Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 30
Found at i:2415532 original size:20 final size:19
Alignment explanation
Indices: 2415497--2415574 Score: 93
Period size: 19 Copynumber: 4.1 Consensus size: 19
2415487 CGCAACACGA
2415497 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGC-G
*
2415517 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
** *
2415536 AAATGAAAATCGCAACGCG
1 AAATGACTATCGCAATGCG
**
2415555 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAATGCG
2415574 A
1 A
2415575 TTTGTGTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 35 0.67
20 17 0.33
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:2415540 original size:19 final size:19
Alignment explanation
Indices: 2415505--2415574 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
2415495 GAAAATGACT
***
2415505 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
2415525 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2415544 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2415563 ATCGCAATGCGA
1 ATCGCAATGCGA
2415575 TTTGTGTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 35 0.78
20 10 0.22
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2415645 original size:20 final size:20
Alignment explanation
Indices: 2415585--2415648 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
2415575 TTTGTGTTTC
*
2415585 GCGATAGCCATTTCCGCGTT
1 GCGATAGCCATTTTCGCGTT
*
2415605 ACGATAGCCA-TTTCTGCGTT
1 GCGATAGCCATTTTC-GCGTT
*
2415625 GCGATAGTCATTTTCGCGTT
1 GCGATAGCCATTTTCGCGTT
2415645 GCGA
1 GCGA
2415649 AAGTAAGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 31 0.82
21 4 0.11
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (20 bp):
GCGATAGCCATTTTCGCGTT
Found at i:2415659 original size:20 final size:20
Alignment explanation
Indices: 2415615--2415674 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
2415605 ACGATAGCCA
* * *
2415615 TTTCTGCGTTGCGATAGTCAT
1 TTTC-GCGTTGCGAAAGTAAG
2415636 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
2415656 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
2415675 ACTATTCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.37
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:2416050 original size:21 final size:21
Alignment explanation
Indices: 2416023--2416077 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2416013 CCTGTTATCC
2416023 CTCAAGAGTCCCCT-TCAATCA
1 CTCAAGAGTCCCCTATC-ATCA
* * *
2416044 TTCAAGAGGCCCCTATCATCC
1 CTCAAGAGTCCCCTATCATCA
2416065 CTCAAGAGTCCCC
1 CTCAAGAGTCCCC
2416078 CCACCGTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.25, C:0.40, G:0.13, T:0.22
Consensus pattern (21 bp):
CTCAAGAGTCCCCTATCATCA
Found at i:2416103 original size:40 final size:41
Alignment explanation
Indices: 2416014--2416103 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 41
2416004 CCCGACTCAC
* * *
2416014 CTGTTATCCCTCAAGAGTCCCCTTCAATCATTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCC-TCAACCATTCAAGAGGCCA
* * *
2416056 CTATCATCCCTCAAGAGTCCCC-CCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCAACCATTCAAGAGGCCA
2416096 CTGTCATC
1 CTGTCATC
2416104 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 21 0.51
42 20 0.49
ACGTcount: A:0.23, C:0.39, G:0.14, T:0.23
Consensus pattern (41 bp):
CTGTCATCCCTCAAGAGTCCCCTCAACCATTCAAGAGGCCA
Found at i:2416112 original size:40 final size:42
Alignment explanation
Indices: 2416044--2416122 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 42
2416034 CCTTCAATCA
*
2416044 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCC-CCCACCG
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACCG
* ** *
2416084 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
2416123 TCATTCCAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 23 0.72
41 5 0.16
42 4 0.12
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.20
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACCG
Found at i:2416704 original size:20 final size:19
Alignment explanation
Indices: 2416653--2416709 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2416643 AAACAATAAT
2416653 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
2416672 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
2416693 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
2416710 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:2416875 original size:22 final size:21
Alignment explanation
Indices: 2416796--2416928 Score: 74
Period size: 22 Copynumber: 6.0 Consensus size: 21
2416786 CAAAGAAACT
*
2416796 AAAA-ATATA-ATGAAAATAA
1 AAAATATATATATAAAAATAA
*
2416815 ATAAATAGTATAAATAAAATAATAA
1 A-AAATA-TATATAT-AAA-AATAA
2416840 AAAATATATATATAAAAATATA
1 AAAATATATATATAAAAATA-A
* * *
2416862 AAAATGTATGTAT-AATATAA
1 AAAATATATATATAAAAATAA
* *
2416882 TAAAATACTAAATAGTAATAATAA
1 -AAAATA-TATATA-TAAAAATAA
* * *
2416906 TAAATAAATAAATGAAAAATAA
1 AAAATATATATAT-AAAAATAA
2416928 A
1 A
2416929 TATACATATA
Statistics
Matches: 86, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
19 1 0.01
20 4 0.05
21 16 0.19
22 33 0.38
23 14 0.16
24 12 0.14
25 6 0.07
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAATATATATATAAAAATAA
Found at i:2416917 original size:24 final size:23
Alignment explanation
Indices: 2416799--2416918 Score: 68
Period size: 24 Copynumber: 4.9 Consensus size: 23
2416789 AGAAACTAAA
2416799 AATATAATGAAAATAAATAAATAGT
1 AATATAAT-AAAAT-AATAAATAGT
* *
2416824 -ATA-AATAAAATAATAAAAAAT
1 AATATAATAAAATAATAAATAGT
*
2416845 -ATATATATAAAAATATAAAAATGTATGTAT
1 AATATA-AT-AAAATA-ATAAA--TA-G--T
*
2416875 AATATAATAAAATACTAAATAGT
1 AATATAATAAAATAATAAATAGT
2416898 AATAATAAT-AAATAAATAAAT
1 AAT-ATAATAAAAT-AATAAAT
2416919 GAAAAATAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
21 11 0.15
22 6 0.08
23 13 0.17
24 20 0.27
25 5 0.07
26 2 0.03
27 1 0.01
28 3 0.04
29 6 0.08
30 3 0.04
31 5 0.07
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (23 bp):
AATATAATAAAATAATAAATAGT
Found at i:2417153 original size:23 final size:23
Alignment explanation
Indices: 2417119--2417165 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
2417109 ACGTAAAGAA
2417119 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
2417142 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
2417165 A
1 A
2417166 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:2417578 original size:37 final size:37
Alignment explanation
Indices: 2417527--2417597 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
2417517 ATAATAGTAG
* * *
2417527 AATTCTATCCTATTTTTATGAGTTTGAATCCTAGCAA
1 AATTATATCATATTTTTAAGAGTTTGAATCCTAGCAA
2417564 AATTATATCATATTTTTAAGAGTTTGAATCCTAG
1 AATTATATCATATTTTTAAGAGTTTGAATCCTAG
2417598 TAGGACGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (37 bp):
AATTATATCATATTTTTAAGAGTTTGAATCCTAGCAA
Found at i:2422473 original size:20 final size:20
Alignment explanation
Indices: 2422420--2422475 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2422410 TTTCAAAGTG
* *
2422420 ATGCACCGATGCAACAATCC
1 ATGCATCGATGCACCAATCC
2422440 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
2422460 ATGCATCGATGCACCA
1 ATGCATCGATGCACCA
2422476 TGGAATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:2422555 original size:26 final size:26
Alignment explanation
Indices: 2422524--2422589 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
2422514 TGTACATACC
2422524 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
*
2422550 ATGCATTGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
2422576 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2422590 AAGCCATGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (26 bp):
ATGCATCGATGCACTCAGTGCATTTG
Found at i:2428436 original size:23 final size:23
Alignment explanation
Indices: 2428367--2428447 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
2428357 ACACCTAACA
*
2428367 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
** *
2428389 GTGCATCGAT--ACACAATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
2428410 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
2428433 GTGCATCGATGCACA
1 GTGCATCGATGCACA
2428448 AGGCCATGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.02
21 14 0.31
22 10 0.22
23 20 0.44
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:2431208 original size:45 final size:45
Alignment explanation
Indices: 2431159--2431246 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
2431149 GAACATCAAA
* *
2431159 TGCATTTTATGCATAGATGCACATA-CCATGCATCGATGCACTCAG
1 TGCATTTGATGCATAGATACACA-AGCCATGCATCGATGCACTCAG
*
2431204 TGCATTTGATGCATCGATACACAAGCCATGCATCGATGCACTC
1 TGCATTTGATGCATAGATACACAAGCCATGCATCGATGCACTC
2431247 TGGCTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (45 bp):
TGCATTTGATGCATAGATACACAAGCCATGCATCGATGCACTCAG
Found at i:2432253 original size:5 final size:5
Alignment explanation
Indices: 2432243--2432267 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2432233 AATATATAAA
2432243 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
2432268 CATGAGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:2434490 original size:12 final size:12
Alignment explanation
Indices: 2434458--2434516 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
2434448 TGGTCCTGCA
2434458 AATATT-ATAAT
1 AATATTAATAAT
*
2434469 AAT-TAGAATAAT
1 AATAT-TAATAAT
*
2434481 AATATTAATAGT
1 AATATTAATAAT
*
2434493 AATATTTATAAT
1 AATATTAATAAT
*
2434505 AATAATAATAAT
1 AATATTAATAAT
2434517 TTAATAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
10 1 0.03
11 3 0.08
12 33 0.87
13 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:2434524 original size:3 final size:3
Alignment explanation
Indices: 2434464--2434516 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
2434454 TGCAAATATT
* * * * * *
2434464 ATA ATA ATT AGA ATA ATA ATA TTA ATA GTA ATA TTT ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2434512 ATA AT
1 ATA AT
2434517 TTAATAATTT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:2434526 original size:27 final size:28
Alignment explanation
Indices: 2434465--2434526 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
2434455 GCAAATATTA
*
2434465 TAATAA-TTAGAATAATAATATTAATAG
1 TAATAATTTAGAATAATAATAATAATAG
* *
2434492 TAAT-ATTTATAATAATAATAATAAT-T
1 TAATAATTTAGAATAATAATAATAATAG
2434518 TAATAATTT
1 TAATAATTT
2434527 TTTTAATCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (28 bp):
TAATAATTTAGAATAATAATAATAATAG
Found at i:2435015 original size:14 final size:15
Alignment explanation
Indices: 2434996--2435028 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2434986 AAAGAAAAAG
2434996 AAATAATAATAA-TA
1 AAATAATAATAATTA
2435010 AAATAATAATAATTA
1 AAATAATAATAATTA
2435025 AAAT
1 AAAT
2435029 TCGGACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAATAATAATTA
Found at i:2435770 original size:41 final size:42
Alignment explanation
Indices: 2435719--2435805 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 42
2435709 GTCCGGAGGT
* * *
2435719 CTTATAGATGACCCATAGGATTT-ATCATCTTGCTCAAAAGA
1 CTTACAGATGACCCAAAGGATTTAATCATCATGCTCAAAAGA
*
2435760 CTTACAGATGACCCAAAGGATTTAATCATCATGCTCAGAAGA
1 CTTACAGATGACCCAAAGGATTTAATCATCATGCTCAAAAGA
2435802 CTTA
1 CTTA
2435806 TTGATGGTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 21 0.51
42 20 0.49
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (42 bp):
CTTACAGATGACCCAAAGGATTTAATCATCATGCTCAAAAGA
Found at i:2437152 original size:19 final size:19
Alignment explanation
Indices: 2437128--2437178 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2437118 GAAAATATTC
2437128 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2437147 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2437166 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2437179 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2437219 original size:12 final size:12
Alignment explanation
Indices: 2437202--2437240 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2437192 TCGATGCATC
2437202 GATGCATGGACT
1 GATGCATGGACT
2437214 GATGCAT---C-
1 GATGCATGGACT
2437222 GATGCATGGACT
1 GATGCATGGACT
2437234 GATGCAT
1 GATGCAT
2437241 CGGTGCATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (12 bp):
GATGCATGGACT
Found at i:2437219 original size:20 final size:20
Alignment explanation
Indices: 2437194--2437249 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2437184 TTAATTCATC
2437194 GATGCATCGATGCATGGACT
1 GATGCATCGATGCATGGACT
2437214 GATGCATCGATGCATGGACT
1 GATGCATCGATGCATGGACT
*
2437234 GATGCATCGGTGCATG
1 GATGCATCGATGCATG
2437250 CCTTTGAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (20 bp):
GATGCATCGATGCATGGACT
Found at i:2437231 original size:65 final size:64
Alignment explanation
Indices: 2437022--2437229 Score: 239
Period size: 65 Copynumber: 3.2 Consensus size: 64
2437012 GCACCAAGTG
* *
2437022 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCATGGTGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
2437086 -
64 A
*
2437086 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
2437148 GA
63 GA
* * * *
2437150 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
2437214 GA
63 GA
2437216 TGCATCGATGCATG
1 TGCATCGATGCATG
2437230 GACTGATGCA
Statistics
Matches: 124, Mismatches: 9, Indels: 21
0.81 0.06 0.14
Matches are distributed among these distances:
63 10 0.08
64 45 0.36
65 65 0.52
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:2437603 original size:31 final size:31
Alignment explanation
Indices: 2437565--2437644 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
2437555 ATCGATTTTG
2437565 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
2437596 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
2437627 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
2437645 TTTGTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:2438794 original size:44 final size:42
Alignment explanation
Indices: 2438680--2438797 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 42
2438670 AAAACCCGAC
* * *
2438680 GGATGCATCGGTGCATGGTCTTATGCATCGATGCATATTCAAG
1 GGATGCATCGGTGCATTGT-TAATGCATCGATACATATTCAAG
* * *
2438723 GCATGCATCGGTGCATCATGGTGATGCATCGATACATATTCAAAG
1 GGATGCATCGGTGCAT--TGTTAATGCATCGATACATATTC-AAG
*
2438768 GGATGCATCGATGCATTGTTAAATGCATCG
1 GGATGCATCGGTGCATTGTT-AATGCATCG
2438798 GTGCATGAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 18 0.29
44 26 0.42
45 18 0.29
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (42 bp):
GGATGCATCGGTGCATTGTTAATGCATCGATACATATTCAAG
Found at i:2444265 original size:64 final size:64
Alignment explanation
Indices: 2444212--2444374 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
2444202 CGGTGCACCA
*
2444212 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
2444276 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
2444341 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
2444375 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:2444346 original size:19 final size:19
Alignment explanation
Indices: 2444322--2444372 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2444312 GAAAATATTC
2444322 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2444341 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2444360 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2444373 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2444414 original size:65 final size:65
Alignment explanation
Indices: 2444216--2444423 Score: 207
Period size: 65 Copynumber: 3.2 Consensus size: 65
2444206 GCACCAAGTG
* * ** *
2444216 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
2444279 G-
64 GA
* * *
2444280 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
2444343 A
65 A
* *
2444344 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
2444406 CTGA
62 CTGA
2444410 TGCATCGGTGCATG
1 TGCATCGGTGCATG
2444424 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.06
64 51 0.41
65 60 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:2449573 original size:3 final size:3
Alignment explanation
Indices: 2449565--2449635 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
2449555 ACACACGGGA
2449565 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2449613 ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
2449636 CTTCTTCTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2450900 original size:2 final size:2
Alignment explanation
Indices: 2450893--2450934 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2450883 CCCGGTTAGT
2450893 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2450935 ATGTATTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2456509 original size:28 final size:24
Alignment explanation
Indices: 2456441--2456487 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2456431 ACCGATACTC
*
2456441 AAAGGAGTATCGATACTACTTTAA
1 AAAGTAGTATCGATACTACTTTAA
2456465 AAAGTAGTATCGATACTACTTTA
1 AAAGTAGTATCGATACTACTTTA
2456488 CCATGAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (24 bp):
AAAGTAGTATCGATACTACTTTAA
Found at i:2456612 original size:21 final size:21
Alignment explanation
Indices: 2456554--2456605 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
2456544 TTAAATATAA
2456554 TAAAGGAAGTACCGATACTCAT
1 TAAAGG-AGTACCGATACTCAT
*
2456576 TAAAGGATTACCGATACTCAT
1 TAAAGGAGTACCGATACTCAT
2456597 TAAAGGAGT
1 TAAAGGAGT
2456606 GTCGATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (21 bp):
TAAAGGAGTACCGATACTCAT
Found at i:2459037 original size:21 final size:21
Alignment explanation
Indices: 2459008--2459144 Score: 139
Period size: 21 Copynumber: 6.4 Consensus size: 21
2458998 AATTGTCCCT
2459008 AAGGACCACATATATGTTCCG
1 AAGGACCACATATATGTTCCG
* * * *
2459029 AATGACCACATAGAATTGTCCCT
1 AAGGACCACATA-TA-TGTTCCG
* *
2459052 AAGAACCACATATATGTTCCA
1 AAGGACCACATATATGTTCCG
** *
2459073 AAATACCAAATATATGTTCCG
1 AAGGACCACATATATGTTCCG
* *
2459094 AAGGACCCCATATATGTTCCA
1 AAGGACCACATATATGTTCCG
* *
2459115 AAGGATCACATATATGTCCCG
1 AAGGACCACATATATGTTCCG
2459136 AAGGACCAC
1 AAGGACCAC
2459145 GTAAAACCCT
Statistics
Matches: 91, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
21 74 0.81
22 2 0.02
23 15 0.16
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCG
Found at i:2459063 original size:23 final size:23
Alignment explanation
Indices: 2458975--2459063 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
2458965 TGCCATATAA
* *
2458975 AATTGTCCCGAAGGACCTCGTAG
1 AATTGTCCCGAAGGACCACATAG
*
2458998 AATTGTCCCTAAGGACCACATA-
1 AATTGTCCCGAAGGACCACATAG
* * *
2459020 TA-TGTTCCGAATGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
* *
2459042 AATTGTCCCTAAGAACCACATA
1 AATTGTCCCGAAGGACCACATA
2459064 TATGTTCCAA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
21 16 0.31
22 2 0.04
23 34 0.65
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:2459128 original size:42 final size:42
Alignment explanation
Indices: 2459001--2459144 Score: 162
Period size: 42 Copynumber: 3.4 Consensus size: 42
2458991 CTCGTAGAAT
* * * *
2459001 TGTCCCTAAGGACCACATATATGTTCCGAATGACCACATAGAA
1 TGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATA-TA
* * * *
2459044 TTGTCCCTAAGAACCACATATATGTTCCAAAATACCAAATATA
1 -TGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATATA
* * * *
2459087 TGTTCCGAAGGACCCCATATATGTTCCAAAGGATCACATATA
1 TGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATATA
2459129 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
2459145 GTAAAACCCT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 48 0.57
43 1 0.01
44 35 0.42
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (42 bp):
TGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATATA
Found at i:2461272 original size:22 final size:22
Alignment explanation
Indices: 2461247--2461289 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2461237 GAAAGCTTAA
2461247 TAAAAGAAAAATAATTA-ATTTC
1 TAAAA-AAAAATAATTATATTTC
*
2461269 TAAAAACAAATAATTATATTT
1 TAAAAAAAAATAATTATATTT
2461290 AAAAATGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAAAAAAAATAATTATATTTC
Found at i:2461294 original size:21 final size:19
Alignment explanation
Indices: 2461247--2461294 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
2461237 GAAAGCTTAA
2461247 TAAAAGAAAAATAATTAATTT
1 TAAAA-AAAAATAATTAA-TT
*
2461268 CTAAAAACAAATAATTATATT
1 -TAAAAAAAAATAATTA-ATT
2461289 TAAAAA
1 TAAAAA
2461295 TGGCAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
22 6 0.25
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAAAAAAATAATTAATT
Found at i:2472791 original size:55 final size:54
Alignment explanation
Indices: 2472732--2473033 Score: 311
Period size: 54 Copynumber: 5.5 Consensus size: 54
2472722 TAGAATTAAC
2472732 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAA-T
* ***
2472787 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGT---G-T-AGCCAAAAT
* ** * *
2472846 GACTGAGCACCTCTGTGCTTCAGCCGAGAGCTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT
* *
2472900 GATTGAGCACCTCTGTGCTTCAATCGAG-GACTGACACCTCTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGTAGCCAA-AAT
* * * * * * ****
2472955 GACTGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA-TTGGAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGA-GCTGACACCTCTGTGTAGCCAAAAT
*
2473009 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
2473034 TAAAATCAAG
Statistics
Matches: 208, Mismatches: 30, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
53 1 0.00
54 74 0.36
55 70 0.34
56 16 0.08
58 1 0.00
59 41 0.20
60 5 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT
Found at i:2472830 original size:27 final size:28
Alignment explanation
Indices: 2472735--2473000 Score: 128
Period size: 27 Copynumber: 9.5 Consensus size: 28
2472725 AATTAACGAT
*
2472735 TGAGCACCTCTGTGCTTCAATCGAGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* ** * *
2472763 TGA-CACCTCTGTG-TAGCCAAAAGTG-AT
1 TGAGCACCTCTGTGCT--TCAATCGAGAAC
2472790 TGAGCACCTCTGTGCTTCAATCGAGAAC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* *** *
2472818 TGA-CACCTCTGTGCAGTTAAAAAAAAATGAC
1 TGAGCACCTCTGTGC--TTCAATCGAGA--AC
** *
2472849 TGAGCACCTCTGTGCTTCAGCCGAGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* *
2472877 TGA-CACCTCTGTG-TAGCTAA--GATG-AT
1 TGAGCACCTCTGTGCT-TC-AATCGA-GAAC
*
2472903 TGAGCACCTCTGTGCTTCAATCGAGGAC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
** *
2472931 TGA-CACCTCTGTGCAGCCAA-CTATG-AC
1 TGAGCACCTCTGTGC-TTCAATCGA-GAAC
*
2472958 TGAGCACCTCTGTGCTTCAATCTA-AATTC
1 TGAGCACCTCTGTGCTTCAATCGAGAA--C
2472987 TG-GCACCTCTGTGC
1 TGAGCACCTCTGTGC
2473001 ATTGGAATGA
Statistics
Matches: 179, Mismatches: 34, Indels: 50
0.68 0.13 0.19
Matches are distributed among these distances:
26 9 0.05
27 75 0.42
28 64 0.36
29 10 0.06
30 5 0.03
31 5 0.03
32 11 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (28 bp):
TGAGCACCTCTGTGCTTCAATCGAGAAC
Found at i:2472874 original size:59 final size:55
Alignment explanation
Indices: 2472732--2473033 Score: 299
Period size: 55 Copynumber: 5.5 Consensus size: 55
2472722 TAGAATTAAC
* * ** *
2472732 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAT
2472787 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAG-T---AAAAAAT
* ** * * *
2472846 GACTGAGCACCTCTGTGCTTCAGCCGAGAGCTGACACCTCTGTGTAGCT--AAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAG-TAAAAAAT
* ** **
2472900 GATTGAGCACCTCTGTGCTTCAATCGAGGACTGACACCTCTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAT
* * * ***
2472955 GACTGAGCACCTCTGTGCTTCAATCTA-AATTCTGGCACCTCTGTGCA-T-TGGAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAA--CTGACACCTCTGTGCAGTAAAAAAT
*
2473009 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
2473034 TAAAATCAAG
Statistics
Matches: 207, Mismatches: 32, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
54 71 0.34
55 73 0.35
56 15 0.07
59 48 0.23
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (55 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAT
Found at i:2472942 original size:113 final size:114
Alignment explanation
Indices: 2472735--2472946 Score: 372
Period size: 113 Copynumber: 1.9 Consensus size: 114
2472725 AATTAACGAT
*
2472735 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
2472800 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
* * *
2472849 TGAGCACCTCTGTGCTTCAGCCGAGAGCTGACACCTCTGTGTAGCTAAGA-TGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
*
2472913 TGTGCTTCAATCGAGGACTGACACCTCTGTGCAG
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG
2472947 CCAACTATGA
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 47 0.51
114 46 0.49
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (114 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
Found at i:2473033 original size:109 final size:110
Alignment explanation
Indices: 2472735--2473033 Score: 343
Period size: 109 Copynumber: 2.7 Consensus size: 110
2472725 AATTAACGAT
* * * * *
2472735 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGA-TGATTGAGCACCTC
2472800 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
65 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG---AAAAAAAATGAC
* * *
2472849 TGAGCACCTCTGTGCTTCAGCCGAGAGCTGACACCTCTGTGTAGCTAAGATGATTGAGCACCTCT
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
* ** **
2472914 GTGCTTCAATCGAGGACTGACACCTCTGTGCAG-CCAACTATGAC
66 GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
* * * * **
2472958 TGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA--TTGGAATGATTGAGCACCT
1 TGAGCACCTCTGTGCTTCAACCGAAA-GCTGACACCTCTGTGCAGCTAAG-ATGATTGAGCACCT
*
2473021 CTGTGCTACAATC
64 CTGTGCTTCAATC
2473034 TAAAATCAAG
Statistics
Matches: 164, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
108 2 0.01
109 55 0.34
110 14 0.09
113 47 0.29
114 46 0.28
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
Found at i:2473815 original size:2 final size:2
Alignment explanation
Indices: 2473808--2473865 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2473798 GGTCACGACA
2473808 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
2473850 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2473866 CATCGACAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2474739 original size:42 final size:42
Alignment explanation
Indices: 2474688--2474767 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
2474678 TTTTAGAAAA
* *
2474688 ATTAAGATATT-AATTAAATTTAAA-ATATAAATTTAAATAATT
1 ATTAAGATATTCAA-TAAA-TTAAATATACAAATATAAATAATT
2474730 ATTAAGATATTCAATAAATTAAATATACAAATATAAAT
1 ATTAAGATATTCAATAAATTAAATATACAAATATAAAT
2474768 TTACATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 5 0.15
42 27 0.79
43 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (42 bp):
ATTAAGATATTCAATAAATTAAATATACAAATATAAATAATT
Found at i:2475032 original size:25 final size:27
Alignment explanation
Indices: 2474979--2475032 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
2474969 AACATTGAAA
** *
2474979 TTATTTTTTATATTTTCATATTTTTTT
1 TTATTTTTTATATTTTCATAAATTATT
2475006 TTATTTTTT-T-TTTTCATAAATTATT
1 TTATTTTTTATATTTTCATAAATTATT
2475031 TT
1 TT
2475033 CTAATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.58
26 1 0.04
27 9 0.38
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (27 bp):
TTATTTTTTATATTTTCATAAATTATT
Found at i:2475655 original size:46 final size:46
Alignment explanation
Indices: 2475589--2475679 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
2475579 TGGGCATCCA
*
2475589 CACAATCCACAACAACGCCTCCGAACTGCGGCTCCAAATTCCGGCC
1 CACAATCCACAACAACGCCTCCGAACGGCGGCTCCAAATTCCGGCC
* * *
2475635 CACAATCCACAACAACGCCTCTGAACGGCGGCTGCAGATTCCGGC
1 CACAATCCACAACAACGCCTCCGAACGGCGGCTCCAAATTCCGGC
2475680 GGCATAGTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.27, C:0.41, G:0.19, T:0.13
Consensus pattern (46 bp):
CACAATCCACAACAACGCCTCCGAACGGCGGCTCCAAATTCCGGCC
Found at i:2480293 original size:21 final size:21
Alignment explanation
Indices: 2480267--2480306 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2480257 GACTATCGTA
2480267 TTGCGATTTCCCAAATTCGCG
1 TTGCGATTTCCCAAATTCGCG
* *
2480288 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
2480307 TAATGCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGCG
Found at i:2480313 original size:21 final size:21
Alignment explanation
Indices: 2480262--2480314 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2480252 ATTCTGACTA
2480262 TCGTATTGCGATTTCCCAAAT
1 TCGTATTGCGATTTCCCAAAT
** * *
2480283 TCGCGTTGCGATTTTCCTAAT
1 TCGTATTGCGATTTCCCAAAT
*
2480304 TCGTAATGCGA
1 TCGTATTGCGA
2480315 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGTATTGCGATTTCCCAAAT
Found at i:2480336 original size:20 final size:20
Alignment explanation
Indices: 2480308--2480395 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
2480298 CCTAATTCGT
2480308 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* ** *
2480328 AACGCGAATTTGGAAAATCGC
1 AATGCGAA-TACGTAAATCGC
* *
2480349 AATGCGATTACGTAAATCCC
1 AATGCGAATACGTAAATCGC
2480369 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
2480389 AATGCGA
1 AATGCGA
2480396 TTTACATAGC
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 40 0.73
21 15 0.27
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:2480353 original size:41 final size:40
Alignment explanation
Indices: 2480308--2480395 Score: 113
Period size: 41 Copynumber: 2.2 Consensus size: 40
2480298 CCTAATTCGT
* **
2480308 AATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGC
1 AATGCGAATACGTAAATCCCAACGCGAA-TACGAAAATCGC
* * *
2480349 AATGCGATTACGTAAATCCCAATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCCCAACGCGAATACGAAAATCGC
2480389 AATGCGA
1 AATGCGA
2480396 TTTACATAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 16 0.39
41 25 0.61
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
AATGCGAATACGTAAATCCCAACGCGAATACGAAAATCGC
Found at i:2480590 original size:22 final size:22
Alignment explanation
Indices: 2480565--2480625 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 22
2480555 GCGACATCCA
2480565 TCCCCATCTCCGACGAAATCAG
1 TCCCCATCTCCGACGAAATCAG
2480587 TCCCCA----CGACGATAA-CAG
1 TCCCCATCTCCGACGA-AATCAG
* *
2480605 TCTCCATCTCCGGCGAAATCA
1 TCCCCATCTCCGACGAAATCA
2480626 TTCACGGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
18 14 0.45
19 2 0.06
21 2 0.06
22 13 0.42
ACGTcount: A:0.28, C:0.39, G:0.15, T:0.18
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAG
Found at i:2480982 original size:20 final size:20
Alignment explanation
Indices: 2480957--2481004 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2480947 CAACGAGTGA
2480957 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
2480977 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2480997 ATCGCAAC
1 ATCGCAAC
2481005 AAGAGAATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2481072 original size:20 final size:20
Alignment explanation
Indices: 2481047--2481096 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2481037 TGCGATTCTT
2481047 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
2481067 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
2481087 GTGTTGCGAT
1 GCGTTGCGAT
2481097 TTAAAGTTTC
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:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:2483007 original size:20 final size:20
Alignment explanation
Indices: 2482982--2483087 Score: 167
Period size: 20 Copynumber: 5.3 Consensus size: 20
2482972 AGAATAGTTT
2482982 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2483002 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2483022 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2483042 ACTATTGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
2483062 ACTATCGCAATGTGAATTTG
1 ACTATCGCAATGCGAAAATG
2483082 ACTATC
1 ACTATC
2483088 ACAACGAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2483250 original size:20 final size:20
Alignment explanation
Indices: 2483225--2483279 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
2483215 GATTCTCTCC
2483225 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
2483245 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
2483265 TTGCGATAGTCATTT
1 TTGCGATAGTCATTT
2483280 GCAGATTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:2483846 original size:21 final size:21
Alignment explanation
Indices: 2483755--2483859 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
2483745 GACTCACCTG
*
2483755 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
2483777 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
2483797 TCATCCATCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
2483818 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
2483839 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
2483860 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:2483852 original size:42 final size:42
Alignment explanation
Indices: 2483752--2483862 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
2483742 CCTGACTCAC
* * * *
2483752 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
2483794 CTATCATCCATCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
2483836 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
2483863 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:2485235 original size:14 final size:14
Alignment explanation
Indices: 2485216--2485251 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2485206 ATTGTTTAAT
2485216 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2485230 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2485244 TGATTTGT
1 TGATTTGT
2485252 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2485394 original size:33 final size:34
Alignment explanation
Indices: 2485357--2485428 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
2485347 CAGACTATCG
2485357 CAACGAGAGAATCGCAATGCG-AAATGAAAATCA
1 CAACGAGAGAATCGCAATGCGAAAATGAAAATCA
* *
2485390 CAACGAGTGAATCGCAATGCGAAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCGAAAATGAAAATCA
2485424 CAACG
1 CAACG
2485429 CGAAACTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (34 bp):
CAACGAGAGAATCGCAATGCGAAAATGAAAATCA
Found at i:2485459 original size:19 final size:19
Alignment explanation
Indices: 2485437--2485581 Score: 228
Period size: 19 Copynumber: 7.8 Consensus size: 19
2485427 CGCGAAACTA
*
2485437 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2485456 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
2485474 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2485490 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2485509 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2485528 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2485547 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2485566 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
2485582 CTCTCGTTAC
Statistics
Matches: 117, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
14 6 0.05
16 7 0.06
17 3 0.03
18 4 0.03
19 85 0.73
20 12 0.10
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:2485616 original size:20 final size:20
Alignment explanation
Indices: 2485586--2485674 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
2485576 GCGATTCTCT
*
2485586 CGTTACGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
2485606 TGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
2485626 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
2485646 CGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
2485666 CGTTGCGAT
1 CGTTGCGAT
2485675 TTTCGCGTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2485681 original size:14 final size:14
Alignment explanation
Indices: 2485662--2485688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2485652 GATAGTCATA
2485662 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
2485676 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2485689 AGTCAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.30, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:2488146 original size:24 final size:24
Alignment explanation
Indices: 2488117--2488174 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
2488107 ATCAAAATCT
2488117 GAGTATTGACCAAGATCAAAGTTC
1 GAGTATTGACCAAGATCAAAGTTC
* *
2488141 GGGTATTGACCAAGATCAAATTTC
1 GAGTATTGACCAAGATCAAAGTTC
*
2488165 GAATATTGAC
1 GAGTATTGAC
2488175 TAGTACTCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (24 bp):
GAGTATTGACCAAGATCAAAGTTC
Found at i:2489035 original size:20 final size:20
Alignment explanation
Indices: 2489012--2489110 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 20
2489002 TTGCGATAGT
* *
2489012 CAGAATCTCGTTGCGATTTA
1 CAGAATCACATTGCGATTTA
* *
2489032 CAGATTCACATTACGATTTA
1 CAGAATCACATTGCGATTTA
*
2489052 C-GTAATCGCATTGCGATTTA
1 CAG-AATCACATTGCGATTTA
* * *
2489072 C-GTATTCGCATTGTGATTTA
1 CAG-AATCACATTGCGATTTA
*
2489092 C-GTAATCGCATTGCGATTT
1 CAG-AATCACATTGCGATTT
2489111 TTCAAATTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
19 1 0.01
20 66 0.99
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (20 bp):
CAGAATCACATTGCGATTTA
Found at i:2489068 original size:40 final size:40
Alignment explanation
Indices: 2489022--2489148 Score: 157
Period size: 40 Copynumber: 3.1 Consensus size: 40
2489012 CAGAATCTCG
*
2489022 TTGCGATTTACAGATTCACATTACGATTTACGTAATCGCA
1 TTGCGATTTACAGATTCACATTGCGATTTACGTAATCGCA
* *
2489062 TTGCGATTTAC-GTATTCGCATTGTGATTTACGTAATCGCA
1 TTGCGATTTACAG-ATTCACATTGCGATTTACGTAATCGCA
* * ** *
2489102 TTGCGATTTTTCAAATTCATGTTGCGATTTACGTATTCGCA
1 TTGCGA-TTTACAGATTCACATTGCGATTTACGTAATCGCA
2489143 TTGCGA
1 TTGCGA
2489149 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 41 0.55
41 32 0.43
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACAGATTCACATTGCGATTTACGTAATCGCA
Found at i:2489146 original size:20 final size:20
Alignment explanation
Indices: 2489022--2489148 Score: 130
Period size: 20 Copynumber: 6.3 Consensus size: 20
2489012 CAGAATCTCG
*
2489022 TTGCGATTTACAG-ATTCACA
1 TTGCGATTTAC-GTATTCGCA
* *
2489042 TTACGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
2489062 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
2489082 TTGTGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** ***
2489102 TTGCGATTTTTCAAATTCATG
1 TTGCGA-TTTACGTATTCGCA
2489123 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2489143 TTGCGA
1 TTGCGA
2489149 ATTAGGAAAA
Statistics
Matches: 84, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
19 1 0.01
20 70 0.83
21 13 0.15
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2489169 original size:21 final size:21
Alignment explanation
Indices: 2489145--2489190 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2489135 TATTCGCATT
2489145 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
2489166 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2489187 GCGA
1 GCGA
2489191 TAGCCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2491775 original size:21 final size:21
Alignment explanation
Indices: 2491749--2491848 Score: 182
Period size: 21 Copynumber: 4.8 Consensus size: 21
2491739 TGCGATTTTG
2491749 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
2491770 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
*
2491791 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
*
2491812 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
2491833 GACTATCGCAACGAAT
1 GACTATCGCAACGAAT
2491849 ATCGCAACGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGAATTTGGA
Found at i:2491802 original size:42 final size:42
Alignment explanation
Indices: 2491749--2491928 Score: 220
Period size: 42 Copynumber: 4.5 Consensus size: 42
2491739 TGCGATTTTG
* *
2491749 GACTATCGCAACGAATTTGGAGACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGA
2491791 GACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGA
2491833 GACTATCG---C-AAC---GA-A-TATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGA
* *
2491866 AACTATCGCAACGCACTTGGAGACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGA
*
2491908 -A-AATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
2491929 CTATTGCAAT
Statistics
Matches: 121, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
33 25 0.21
34 1 0.01
35 2 0.02
36 1 0.01
37 2 0.02
38 3 0.02
39 1 0.01
40 9 0.07
41 2 0.02
42 75 0.62
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGA
Found at i:2491857 original size:33 final size:33
Alignment explanation
Indices: 2491815--2491878 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
2491805 ACTTGGAGAC
*
2491815 TATCGCAACGAACTTGGAGACTATCGCAACGAA
1 TATCGCAACGAACTTGGAAACTATCGCAACGAA
2491848 TATCGCAACGAACTTGGAAACTATCGCAACG
1 TATCGCAACGAACTTGGAAACTATCGCAACG
2491879 CACTTGGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (33 bp):
TATCGCAACGAACTTGGAAACTATCGCAACGAA
Found at i:2491874 original size:21 final size:21
Alignment explanation
Indices: 2491848--2491928 Score: 112
Period size: 21 Copynumber: 3.9 Consensus size: 21
2491838 TCGCAACGAA
2491848 TATCGCAACGAACTTGGAAAC
1 TATCGCAACGAACTTGGAAAC
* *
2491869 TATCGCAACGCACTTGGAGAC
1 TATCGCAACGAACTTGGAAAC
2491890 TATCGCAACGAACTTGGAAA-
1 TATCGCAACGAACTTGGAAAC
2491910 -ATCGCAACGCGAACTTGGA
1 TATCGCAA--CGAACTTGGA
2491929 CTATTGCAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
19 7 0.13
21 47 0.87
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (21 bp):
TATCGCAACGAACTTGGAAAC
Found at i:2491876 original size:54 final size:54
Alignment explanation
Indices: 2491794--2491901 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
2491784 ATTTGGAGAC
*
2491794 TATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAA
1 TATCGCAACGAACTTGGAAACTATCGCAACGAACTTGGAGACTATCGCAACGAA
*
2491848 TATCGCAACGAACTTGGAAACTATCGCAACGCACTTGGAGACTATCGCAACGAA
1 TATCGCAACGAACTTGGAAACTATCGCAACGAACTTGGAGACTATCGCAACGAA
2491902 CTTGGAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (54 bp):
TATCGCAACGAACTTGGAAACTATCGCAACGAACTTGGAGACTATCGCAACGAA
Found at i:2491937 original size:21 final size:21
Alignment explanation
Indices: 2491848--2491943 Score: 78
Period size: 21 Copynumber: 4.7 Consensus size: 21
2491838 TCGCAACGAA
2491848 TATCGCAA--CGAACTTGGAAAC
1 TATCGCAACGCGAACTTGG--AC
2491869 TATCGCAACGC--ACTTGGAGAC
1 TATCGCAACGCGAACTT-G-GAC
*
2491890 TATCGCAA--CGAACTTGGAA
1 TATCGCAACGCGAACTTGGAC
*
2491909 AATCGCAACGCGAACTTGGAC
1 TATCGCAACGCGAACTTGGAC
* *
2491930 TATTGCAATGCGAA
1 TATCGCAACGCGAA
2491944 TATGTAAATC
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
19 10 0.16
20 1 0.02
21 47 0.77
22 1 0.02
23 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
TATCGCAACGCGAACTTGGAC
Found at i:2491946 original size:96 final size:96
Alignment explanation
Indices: 2491752--2491928 Score: 277
Period size: 96 Copynumber: 1.8 Consensus size: 96
2491742 GATTTTGGAC
* * * *
2491752 TATCGCAACGAATTTGGAGACTATCGCAACGAATTTGGAGACTATCGCAACGAACTTGGAGACTA
1 TATCGCAACGAACTTGGAAACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACAA
2491817 TCGCAACGAACTTGGAGACTATCGCAACGAA
66 TCGCAACGAACTTGGAGACTATCGCAACGAA
*
2491848 TATCGCAACGAACTTGGAAACTATCGCAACGCACTTGGAGACTATCGCAACGAACTTGGA-A-AA
1 TATCGCAACGAACTTGGAAACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACAA
2491911 TCGCAACGCGAACTTGGA
66 TCGCAA--CGAACTTGGA
2491929 CTATTGCAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
94 7 0.09
95 1 0.01
96 66 0.89
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (96 bp):
TATCGCAACGAACTTGGAAACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACAA
TCGCAACGAACTTGGAGACTATCGCAACGAA
Found at i:2499119 original size:2 final size:2
Alignment explanation
Indices: 2499114--2499144 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2499104 TTGTGTGTCA
2499114 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
2499145 ATAAAGTATC
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:2505040 original size:3 final size:3
Alignment explanation
Indices: 2505032--2505056 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2505022 ATTTTTATAT
2505032 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2505057 AAATTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2506496 original size:4 final size:4
Alignment explanation
Indices: 2506487--2506521 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
2506477 GTTTTTATTA
2506487 TTAT TTAT TTAT TTAT TTAT TTAT TTATT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TT
2506522 TCTTTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2508004 original size:14 final size:14
Alignment explanation
Indices: 2507985--2508011 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2507975 TTTACTCCTT
2507985 TTTATTTTATTTTA
1 TTTATTTTATTTTA
2507999 TTTATTTTATTTT
1 TTTATTTTATTTT
2508012 TTATGTAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:2509735 original size:31 final size:31
Alignment explanation
Indices: 2509670--2509818 Score: 220
Period size: 31 Copynumber: 5.0 Consensus size: 31
2509660 CCCGAAGGAC
*
2509670 CAGTCCATA-GATTCCGAAGAAC-TAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
2509700 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2509731 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2509762 CAGTCC--ATGTT-CGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2509790 -AGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
2509819 CCCTCGACCC
Statistics
Matches: 109, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
27 5 0.05
28 17 0.16
29 10 0.09
30 34 0.31
31 43 0.39
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:2509805 original size:58 final size:61
Alignment explanation
Indices: 2509670--2509818 Score: 218
Period size: 58 Copynumber: 2.5 Consensus size: 61
2509660 CCCGAAGGAC
* *
2509670 CAGTCCATA-GATTCCGAAGAAC-TAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAACAGTCCA-ATGTCCCGAAGAACATAGGTAAA
*
2509731 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCC-ATGT-TCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCAATGTCCCGAAGAACATAGGTAAA
2509790 -AGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
2509819 CCCTCGACCC
Statistics
Matches: 83, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
58 29 0.35
59 16 0.19
60 4 0.05
61 20 0.24
62 14 0.17
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (61 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCAATGTCCCGAAGAACATAGGTAAA
Found at i:2510593 original size:21 final size:21
Alignment explanation
Indices: 2510563--2510607 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2510553 AATTCTGTCG
* *
2510563 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2510584 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2510605 TTG
1 TTG
2510608 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2513555 original size:31 final size:31
Alignment explanation
Indices: 2513517--2513669 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
2513507 CCCGAAGGAC
* *
2513517 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
2513548 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2513579 CAGTCCATATGTTCCGAAGAACATA-GTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2513609 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2513640 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
2513670 CCCTCGACCC
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
30 30 0.26
31 83 0.73
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:2513633 original size:61 final size:61
Alignment explanation
Indices: 2513517--2513665 Score: 237
Period size: 61 Copynumber: 2.4 Consensus size: 61
2513507 CCCGAAGGAC
* * *
2513517 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATA-GTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2513579 CAGTCCATATGTTCCGAAGAACATAGTAAACAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
2513640 CAGTCCATATGTTCCGAAGAACATAG
1 CAGTCCATATGTTCCGAAGAACATAG
2513666 GTAACCCTCG
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
61 59 0.72
62 22 0.27
63 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (61 bp):
CAGTCCATATGTTCCGAAGAACATAGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2514068 original size:16 final size:16
Alignment explanation
Indices: 2514032--2514070 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2514022 GCATGTTAAC
2514032 ACATATAATCATGCAT
1 ACATATAATCATGCAT
2514048 ACATA-AATCATGTCAT
1 ACATATAATCATG-CAT
*
2514064 TCATATA
1 ACATATA
2514071 CGTATAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 7 0.35
16 12 0.60
17 1 0.05
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (16 bp):
ACATATAATCATGCAT
Found at i:2514448 original size:21 final size:20
Alignment explanation
Indices: 2514418--2514457 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2514408 ATTCTGTCGT
* *
2514418 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
2514438 TTGAATGGGTACCGATTCCC
1 TTGAA-GGGTACCGATTCCC
2514458 TTGCCCAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:2515282 original size:13 final size:13
Alignment explanation
Indices: 2515264--2515290 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2515254 GGTTGTGCTC
2515264 AATTACTTACTGT
1 AATTACTTACTGT
2515277 AATTACTTACTGT
1 AATTACTTACTGT
2515290 A
1 A
2515291 TGGATCAGAA
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:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (13 bp):
AATTACTTACTGT
Found at i:2524271 original size:8 final size:8
Alignment explanation
Indices: 2524260--2524303 Score: 65
Period size: 7 Copynumber: 5.6 Consensus size: 8
2524250 AAGAAAAGAC
2524260 AAAAATGA
1 AAAAATGA
2524268 AAAAATG-
1 AAAAATGA
2524275 AAAAATG-
1 AAAAATGA
2524282 AAAAATGA
1 AAAAATGA
2524290 GAAAAATGA
1 -AAAAATGA
2524299 AAAAA
1 AAAAA
2524304 AAGAAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.41
8 12 0.35
9 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AAAAATGA
Found at i:2524272 original size:9 final size:9
Alignment explanation
Indices: 2524260--2524325 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
2524250 AAGAAAAGAC
2524260 AAAAATG-A
1 AAAAATGAA
2524268 AAAAATG--
1 AAAAATGAA
2524275 AAAAATG--
1 AAAAATGAA
*
2524282 AAAAATGAG
1 AAAAATGAA
2524291 AAAAATGAA
1 AAAAATGAA
*
2524300 AAAAAAGAA
1 AAAAATGAA
2524309 GAAAAAT-AA
1 -AAAAATGAA
*
2524318 ATAAATGA
1 AAAAATGA
2524326 TGGTTCAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
7 14 0.28
8 12 0.24
9 19 0.38
10 5 0.10
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (9 bp):
AAAAATGAA
Found at i:2524272 original size:16 final size:16
Alignment explanation
Indices: 2524237--2524303 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
2524227 CTTGAAGAAG
*
2524237 AAAAGACAAAAA-AAA
1 AAAAGACAAAAATGAA
2524252 GAAAAGACAAAAATGAA
1 -AAAAGACAAAAATGAA
2524269 AAAATG--AAAAATGAA
1 AAAA-GACAAAAATGAA
* *
2524284 AAATGAGAAAAATGAA
1 AAAAGACAAAAATGAA
2524300 AAAA
1 AAAA
2524304 AAGAAGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 1 0.02
15 12 0.27
16 28 0.64
17 3 0.07
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAAGACAAAAATGAA
Found at i:2524277 original size:22 final size:22
Alignment explanation
Indices: 2524245--2524302 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
2524235 AGAAAAGACA
*
2524245 AAAAAAAGAAAAGA-CAAAAATG
1 AAAAAATGAAAA-ATCAAAAATG
*
2524267 AAAAAATGAAAAATGAAAAATG
1 AAAAAATGAAAAATCAAAAATG
2524289 AGAAAAATGAAAAA
1 A-AAAAATGAAAAA
2524303 AAAGAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 1 0.03
22 19 0.59
23 12 0.38
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAATGAAAAATCAAAAATG
Found at i:2524308 original size:16 final size:16
Alignment explanation
Indices: 2524260--2524308 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
2524250 AAGAAAAGAC
*
2524260 AAAAATG-AAAAAATG
1 AAAAATGAAAAAAAAG
**
2524275 AAAAATGAAAAATGAG
1 AAAAATGAAAAAAAAG
2524291 AAAAATGAAAAAAAAG
1 AAAAATGAAAAAAAAG
2524307 AA
1 AA
2524309 GAAAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (16 bp):
AAAAATGAAAAAAAAG
Found at i:2525721 original size:3 final size:3
Alignment explanation
Indices: 2525713--2525737 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2525703 TTTTATTTAT
2525713 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2525738 AAATTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2531883 original size:3 final size:3
Alignment explanation
Indices: 2531875--2531900 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2531865 GAATTGGGTT
2531875 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2531901 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2531921 original size:17 final size:17
Alignment explanation
Indices: 2531899--2531931 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2531889 GTTGTTGTTG
2531899 TTTA-TTATTATTATTTA
1 TTTATTTATT-TTATTTA
2531916 TTTATTTATTTTATTT
1 TTTATTTATTTTATTT
2531932 TCTTTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTTTATTTA
Found at i:2536469 original size:37 final size:36
Alignment explanation
Indices: 2536397--2536470 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
2536387 GTTAGAAAAT
*
2536397 ATTTATATATTTTCTTTAAAAAATTAAATTAATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATAATAAA
* *
2536433 ATTTATATAATTTTTTTTACAAAATTAAAA-ATATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAATA-ATAAA
2536470 A
1 A
2536471 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 9 0.27
37 24 0.73
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATAATAAA
Found at i:2538654 original size:3 final size:3
Alignment explanation
Indices: 2538646--2538722 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
2538636 TTAATATATT
* *
2538646 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2538694 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2538723 TGGGTAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2539063 original size:116 final size:116
Alignment explanation
Indices: 2538877--2539716 Score: 1249
Period size: 116 Copynumber: 7.3 Consensus size: 116
2538867 TTCTTCAGAT
* ** * * * *
2538877 GAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATCAAATGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGCAAA
2538942 AGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* * * * *
2538994 GAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCCATCAAATGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGCAAA
2539058 AGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---
65 AGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* * * *
2539107 GAGTTCTTCTCATTTTGAACCTTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTC-AGAAAA
1 GAGTTCTTCTCATTATGAACCTTCTCTGG-AAAAGCTGATCCATCAAGTGATGAATTCGAG-CAA
* *
2539170 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---
64 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
2539220 GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAA
1 GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGCAAAA
2539285 GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* * * *
2539336 GAGTTCTTCTCATTATGAACTTTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTC-AGAAAA
1 GAGTTCTTCTCATTATGAACCTTCTCTGG-AAAAGCTGATCCATCAAGTGATGAATTCGAG-CAA
* *
2539399 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---
64 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
2539449 GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAA
1 GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGCAAAA
2539514 GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
2539565 GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAA
1 GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGCAAAA
2539630 GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
2539681 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCT
1 GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCT
2539717 AATCTTTCAA
Statistics
Matches: 667, Mismatches: 40, Indels: 33
0.90 0.05 0.04
Matches are distributed among these distances:
112 13 0.02
113 287 0.43
114 7 0.01
115 2 0.00
116 332 0.50
117 24 0.04
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (116 bp):
GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGCAAAA
GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:2539321 original size:229 final size:229
Alignment explanation
Indices: 2538859--2539739 Score: 1289
Period size: 229 Copynumber: 3.8 Consensus size: 229
2538849 TTGAATAAAC
* * ** ** *
2538859 TCTTC-TCTTTCTTCAGAT-GAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACCTTCT-CTGGCAAAAATAATCCATC
* * *
2538922 AAATGATGAATTCA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
65 AAGTGATGAATTCAGAGAAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
* * * *
2538986 CAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCCATCAAATGATGAATT
130 CAGAT-A-GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGCTGATCCATCAAATGATGGATT
**
2539050 CAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACT
192 TGAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACT
*
2539088 TCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTTTGAACCTTCTCTGGCAAAAATAATCCATCA
1 TCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCA
*
2539152 AGTGATGAATTCAGA-AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
66 AGTGATGAATTCAGAGAAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
*
2539216 AGAT-GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
131 AGATAGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
2539280 CAAAAGATTGAACAAGTTCTTCTCATTATGAACT
196 CAAAAGATTGAACAAGTTCTTCTCATTATGAACT
*
2539314 TCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAAATAATCCAT
1 TCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCAT
*
2539379 CAAGTGATGAATTCAGA-AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
64 CAAGTGATGAATTCAGAGAAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
*
2539443 TCAGAT-GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
129 TCAGATAGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTG
2539507 AGCAAAAGATTGAACAAGTTCTTCTCATTATGAACT
194 AGCAAAAGATTGAACAAGTTCTTCTCATTATGAACT
* *
2539543 TCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGG-AAAAGCTGATCCA
1 TCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACCTTCTCTGGCAAAA-ATAATCCA
* * * *
2539607 TCAAGTGATGGATT-TGAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
63 TCAAGTGATGAATTCAGAGAAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
* * ** *
2539671 TTCAGATGACGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGATAGAT
128 TTCAGAT-A-GAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
2539736 TTGA
191 TTGA
2539740 ATCTTTGCTA
Statistics
Matches: 606, Mismatches: 35, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
225 3 0.00
226 102 0.17
228 6 0.01
229 406 0.67
230 36 0.06
232 53 0.09
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (229 bp):
TCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCA
AGTGATGAATTCAGAGAAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
AGATAGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
CAAAAGATTGAACAAGTTCTTCTCATTATGAACT
Found at i:2540419 original size:84 final size:84
Alignment explanation
Indices: 2540319--2540877 Score: 1068
Period size: 84 Copynumber: 6.7 Consensus size: 84
2540309 ATAATTTTTA
2540319 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
*
2540384 AATTCAATGATTGGTTCTA
66 AATTCAATGATTGGTTCTG
2540403 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
2540468 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
2540487 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
*
2540552 AATTCAATGATTGGTTCTA
66 AATTCAATGATTGGTTCTG
2540571 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
2540636 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
*
2540655 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTACATTTTCT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT-CATCTTCT
2540719 AAATTCAATGATTGGTTCTG
65 AAATTCAATGATTGGTTCTG
2540739 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
2540804 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
2540823 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
2540878 ACATTTGTTC
Statistics
Matches: 468, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
83 14 0.03
84 447 0.96
85 7 0.01
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
AATTCAATGATTGGTTCTG
Found at i:2541926 original size:5 final size:5
Alignment explanation
Indices: 2541909--2541955 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
2541899 TGACCCCCCT
*
2541909 TTTTC TTTT- TTTTC TTTTTC TTTTC TTTT- TTTTT TCTTTC TTTTC TT
1 TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC TT
2541956 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
4 8 0.22
5 20 0.54
6 9 0.24
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:2541927 original size:15 final size:15
Alignment explanation
Indices: 2541907--2541955 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
2541897 CTTGACCCCC
2541907 CTTTTTCTTTTTTTT
1 CTTTTTCTTTTTTTT
2541922 CTTTTTCTTTTCTTTT
1 CTTTTTCTTTT-TTTT
* *
2541938 TTTTTTCTTTCTTTT
1 CTTTTTCTTTTTTTT
2541953 CTT
1 CTT
2541956 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Found at i:2541934 original size:20 final size:20
Alignment explanation
Indices: 2541909--2541955 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2541899 TGACCCCCCT
2541909 TTTTCTTTTTTTTCTT-TTTC
1 TTTTCTTTTTTTT-TTCTTTC
2541929 TTTTCTTTTTTTTTTCTTTC
1 TTTTCTTTTTTTTTTCTTTC
2541949 TTTTCTT
1 TTTTCTT
2541956 CAAGCATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTCTTTTTTTTTTCTTTC
Found at i:2552598 original size:18 final size:18
Alignment explanation
Indices: 2552575--2552624 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2552565 AAAATACTTG
2552575 TAAATAAAATAAAACAT-A
1 TAAATAAAATAAAA-ATAA
**
2552593 TAAATATTATAAAAATAA
1 TAAATAAAATAAAAATAA
2552611 TAAAT-AAATAAAAA
1 TAAATAAAATAAAAA
2552625 ATTTGAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATAAAATAAAAATAA
Found at i:2554298 original size:21 final size:22
Alignment explanation
Indices: 2554273--2554318 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2554263 CTTTCTCCGG
*
2554273 TTCTGT-CT-CTCTTTTTTTCTT
1 TTCTGTCCTCCTCCTTTTTT-TT
2554294 TTCTGTCCTCCTCCTTTTTTTT
1 TTCTGTCCTCCTCCTTTTTTTT
2554316 TTC
1 TTC
2554319 AGGTGGGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 7 0.32
23 9 0.41
ACGTcount: A:0.00, C:0.28, G:0.04, T:0.67
Consensus pattern (22 bp):
TTCTGTCCTCCTCCTTTTTTTT
Found at i:2554723 original size:3 final size:3
Alignment explanation
Indices: 2554715--2554794 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
2554705 TTAATATATT
* *
2554715 TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2554763 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2554795 TGGGTAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2557437 original size:79 final size:79
Alignment explanation
Indices: 2557306--2557463 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
2557296 TATTGATCCA
2557306 GTGTTCTATGCTTACTTTGTTGTTTAATTTGTTTCTTCTTAATATTAAGATTTTGGAGGCTCTTC
1 GTGTTCTATGCTTACTTTGTTGTTTAATTTGTTTCTTCTTAATATTAAGATTTTGGAGGCTCTTC
2557371 ATACAGGCTTATGC
66 ATACAGGCTTATGC
2557385 GTGTTCTATGCTTACTTTGTTGTTTAATTTGTTTCTTCTTAATATTAAGATTTTGGAGGCTCTTC
1 GTGTTCTATGCTTACTTTGTTGTTTAATTTGTTTCTTCTTAATATTAAGATTTTGGAGGCTCTTC
2557450 ATACAGGCTTATGC
66 ATACAGGCTTATGC
2557464 TGAACTCTTA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (79 bp):
GTGTTCTATGCTTACTTTGTTGTTTAATTTGTTTCTTCTTAATATTAAGATTTTGGAGGCTCTTC
ATACAGGCTTATGC
Found at i:2559869 original size:184 final size:183
Alignment explanation
Indices: 2559560--2559933 Score: 633
Period size: 184 Copynumber: 2.0 Consensus size: 183
2559550 AACCGAAATT
* * ** *
2559560 AAATATTAAATATATTATATATAACATATGGGTTCAGTCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAAAATATTATATATAACATATGAGTTCAACCCAAACCATTTAAAACCCAATTAATAA
**
2559625 TTTAAGATCCAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAATTTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAAATTATATAAAATTT
2559690 TTATTTGATAATTATATATTATTTAAATTAATT-GTAAACTGTTTTTTTAATTAA
131 TTATTTGATAATTATATATTATTTAAATTAATTAG-AAACTG-TTTTTTAATTAA
2559744 AAATATTAAAAATATTATATATAACATATGAGTTCAACCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAAAATATTATATATAACATATGAGTTCAACCCAAACCATTTAAAACCCAATTAATAA
**
2559809 TTTAAGATCCAATAACTTTTAAATTTAAATTAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAAATTATATAAAATTT
*
2559874 TTATTTTATAATTATATATTATTTAAATTAATTAGAAACTGTTTTTTAATTAA
131 TTATTTGATAATTATATATTATTTAAATTAATTAGAAACTGTTTTTTAATTAA
2559927 AAATATT
1 AAATATT
2559934 TAATTTTTAT
Statistics
Matches: 179, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
183 19 0.11
184 159 0.89
185 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAAAATATTATATATAACATATGAGTTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTGATAATTATATATTATTTAAATTAATTAGAAACTGTTTTTTAATTAA
Found at i:2571211 original size:3 final size:3
Alignment explanation
Indices: 2571203--2571247 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
2571193 AGGTGGGGGC
*
2571203 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2571248 ATTTTCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2573337 original size:23 final size:23
Alignment explanation
Indices: 2573311--2573356 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2573301 CTAACGTTGA
* * *
2573311 GTGATTATTTTGTAATAAACGAT
1 GTGATCATTTCGTAACAAACGAT
2573334 GTGATCATTTCGTAACAAACGAT
1 GTGATCATTTCGTAACAAACGAT
2573357 AACGTTAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (23 bp):
GTGATCATTTCGTAACAAACGAT
Found at i:2573421 original size:16 final size:16
Alignment explanation
Indices: 2573400--2573434 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2573390 TCAATAGTGA
2573400 AAACGAACATTTACCC
1 AAACGAACATTTACCC
2573416 AAACGAACATTTACCC
1 AAACGAACATTTACCC
2573432 AAA
1 AAA
2573435 TATTAGTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.29, G:0.06, T:0.17
Consensus pattern (16 bp):
AAACGAACATTTACCC
Found at i:2574428 original size:149 final size:149
Alignment explanation
Indices: 2574083--2574464 Score: 427
Period size: 150 Copynumber: 2.6 Consensus size: 149
2574073 AGAAATATGC
* * * * * * *
2574083 CTTGATTGATAAAGAGTGTGTTTTCGAGGATTGTTCAAATAAAATAGTACTTTCATGTT-TATTC
1 CTTGACTGATAATGAGTGTGTTTTCAAGGATTGCTCATACAAAATAATACTTT--T-TTATATTC
* *
2574147 GAGTGATTTTT-AAATATATGAAACATATGTAATTTATTAAAATACAAGTCCATAATATTTGATG
63 GAGTGATTTTTGAAATATATTAAACATATGTAATTTATTAAAATACAAGGCCATAATATTTGATG
* * *
2574211 AGGGTAATCTATGAAAATATGA
128 AGGGGAATCTATGAAAACACGA
* * * * *
2574233 CTTGACTGACAATTATTGTGTTTTCCAGGATTGGC-CGTACAAAATAATATCTTTTTTATATTCG
1 CTTGACTGATAATGAGTGTGTTTTCAAGGATT-GCTCATACAAAATAATA-CTTTTTTATATTCG
* ** * * * *
2574297 TGTGATTTTTGAAATATATTAAATGTATGTAATTTATTTAAATATAAGGCGATGATATTTTG-TG
64 AGTGATTTTTGAAATATATTAAACATATGTAATTTATTAAAATACAAGGCCATAATA-TTTGATG
*
2574361 AGGGGAATTTATGAAAACACG-
128 AGGGGAATCTATGAAAACACGA
2574382 CTTGACTGATAATGAGTGTGTTTTCAAGGATTGCTCATACAAAATAATAGC-TTTTTATATTCGA
1 CTTGACTGATAATGAGTGTGTTTTCAAGGATTGCTCATACAAAATAATA-CTTTTTTATATTCGA
2574446 GTGATTTTTG-AATATATTA
65 GTGATTTTTGAAATATATTA
2574465 TATAGGAAAA
Statistics
Matches: 195, Mismatches: 31, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
147 9 0.05
148 26 0.13
149 58 0.30
150 93 0.48
151 9 0.05
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.40
Consensus pattern (149 bp):
CTTGACTGATAATGAGTGTGTTTTCAAGGATTGCTCATACAAAATAATACTTTTTTATATTCGAG
TGATTTTTGAAATATATTAAACATATGTAATTTATTAAAATACAAGGCCATAATATTTGATGAGG
GGAATCTATGAAAACACGA
Found at i:2576745 original size:13 final size:13
Alignment explanation
Indices: 2576727--2576752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2576717 CTGCGGGGGT
2576727 ATGATTATTCGTA
1 ATGATTATTCGTA
2576740 ATGATTATTCGTA
1 ATGATTATTCGTA
2576753 GCTATCGTGT
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:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATGATTATTCGTA
Found at i:2584574 original size:6 final size:6
Alignment explanation
Indices: 2584553--2584587 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
2584543 AGAAAGCACA
2584553 CTGAGT CTGAGCT CTGAGT CTGAGT CTGAGT CTGA
1 CTGAGT CTGAG-T CTGAGT CTGAGT CTGAGT CTGA
2584588 ATCATCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.31
Consensus pattern (6 bp):
CTGAGT
Found at i:2585099 original size:31 final size:29
Alignment explanation
Indices: 2585061--2585135 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 29
2585051 CTAACACATT
*
2585061 TTTTTGGTCAAAATAAATACCTAAAGTTATC
1 TTTTTGGTCAAAATAAATA-CTAAA-ATATC
* *
2585092 TTTTTGGTCAAAATAAGTACTAAAATATT
1 TTTTTGGTCAAAATAAATACTAAAATATC
2585121 TTTTTGGTCAAAATA
1 TTTTTGGTCAAAATA
2585136 GATGTCTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.44
30 5 0.12
31 18 0.44
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (29 bp):
TTTTTGGTCAAAATAAATACTAAAATATC
Found at i:2588074 original size:21 final size:23
Alignment explanation
Indices: 2588048--2588094 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2588038 ACATGATATA
* *
2588048 TACCCG-ACATGCTTT-TATTCC
1 TACCCGAACATGATTTATAATCC
2588069 TACCCGAACATGATTTATAATCC
1 TACCCGAACATGATTTATAATCC
2588092 TAC
1 TAC
2588095 ATGTTTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (23 bp):
TACCCGAACATGATTTATAATCC
Found at i:2588317 original size:14 final size:14
Alignment explanation
Indices: 2588298--2588329 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2588288 TGAACCTACC
2588298 AAACCCTCAATCCT
1 AAACCCTCAATCCT
*
2588312 AAACCCTCAATCTT
1 AAACCCTCAATCCT
2588326 AAAC
1 AAAC
2588330 TCAAGATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.22
Consensus pattern (14 bp):
AAACCCTCAATCCT
Found at i:2597989 original size:65 final size:64
Alignment explanation
Indices: 2597872--2598080 Score: 239
Period size: 65 Copynumber: 3.2 Consensus size: 64
2597862 TTTCAAAGTG
* * * * **
2597872 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CTAGCCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
2597935 TC
63 TC
*
2597937 ATGCATCGATGCACATA-CTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCAT
1 ATGCATCGATGCAC-TAGCCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCAT
*
2597999 TTG
62 TTC
*
2598002 ATGCATCGATGCACTAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
2598066 ATGCATCGATGCACT
1 ATGCATCGATGCACT
2598081 CTTAGTGCAG
Statistics
Matches: 127, Mismatches: 8, Indels: 19
0.82 0.05 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 52 0.41
65 68 0.54
66 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACTAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Done.