* *
1430519 TGAATATTGTACAGATCACTCGATAAAACTTGTGTACCTTTGTGGTGCATGAGGTGGA
1 TGAATACTGTACAGATCACTCGATAAAACTCGTGTACCTTTGTGGTGCATGAGGTGGA
1430577 GTGACTATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (66 bp):
TGAATACTGTACAGATCACTCGATAAAACTCGTGTACCTTTGTGGTGCATGAGGTGGACTGATAA
T
Found at i:1430969 original size:12 final size:12
Alignment explanation
Indices: 1430952--1430978 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1430942 AACGGTACAA
1430952 AAAAATAAATAT
1 AAAAATAAATAT
1430964 AAAAATAAATAT
1 AAAAATAAATAT
1430976 AAA
1 AAA
1430979 TAGTACAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAATAAATAT
Found at i:1431314 original size:15 final size:15
Alignment explanation
Indices: 1431294--1431324 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1431284 TTAGGGCAAG
1431294 TAGTATCGATATTGT
1 TAGTATCGATATTGT
1431309 TAGTATCGATATTGT
1 TAGTATCGATATTGT
1431324 T
1 T
1431325 CTTGTAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (15 bp):
TAGTATCGATATTGT
Found at i:1433203 original size:8 final size:8
Alignment explanation
Indices: 1433185--1433214 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1433175 ATTCAAATTA
1433185 TAAAATA-
1 TAAAATAT
1433192 TAAAATAT
1 TAAAATAT
1433200 TAAAATAT
1 TAAAATAT
1433208 TAAAATA
1 TAAAATA
1433215 AATAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAATAT
Found at i:1433205 original size:23 final size:22
Alignment explanation
Indices: 1433161--1433229 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
1433151 TAATATATAA
* *
1433161 ATAAAAAATAAGAAATTCAAATT
1 ATAAAATATAAGAAATT-AAAAT
1433184 ATAAAATATAA-AATATTAAAAT
1 ATAAAATATAAGAA-ATTAAAAT
* *
1433206 ATTAAAATA-AATAAATAAAAAT
1 A-TAAAATATAAGAAATTAAAAT
1433228 AT
1 AT
1433230 TAATAATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.03
22 17 0.43
23 22 0.55
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (22 bp):
ATAAAATATAAGAAATTAAAAT
Found at i:1433234 original size:16 final size:16
Alignment explanation
Indices: 1433187--1433235 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1433177 TCAAATTATA
1433187 AAATATAAAATATTAA-
1 AAATA-AAAATATTAAT
*
1433203 AATATTAAAATA--AAT
1 AA-ATAAAAATATTAAT
1433218 AAATAAAAATATTAAT
1 AAATAAAAATATTAAT
1433234 AA
1 AA
1433236 TGTAAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.37
15 2 0.07
16 13 0.48
17 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAAAAATATTAAT
Found at i:1437069 original size:2 final size:2
Alignment explanation
Indices: 1437062--1437086 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1437052 AAGTTTTCAA
1437062 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 A
1437087 ATTCAAAGTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1438977 original size:21 final size:20
Alignment explanation
Indices: 1438953--1438994 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1438943 TGTAGAGATT
1438953 TCATCCCCAAACGACTAGAAA
1 TCATCCCC-AACGACTAGAAA
* *
1438974 TCATCCGCAATGACTAGAAA
1 TCATCCCCAACGACTAGAAA
1438994 T
1 T
1438995 GACCATATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (20 bp):
TCATCCCCAACGACTAGAAA
Found at i:1441890 original size:24 final size:24
Alignment explanation
Indices: 1441861--1441906 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1441851 TTTTTATATA
*
1441861 TTTTCCAACAGTTAGTATCTTTAT
1 TTTTCCAACAATTAGTATCTTTAT
*
1441885 TTTTCCAACAATTGGTATCTTT
1 TTTTCCAACAATTAGTATCTTT
1441907 TTCATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (24 bp):
TTTTCCAACAATTAGTATCTTTAT
Found at i:1442342 original size:23 final size:24
Alignment explanation
Indices: 1442293--1442343 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1442283 CGATACCCAA
* * *
1442293 AGTAGTATTGATACTACTTTGTAT
1 AGTAGTATCGATACCACTATGTAT
1442317 AGTAGTATCGATACCA-TATGTAT
1 AGTAGTATCGATACCACTATGTAT
1442340 AGTA
1 AGTA
1442344 TCGATACCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (24 bp):
AGTAGTATCGATACCACTATGTAT
Done.