Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 24
Found at i:2642133 original size:22 final size:22
Alignment explanation
Indices: 2642107--2642169 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
2642097 GACATCCGTT
2642107 CCCATCTCTGACGAAATCAGTC
1 CCCATCTCTGACGAAATCAGTC
* *
2642129 CCCATCTCCGACGATATCAGTC
1 CCCATCTCTGACGAAATCAGTC
* *
2642151 TCCATCTCTGGCGAAATCA
1 CCCATCTCTGACGAAATCA
2642170 TTCACGGTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.37, G:0.14, T:0.24
Consensus pattern (22 bp):
CCCATCTCTGACGAAATCAGTC
Found at i:2642588 original size:20 final size:20
Alignment explanation
Indices: 2642535--2642590 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2642525 GATAGTTAAA
* **
2642535 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
2642555 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
2642575 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
2642591 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:2642597 original size:20 final size:20
Alignment explanation
Indices: 2642554--2642597 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2642544 CGATAGTCAT
* *
2642554 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
2642574 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
2642594 TTTC
1 TTTC
2642598 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:2644581 original size:19 final size:20
Alignment explanation
Indices: 2644554--2644611 Score: 91
Period size: 19 Copynumber: 3.0 Consensus size: 20
2644544 CGCAACACAC
2644554 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
2644574 GC-AAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
**
2644593 GCGAATTTGACTATCGCAA
1 GCGAAAATGACTATCGCAA
2644612 CGAAAGAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAT
Found at i:2644710 original size:20 final size:20
Alignment explanation
Indices: 2644657--2644721 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
2644647 CGATTCTCTT
** *
2644657 GTTGCGATAGTCAAATTAGC
1 GTTGCGATAGTCATTTTCGC
*
2644677 ATTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
2644697 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
2644717 GTTGC
1 GTTGC
2644722 AATTTTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:2645263 original size:42 final size:42
Alignment explanation
Indices: 2645204--2645296 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
2645194 GCCCGACTCA
** * *
2645204 CCTATCATCGTTCAAGAGGCCTCTC-CTATCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCATCTCTC-ACCGTTCAAGAGGCC
*
2645246 CCTATCATCCCTCAAGAGTCATCTCTCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCATCTCTCACCGTTCAAGAGGCC
* *
2645288 ACTGTCATC
1 CCTATCATC
2645297 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGGCATCTCTCACCGTTCAAGAGGCC
Found at i:2645299 original size:21 final size:20
Alignment explanation
Indices: 2645208--2645306 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
2645198 GACTCACCTA
*
2645208 TCATCGTTCAAGAGGCCTCT
1 TCATCGTTCAAGAGGCCACT
* *
2645228 CCTATCGTTCAAGAGGCCCCT
1 TC-ATCGTTCAAGAGGCCACT
** *
2645249 ATCATCCCTCAAGA-GTCATCT
1 -TCATCGTTCAAGAGGCCA-CT
*
2645270 CTCACCGTTCAAGAGGCCACT
1 -TCATCGTTCAAGAGGCCACT
*
2645291 GTCATCGTTGAAGAGG
1 -TCATCGTTCAAGAGG
2645307 TCCCTCCCAA
Statistics
Matches: 60, Mismatches: 15, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
20 3 0.05
21 53 0.88
22 4 0.07
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCACT
Found at i:2646715 original size:14 final size:14
Alignment explanation
Indices: 2646696--2646731 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2646686 ATTGTTTAAT
2646696 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2646710 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2646724 TGATTTGT
1 TGATTTGT
2646732 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:2646907 original size:20 final size:20
Alignment explanation
Indices: 2646870--2646923 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2646860 GCAACGAGAG
2646870 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
2646889 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
2646909 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
2646924 CTAAATTCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:2646972 original size:19 final size:20
Alignment explanation
Indices: 2646929--2646981 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2646919 CGAAACTAAA
*
2646929 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
2646949 TTCGCATTGCGATTTTCA-T
1 TTCGCATTGCGATTTTCATT
2646968 TTCGCATTGCGATT
1 TTCGCATTGCGATT
2646982 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:2647011 original size:20 final size:20
Alignment explanation
Indices: 2646986--2647060 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
2646976 GCGATTCTCT
2646986 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
2647006 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
* *
2647026 TGTTGCGATAGTCACATT-CA
1 CGTTGCGATAGTCA-ATTCCG
2647046 CGTTGCGATAGTCAA
1 CGTTGCGATAGTCAA
2647061 ATGAATGTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.02
20 46 0.94
21 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:2650395 original size:20 final size:20
Alignment explanation
Indices: 2650370--2650476 Score: 169
Period size: 20 Copynumber: 5.3 Consensus size: 20
2650360 AAATTCAGTA
*
2650370 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCTCG
2650390 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
2650410 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
2650430 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* * * *
2650450 TTACGATAGTTAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
2650470 TTGCGAT
1 TTGCGAT
2650477 TTACGTATTC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:2650486 original size:20 final size:20
Alignment explanation
Indices: 2650463--2650535 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
2650453 CGATAGTTAG
*
2650463 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2650483 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2650503 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2650523 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2650536 ATTAGGAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2650556 original size:21 final size:21
Alignment explanation
Indices: 2650532--2650577 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2650522 TATTCGCATT
*
2650532 GCGAATTAGGAAAGTCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
2650553 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2650574 GCGA
1 GCGA
2650578 TAGTCAGAAT
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:2659533 original size:13 final size:13
Alignment explanation
Indices: 2659517--2659551 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2659507 AAGTTGAAGC
2659517 AGTTAGTTGTTGA
1 AGTTAGTTGTTGA
*
2659530 AGTTTGTTGTTGA
1 AGTTAGTTGTTGA
2659543 AGATTAGTT
1 AG-TTAGTT
2659552 ACATCATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (13 bp):
AGTTAGTTGTTGA
Found at i:2662846 original size:14 final size:14
Alignment explanation
Indices: 2662827--2662853 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2662817 TGCTCTTGAA
2662827 CATGGCATGATGCG
1 CATGGCATGATGCG
2662841 CATGGCATGATGC
1 CATGGCATGATGC
2662854 CTTCAACAAA
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:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (14 bp):
CATGGCATGATGCG
Found at i:2677146 original size:4 final size:4
Alignment explanation
Indices: 2677137--2677350 Score: 320
Period size: 4 Copynumber: 53.5 Consensus size: 4
2677127 CTTTTTCCCC
* * * *
2677137 TATG TATG TATA TATG TATG TATG TATG TATG TATG TATA CATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
2677185 CATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2677233 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
2677281 TATG TATG TATG TATA TATG TATG TATG TATG TATG TATA TATA TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2677329 TATG TATA TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TA
2677351 CAACAATGAT
Statistics
Matches: 192, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 192 1.00
ACGTcount: A:0.29, C:0.01, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:2685328 original size:23 final size:23
Alignment explanation
Indices: 2685302--2685365 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
2685292 CAGCTCATAT
*
2685302 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
2685325 AATTGCACCGGAGTTCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
2685348 AATTGCATCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
2685366 TATAATAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:2685512 original size:103 final size:103
Alignment explanation
Indices: 2685381--2685598 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
2685371 TAATGTTCAT
*
2685381 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2685446 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCA
*
2685484 AAGGACCACATATCATTCCTTAAGAATCATATAGATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
2685549 GACCTCACACATGTTCCAAAGAATACATATATGTCCCA
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCA
2685587 AAGGACCACATA
1 AAGGACCACATA
2685599 GTCCATCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCA
Found at i:2686116 original size:18 final size:19
Alignment explanation
Indices: 2686079--2686115 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2686069 TTTTTTATTA
*
2686079 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
2686098 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2686116 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:2687446 original size:20 final size:20
Alignment explanation
Indices: 2687421--2687463 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2687411 TATAAGAGCC
*
2687421 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
2687441 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
2687461 CAT
1 CAT
2687464 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:2697687 original size:20 final size:20
Alignment explanation
Indices: 2697662--2697704 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2697652 TCTAAAAGCC
*
2697662 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
2697682 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
2697702 CAT
1 CAT
2697705 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:2703083 original size:31 final size:31
Alignment explanation
Indices: 2703045--2703229 Score: 300
Period size: 31 Copynumber: 6.0 Consensus size: 31
2703035 CCCGAAGGAC
* * *
2703045 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
2703076 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2703107 CAGTCCACATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2703138 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2703169 CAGTCCATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2703200 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
2703230 CCCTCGACCC
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
31 143 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2706761 original size:23 final size:22
Alignment explanation
Indices: 2706735--2706798 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
2706725 CAACTCATAT
2706735 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
2706758 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
*
2706781 AATTTCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
2706799 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:2706939 original size:103 final size:103
Alignment explanation
Indices: 2706814--2707031 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
2706804 TAATGTCCAT
*
2706814 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
2706879 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
2706917 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2706982 GACCTTACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
2707020 AAGGACCACATA
1 AAGGACCACATA
2707032 GACCCTCTAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2707551 original size:19 final size:20
Alignment explanation
Indices: 2707514--2707551 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2707504 TTTTTTATTA
*
2707514 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
2707534 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2707552 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:2709369 original size:12 final size:12
Alignment explanation
Indices: 2709349--2709383 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2709339 CGATTTCGCT
*
2709349 TGAACTTGATTC
1 TGAATTTGATTC
2709361 TGAATTTGATTC
1 TGAATTTGATTC
*
2709373 TGGATTTGATT
1 TGAATTTGATT
2709384 GTTATCTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.49
Consensus pattern (12 bp):
TGAATTTGATTC
Found at i:2719701 original size:50 final size:51
Alignment explanation
Indices: 2719621--2719761 Score: 198
Period size: 50 Copynumber: 2.8 Consensus size: 51
2719611 CTAAAAACCC
* *
2719621 TAACCTCCAAAAAAAT-AAAAATCCCAAAAATCATAACCCCATTGAAAATCA
1 TAACCTCCAAAAAAATCAAAAAT-CCAAAAATCATAACCCCATTAAAAATAA
* * *
2719672 TAAGCTCC-ACAAAATCAGAAATCCAAAAATCATAA-CCCATTAAAAATAA
1 TAACCTCCAAAAAAATCAAAAATCCAAAAATCATAACCCCATTAAAAATAA
*
2719721 TAACCTCCAAAAAAATCAAAAACCCAAAAATCATAACCCCA
1 TAACCTCCAAAAAAATCAAAAATCCAAAAATCATAACCCCA
2719762 CAAAATGATT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
49 19 0.24
50 43 0.55
51 16 0.21
ACGTcount: A:0.55, C:0.26, G:0.02, T:0.16
Consensus pattern (51 bp):
TAACCTCCAAAAAAATCAAAAATCCAAAAATCATAACCCCATTAAAAATAA
Found at i:2719765 original size:17 final size:17
Alignment explanation
Indices: 2719645--2719766 Score: 67
Period size: 17 Copynumber: 7.3 Consensus size: 17
2719635 ATAAAAATCC
2719645 CAAAAATCATAACCCCA
1 CAAAAATCATAACCCCA
** *
2719662 TTGAAAATCATAAGCTCCA
1 -CAAAAATCATAA-CCCCA
* **
2719681 C-AAAATCAGAA-ATC-
1 CAAAAATCATAACCCCA
2719695 CAAAAATCATAA-CCCA
1 CAAAAATCATAACCCCA
* *
2719711 TTAAAAATAATAACCTCCA
1 -CAAAAATCATAACC-CCA
* **
2719730 AAAAAATCA-AAAACC-
1 CAAAAATCATAACCCCA
2719745 CAAAAATCATAACCCCA
1 CAAAAATCATAACCCCA
2719762 CAAAA
1 CAAAA
2719767 TGATTCTCCA
Statistics
Matches: 77, Mismatches: 19, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
14 1 0.01
15 19 0.25
16 6 0.08
17 26 0.34
18 18 0.23
19 7 0.09
ACGTcount: A:0.56, C:0.26, G:0.02, T:0.16
Consensus pattern (17 bp):
CAAAAATCATAACCCCA
Found at i:2720470 original size:17 final size:17
Alignment explanation
Indices: 2720448--2720489 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2720438 TTTGGGTTTT
2720448 TGATTTTGTAAA-GGTTA
1 TGATTTT-TAAAGGGTTA
2720465 TGA-TTTTAAATGGGTTA
1 TGATTTTTAAA-GGGTTA
2720482 TGATTTTT
1 TGATTTTT
2720490 GCGTTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.18
16 3 0.14
17 11 0.50
18 4 0.18
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.52
Consensus pattern (17 bp):
TGATTTTTAAAGGGTTA
Found at i:2720545 original size:14 final size:14
Alignment explanation
Indices: 2720526--2720553 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2720516 ATTTTCAGTG
2720526 GAGTTATGATTTTT
1 GAGTTATGATTTTT
2720540 GAGTTATGATTTTT
1 GAGTTATGATTTTT
2720554 TTGGAGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (14 bp):
GAGTTATGATTTTT
Found at i:2720559 original size:50 final size:50
Alignment explanation
Indices: 2720427--2720563 Score: 170
Period size: 49 Copynumber: 2.8 Consensus size: 50
2720417 ATATTTTGTA
* ** *
2720427 GAGTTATGATTTTTGGGTTTTTGATTTTGTAAAGGTTATGATTTTAAATG
1 GAGTTATGATTTTTGAGTTTTTGATTTTGTGGAGGTTATAATTTTAAATG
* * *
2720477 G-GTTATGATTTTTGCGTTTTTGATTTTGTGGAGGTTATAATTTTCAGTG
1 GAGTTATGATTTTTGAGTTTTTGATTTTGTGGAGGTTATAATTTTAAATG
* *
2720526 GAGTTATGATTTTTGAG-TTATGATTTTTTTGGAGGTTA
1 GAGTTATGATTTTTGAGTTTTTGA-TTTTGTGGAGGTTA
2720564 GGGTTTTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
49 48 0.63
50 28 0.37
ACGTcount: A:0.20, C:0.01, G:0.26, T:0.53
Consensus pattern (50 bp):
GAGTTATGATTTTTGAGTTTTTGATTTTGTGGAGGTTATAATTTTAAATG
Found at i:2721758 original size:37 final size:37
Alignment explanation
Indices: 2721698--2721801 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 37
2721688 CCTTTTTGTC
* * **
2721698 TTACTAGGATTTAAATTTTTAAAAATAGGATAGAATT
1 TTACTAGGATTCAAACTCATAAAAATAGGATAGAATT
** * *
2721735 TTGTTAGGATTCAAACTCCTAAAAATAGAATAGAATT
1 TTACTAGGATTCAAACTCATAAAAATAGGATAGAATT
* * *
2721772 TTACTATGATTTAAACTCATAAAGATAGGA
1 TTACTAGGATTCAAACTCATAAAAATAGGA
2721802 GCCACAAGCA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (37 bp):
TTACTAGGATTCAAACTCATAAAAATAGGATAGAATT
Found at i:2722321 original size:20 final size:19
Alignment explanation
Indices: 2722294--2722341 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
2722284 TTATTATTAT
2722294 TATTTTACTTATATATATA
1 TATTTTACTTATATATATA
* * *
2722313 TACTTTTACTTTTTTTTATA
1 TA-TTTTACTTATATATATA
2722333 TATTTTACT
1 TATTTTACT
2722342 CATTTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTACTTATATATATA
Found at i:2722364 original size:39 final size:42
Alignment explanation
Indices: 2722264--2722365 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 42
2722254 AATACGTATA
* *
2722264 TTATTT-TTTATTTTCTTTTTTTATTATTATTATTTTACTTAT
1 TTATTTATCTATTTTC-TTTTTTATTATTATTATTTTACTCAT
* * *
2722306 ATATATATACT-TTTACTTTTTT-TTA-TA-TATTTTACTCAT
1 TTATTTAT-CTATTTTCTTTTTTATTATTATTATTTTACTCAT
2722345 TTATTTATCTATTTTCTTTTT
1 TTATTTATCTATTTTCTTTTT
2722366 ATCTTTATCC
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
38 2 0.04
39 26 0.53
40 2 0.04
41 3 0.06
42 10 0.20
43 5 0.10
44 1 0.02
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (42 bp):
TTATTTATCTATTTTCTTTTTTATTATTATTATTTTACTCAT
Found at i:2725573 original size:25 final size:24
Alignment explanation
Indices: 2725528--2725574 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
2725518 TCCAATCAAG
2725528 AACAAAAAAGAAAAGAAACAAATA
1 AACAAAAAAGAAAAGAAACAAATA
2725552 AACAAATAAA-AAAGAGAAACAAA
1 AACAAA-AAAGAAA-AGAAACAAA
2725575 AGAAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.79, C:0.09, G:0.09, T:0.04
Consensus pattern (24 bp):
AACAAAAAAGAAAAGAAACAAATA
Found at i:2725585 original size:16 final size:16
Alignment explanation
Indices: 2725525--2725586 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
2725515 AGATCCAATC
* *
2725525 AAGAACAAA-AAAGAA
1 AAGAAAAAAGAAACAA
*
2725540 AAGAAACAAATAAACAA
1 AAGAAA-AAAGAAACAA
2725557 ATA-AAAAAGAGAAACAA
1 A-AGAAAAA-AGAAACAA
2725574 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
2725587 GAACAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 5 0.13
16 11 0.28
17 22 0.56
18 1 0.03
ACGTcount: A:0.79, C:0.06, G:0.11, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAGAAACAA
Found at i:2725595 original size:20 final size:18
Alignment explanation
Indices: 2725532--2725608 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 18
2725522 ATCAAGAACA
* *
2725532 AAAAAGAAAAGAAACAA-
1 AAAAACAAAAGAAAAAAG
* *
2725549 ATAAAC-AAATAAAAAAG
1 AAAAACAAAAGAAAAAAG
*
2725566 AGAAACAAAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
2725584 AAAGAACAAAA-ATCAAAAAG
1 AAA-AACAAAAGA--AAAAAG
2725604 AAAAA
1 AAAAA
2725609 GGGACAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
16 8 0.17
17 9 0.19
18 13 0.27
19 9 0.19
20 9 0.19
ACGTcount: A:0.79, C:0.06, G:0.10, T:0.04
Consensus pattern (18 bp):
AAAAACAAAAGAAAAAAG
Found at i:2727297 original size:106 final size:106
Alignment explanation
Indices: 2727167--2728230 Score: 1698
Period size: 106 Copynumber: 10.0 Consensus size: 106
2727157 ATATCGTGCC
* * * * ** *
2727167 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGAAGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
2727232 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
2727273 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2727338 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
2727379 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
2727444 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2727485 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
2727550 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * **
2727591 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAATAAACAATTTCTT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2727656 AATTTCAAAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** *
2727697 ACTTAAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
2727762 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2727803 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2727868 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATGTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
2727909 ACTCCAGACAACACAAGTTCAACTTCATGATGAAGGGACCACTGGTTGTTAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2727974 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** *
2728015 ACTCAAGACAACAAAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2728080 AATTTCAGAGTCAATTTCGACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
2728121 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2728186 AATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
2728227 ACTC
1 ACTC
2728231 GGAACAATGC
Statistics
Matches: 886, Mismatches: 71, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
105 1 0.00
106 885 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2729048 original size:37 final size:37
Alignment explanation
Indices: 2728958--2729062 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
2728948 CCTTTTCGTC
2728958 CTACTAGGATTTAAACTCCTAAAAATAGGATGAAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATGAAATT
* * * *
2728995 TTGCTAGGATTCAAACTCCTAAAAATAGGAT-AGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATGA-AATT
* * *
2729032 CTACTATGATTTAAACTCATAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
2729063 CCACAAACAC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 1 0.02
37 56 0.98
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATGAAATT
Found at i:2729144 original size:21 final size:22
Alignment explanation
Indices: 2729115--2729158 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2729105 ACACGATTTA
*
2729115 CACACAAAACACAGAGG-AAAG
1 CACACAAAACACAAAGGCAAAG
* *
2729136 CACAGAAAATACAAAGGCAAAG
1 CACACAAAACACAAAGGCAAAG
2729158 C
1 C
2729159 TATTGTAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.23, G:0.18, T:0.02
Consensus pattern (22 bp):
CACACAAAACACAAAGGCAAAG
Found at i:2729583 original size:20 final size:20
Alignment explanation
Indices: 2729558--2729595 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2729548 ATTATTATTA
2729558 TTTTACTTATATATATATAC
1 TTTTACTTATATATATATAC
* *
2729578 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
2729596 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATAC
Found at i:2729624 original size:37 final size:35
Alignment explanation
Indices: 2729532--2729625 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 35
2729522 TATATTATTT
*
2729532 TTTATTT-TCTTTTT-TTATTATTATTATTTTACTTA
1 TTTATTTATCTTTTTCTT-TT-TTATTATTTTACTCA
* * *
2729567 TATATATATACTTTTACTTTTTTATATATTTTACTCA
1 TTTATTTAT-CTTTTTCTTTTTTAT-TATTTTACTCA
2729604 TTTATTTATCTATTTTCTTTTT
1 TTTATTTATCT-TTTTCTTTTT
2729626 ATCTTTATCA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
35 5 0.11
36 7 0.15
37 33 0.70
38 2 0.04
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (35 bp):
TTTATTTATCTTTTTCTTTTTTATTATTTTACTCA
Found at i:2731595 original size:23 final size:23
Alignment explanation
Indices: 2731528--2731597 Score: 95
Period size: 25 Copynumber: 2.9 Consensus size: 23
2731518 TGTAAAATTT
2731528 TAAATATATATTTTTGAATAATAA
1 TAAA-ATATATTTTTGAATAATAA
*
2731552 TAAAATATAACATTTTGAATAATAA
1 TAAAATAT-A-TTTTTGAATAATAA
*
2731577 TAAAATATATTTTTAAATAAT
1 TAAAATATATTTTTGAATAAT
2731598 TTGATATTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 14 0.34
24 6 0.15
25 21 0.51
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (23 bp):
TAAAATATATTTTTGAATAATAA
Found at i:2732906 original size:9 final size:9
Alignment explanation
Indices: 2732892--2732920 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2732882 CTCTAAAGAG
2732892 ACCACCTAT
1 ACCACCTAT
2732901 ACCACCTAT
1 ACCACCTAT
2732910 ACCACCTAT
1 ACCACCTAT
2732919 AC
1 AC
2732921 ATGCCCACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (9 bp):
ACCACCTAT
Found at i:2738575 original size:24 final size:24
Alignment explanation
Indices: 2738543--2738600 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
2738533 TTCTCTTTAT
2738543 TCTTCATCTATCTCTTTTCTCTCC
1 TCTTCATCTATCTCTTTTCTCTCC
*
2738567 TCTTCATCTATCTCTTTTCTCTCT
1 TCTTCATCTATCTCTTTTCTCTCC
*
2738591 TCTTCGTCTA
1 TCTTCATCTA
2738601 ATTTTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.09, C:0.34, G:0.02, T:0.55
Consensus pattern (24 bp):
TCTTCATCTATCTCTTTTCTCTCC
Found at i:2749398 original size:62 final size:62
Alignment explanation
Indices: 2749301--2749424 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
2749291 GTATAAAATG
2749301 ACGGATACAAATCATGTTCAGGGTGAACAAGTAGAGACGTGTCTACCTTGAAATCTGATTTT
1 ACGGATACAAATCATGTTCAGGGTGAACAAGTAGAGACGTGTCTACCTTGAAATCTGATTTT
2749363 ACGGATACAAATCATGTTCAGGGTGAACAAGTAGAGACGTGTCTACCTTGAAATCTGATTTT
1 ACGGATACAAATCATGTTCAGGGTGAACAAGTAGAGACGTGTCTACCTTGAAATCTGATTTT
2749425 TTTTATATTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (62 bp):
ACGGATACAAATCATGTTCAGGGTGAACAAGTAGAGACGTGTCTACCTTGAAATCTGATTTT
Found at i:2772242 original size:21 final size:21
Alignment explanation
Indices: 2772215--2772306 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 21
2772205 ATCGAAAAAT
*
2772215 GAAGCAGTGGAAGCAGAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* *
2772236 GCAGCAGCGGAAGCA-ACCAGA
1 GAAGCAGCGGAAGCAGA-GAGA
* * * * * *
2772257 GCAGTAGTGGAAGTAGAAAAA
1 GAAGCAGCGGAAGCAGAGAGA
* *
2772278 GAAGCAGCGGCAGCACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
2772299 GAAGCAGC
1 GAAGCAGC
2772307 ATATCAGTAG
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.37, T:0.04
Consensus pattern (21 bp):
GAAGCAGCGGAAGCAGAGAGA
Found at i:2772704 original size:43 final size:43
Alignment explanation
Indices: 2772621--2772762 Score: 146
Period size: 43 Copynumber: 3.3 Consensus size: 43
2772611 ATTATGTGTT
* * * *
2772621 ATTTAGCGACGTTTGTAA-AAAAAACGCCGCCATATGCCATAC
1 ATTTAGCGGCGTTTGTAACTAAAAACGCCGCAATATACCATAC
*
2772663 ATTTAGCGGCGTTTGTAACTACAAACGCCGCAATATACCATAC
1 ATTTAGCGGCGTTTGTAACTAAAAACGCCGCAATATACCATAC
* * * * *
2772706 ATTTAGCAGTGTTTGTATACTAGAAACGTCGCTATATACCGA-AC
1 ATTTAGCGGCGTTTGTA-ACTAAAAACGCCGCAATATACC-ATAC
*
2772750 -TTTAGCGGTGTTT
1 ATTTAGCGGCGTTT
2772763 ATATGAAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
42 17 0.20
43 47 0.55
44 21 0.24
45 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGTAACTAAAAACGCCGCAATATACCATAC
Found at i:2772979 original size:43 final size:43
Alignment explanation
Indices: 2772759--2772976 Score: 122
Period size: 43 Copynumber: 5.1 Consensus size: 43
2772749 CTTTAGCGGT
* * * * *
2772759 GTTTATATG-AAAATGCCGCTAAATATCAACACCTATTGCGGC
1 GTTTATAAGTAAAATGCCGCTAAATCTCAAAACCTACTGCGAC
* * * * * *
2772801 G-TTATAAATAAAAACGCCGCTAATTCTC-AACCCTTATTGCAAC
1 GTTTATAAGT-AAAATGCCGCTAAATCTCAAAACC-TACTGCGAC
* * * *
2772844 GTTT-T-CGATACAAATGCCGCTAAATCTGAAAACCTACTACGAA
1 GTTTATAAG-TA-AAATGCCGCTAAATCTCAAAACCTACTGCGAC
** * * * * * * *
2772887 GTTTATGGGAAAAACGCCGCAAAATATCAAAACCTTCTACGTC
1 GTTTATAAGTAAAATGCCGCTAAATCTCAAAACCTACTGCGAC
* * *
2772930 ATTTGTAAGTAAAATGCCGCTAAATCTCAATACCTACTGCGAC
1 GTTTATAAGTAAAATGCCGCTAAATCTCAAAACCTACTGCGAC
2772973 GTTT
1 GTTT
2772977 GTAGGGAAAA
Statistics
Matches: 126, Mismatches: 41, Indels: 17
0.68 0.22 0.09
Matches are distributed among these distances:
41 5 0.04
42 5 0.04
43 107 0.85
44 8 0.06
45 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (43 bp):
GTTTATAAGTAAAATGCCGCTAAATCTCAAAACCTACTGCGAC
Found at i:2773371 original size:52 final size:52
Alignment explanation
Indices: 2773283--2773402 Score: 161
Period size: 52 Copynumber: 2.3 Consensus size: 52
2773273 CTAAATATAC
* * ** *
2773283 TAATTCTTTTATTAAACCTACCAAATGATTGGTGTAATGATTATGTTTTTTTT
1 TAATT-TTTTATTAAAACTACCAAAAGATTAATGTAATGATTATATTTTTTTT
*
2773336 CTATTTTTTTATTAAAAC-ACCAAAAGATTAATGTAATGATTATATTTTTTTT
1 -TAATTTTTTATTAAAACTACCAAAAGATTAATGTAATGATTATATTTTTTTT
2773388 TAATTTTTTATTAAA
1 TAATTTTTTATTAAA
2773403 GCTTTTTATC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 14 0.24
52 30 0.51
53 11 0.19
54 4 0.07
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (52 bp):
TAATTTTTTATTAAAACTACCAAAAGATTAATGTAATGATTATATTTTTTTT
Found at i:2776725 original size:18 final size:19
Alignment explanation
Indices: 2776680--2776726 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 19
2776670 TTCATGCAAC
2776680 AAAATAAAAAAGA-TATAAT
1 AAAATAAAAAA-ATTATAAT
2776699 AAAAT---AAAATTAT-AT
1 AAAATAAAAAAATTATAAT
2776714 AAAATAAAAAAAT
1 AAAATAAAAAAAT
2776727 CAGACCCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
18 5 0.21
19 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAATAAAAAAATTATAAT
Found at i:2777032 original size:26 final size:26
Alignment explanation
Indices: 2776995--2777050 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
2776985 GACAGAAAAA
2776995 AATTGTTATTTCCAACATATTTGACT
1 AATTGTTATTTCCAACATATTTGACT
* *
2777021 AATTGTTGTTTCCAACATGTTTGACT
1 AATTGTTATTTCCAACATATTTGACT
2777047 AATT
1 AATT
2777051 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (26 bp):
AATTGTTATTTCCAACATATTTGACT
Found at i:2777205 original size:18 final size:18
Alignment explanation
Indices: 2777174--2777217 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2777164 ACCGGAAACA
2777174 TTATTATTTCTACCGATT
1 TTATTATTTCTACCGATT
* * *
2777192 TTATTTTTTTTACCGGTT
1 TTATTATTTCTACCGATT
*
2777210 TTGTTATT
1 TTATTATT
2777218 GTTGGGCACT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.09, T:0.64
Consensus pattern (18 bp):
TTATTATTTCTACCGATT
Found at i:2779735 original size:17 final size:16
Alignment explanation
Indices: 2779713--2779755 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
2779703 TTTAGGATAA
2779713 AAAAATAATATTATTAT
1 AAAAATAATATTATT-T
2779730 AAAAAT-ATAATTATTT
1 AAAAATAAT-ATTATTT
2779746 -AAAATAATAT
1 AAAAATAATAT
2779756 ATAAATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAATAATATTATTT
Found at i:2781118 original size:6 final size:6
Alignment explanation
Indices: 2781107--2781133 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2781097 TCCCGTCTCG
2781107 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
2781134 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2781255 original size:21 final size:21
Alignment explanation
Indices: 2781226--2781351 Score: 130
Period size: 21 Copynumber: 5.8 Consensus size: 21
2781216 ATTTTGGACT
2781226 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
2781247 ATCGTAACGTGAACTTCGACT--
1 ATCGCAAC--GAACTTGGAATAA
* *
2781268 ATCGCAACGAATTTGAAATAA
1 ATCGCAACGAACTTGGAATAA
2781289 ATCGCAATGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
2781312 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
2781333 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
2781352 CTATCGCAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
19 7 0.08
21 41 0.48
23 37 0.44
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:2781288 original size:42 final size:42
Alignment explanation
Indices: 2781219--2781360 Score: 203
Period size: 42 Copynumber: 3.3 Consensus size: 42
2781209 CGTTGCGATT
* * *
2781219 TTGGACTATCGCAACGAACTTGGAATAAATCGTAACGTGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
2781261 TTCGACTATCGCAACGAATTTGAAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
2781303 TTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
2781347 TTGGACTATCGCAA
1 TTGGACTATCGCAA
2781361 TGCGAATATG
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 48 0.55
44 39 0.45
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:2781321 original size:86 final size:84
Alignment explanation
Indices: 2781226--2781385 Score: 232
Period size: 86 Copynumber: 1.9 Consensus size: 84
2781216 ATTTTGGACT
* * *
2781226 ATCGCAACGAACTTGGAATAAATCGTAACGTGAACTTCGACTATCGCAA-CGAATTTGAAATAAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAGCGAATATG---TAAA
2781290 TCGCAATGCGAACTTGGAATAA
63 TCGCAATGCGAACTTGGAATAA
* *
2781312 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATC
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-GCGAATATGTAAATC
2781377 GCAATGCGA
65 GCAATGCGA
2781386 TAGTCGAAGT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
85 15 0.22
86 45 0.67
88 7 0.10
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (84 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAGCGAATATGTAAATCG
CAATGCGAACTTGGAATAA
Found at i:2781357 original size:21 final size:21
Alignment explanation
Indices: 2781226--2781366 Score: 103
Period size: 21 Copynumber: 6.6 Consensus size: 21
2781216 ATTTTGGACT
2781226 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* * * *
2781247 ATCGTAACGTGAACTTCGACT-
1 ATCGCAA-GCGAACTTGGAATA
* *
2781268 ATCGCAA-CGAATTTGAAATAA
1 ATCGCAAGCGAACTTGGAAT-A
2781289 ATCGCAATGCGAACTTGGAATAA
1 ATCGCAA-GCGAACTTGGAAT-A
*
2781312 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
*
2781333 ATCGCAACGCGAACTTGGACT-
1 ATCGCAA-GCGAACTTGGAATA
2781354 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
2781367 TATGTAAATC
Statistics
Matches: 96, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
19 7 0.07
21 51 0.53
23 38 0.40
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAAGCGAACTTGGAATA
Found at i:2785765 original size:15 final size:15
Alignment explanation
Indices: 2785741--2785775 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2785731 TTGCTTAATG
2785741 ATATCGATACCCCCA
1 ATATCGATACCCCCA
*
2785756 ATATCTATACCCCCA
1 ATATCGATACCCCCA
2785771 ATATC
1 ATATC
2785776 AATATTACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (15 bp):
ATATCGATACCCCCA
Found at i:2789444 original size:25 final size:25
Alignment explanation
Indices: 2789416--2789472 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
2789406 AGTAACTATT
2789416 TGTCAAAAGAACCCACTAGTGACAC
1 TGTCAAAAGAACCCACTAGTGACAC
*
2789441 TGTCAAAAGAACCCACTAGTGTCAC
1 TGTCAAAAGAACCCACTAGTGACAC
*
2789466 TGACAAA
1 TGTCAAA
2789473 TACACATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (25 bp):
TGTCAAAAGAACCCACTAGTGACAC
Found at i:2798866 original size:65 final size:63
Alignment explanation
Indices: 2798797--2798955 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
2798787 GAATAAATTG
* *
2798797 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATCGATGAACTTAGAG-T-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACA-ACCATGCATCGATGAACTCAG-GCTATTT-TG
2798860 AA
63 -A
* * * *
2798862 AACATCGAATGCATTTGATGCATCGATACACAGCCATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACAACCATGCATCGATGAACTCAGGCTATTTTGA
*
2798925 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
2798956 TAAGGGTCCA
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 31 0.37
64 20 0.24
65 33 0.39
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACCATGCATCGATGAACTCAGGCTATTTTGA
Found at i:2802949 original size:24 final size:24
Alignment explanation
Indices: 2802905--2802953 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2802895 GGTGGTTGAA
*
2802905 TTAATGGTTGTTTAAACTTTATTT
1 TTAATGGTTATTTAAACTTTATTT
*
2802929 TTAATGGTATATTT-AAGTTTATTT
1 TTAATGGT-TATTTAAACTTTATTT
2802953 T
1 T
2802954 AAGTTCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (24 bp):
TTAATGGTTATTTAAACTTTATTT
Found at i:2803460 original size:17 final size:16
Alignment explanation
Indices: 2803429--2803462 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2803419 CACGTGAGGA
2803429 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
2803445 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
2803462 T
1 T
2803463 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:2809823 original size:19 final size:21
Alignment explanation
Indices: 2809786--2809828 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2809776 TAACTTTTTC
2809786 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
2809806 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
2809826 TTT
1 TTT
2809829 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:2809834 original size:19 final size:20
Alignment explanation
Indices: 2809785--2809834 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2809775 TTAACTTTTT
*
2809785 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
2809805 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
2809824 CTTTTACCTTT
1 CTTTTACCTTT
2809835 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:2813147 original size:24 final size:24
Alignment explanation
Indices: 2813118--2813167 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2813108 TGATGGTTGA
*
2813118 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
2813142 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
2813166 TT
1 TT
2813168 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:2813671 original size:16 final size:15
Alignment explanation
Indices: 2813641--2813674 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2813631 CACGTGAGGA
2813641 TTATTTTCTTCTTAT
1 TTATTTTCTTCTTAT
*
2813656 TTATTTATCTTTTTAT
1 TTATTT-TCTTCTTAT
2813672 TTA
1 TTA
2813675 CTGTCTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTCTTCTTAT
Found at i:2816687 original size:21 final size:22
Alignment explanation
Indices: 2816658--2816716 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
2816648 TGCATCCCTT
2816658 TGAATGTGCATCGATACA-CCA
1 TGAATGTGCATCGATACAGCCA
* * * *
2816679 TGAAGGTGCACCGATGCATGCCT
1 TGAATGTGCATCGATACA-GCCA
2816702 TGAATGTGCATCGAT
1 TGAATGTGCATCGAT
2816717 GCACACTGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.50
23 15 0.50
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (22 bp):
TGAATGTGCATCGATACAGCCA
Found at i:2816710 original size:23 final size:22
Alignment explanation
Indices: 2816639--2816719 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
2816629 ACACTTAACA
2816639 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* * *
2816663 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
2816684 GTGCACCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
2816707 GTGCATCGATGCA
1 GTGCATCGATGCA
2816720 CACTGTCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 18 0.38
24 12 0.26
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:2819448 original size:65 final size:63
Alignment explanation
Indices: 2819331--2819538 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 63
2819321 TTTCAAAGTG
* * * ** *
2819331 ATGCACCGATGCACCAATCCATACATCGATGCAC-CATGGAATAAATTG-AACATCGAATGTATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
2819394 TC
62 TC
*
2819396 ATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATT
*
2819459 TG
62 TC
* * *
2819461 ATGCATCGATGCACCAGCCATGCATTGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
2819525 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2819539 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 48 0.39
65 65 0.53
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Found at i:2820886 original size:22 final size:23
Alignment explanation
Indices: 2820858--2820906 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2820848 TTAATTTATG
2820858 TTTGGGTGCTA-TTTATGTAAA-A
1 TTTGGGTGCTAGTTTA-GTAAATA
*
2820880 TTTGGGTGTTAGTTTAGTAAATA
1 TTTGGGTGCTAGTTTAGTAAATA
2820903 TTTG
1 TTTG
2820907 CAGAATGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (23 bp):
TTTGGGTGCTAGTTTAGTAAATA
Found at i:2823788 original size:57 final size:57
Alignment explanation
Indices: 2823562--2823790 Score: 332
Period size: 57 Copynumber: 4.0 Consensus size: 57
2823552 GTTGGAGGAA
* * **
2823562 GAATACTTGCAGGTTCCTCAGCTTTGTGCTGAGAGCCTTACTATTCGTGACGGGGAA
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* *
2823619 GAATACTTGTAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGATGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * * *
2823676 GAATACTTGTAGGTTCCTCGACTTTGTGCTGAGAGCCTTACTGTTTGTGATGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * * *
2823733 GATTACTTGCAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
2823790 G
1 G
2823791 TATGATTATG
Statistics
Matches: 156, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 156 1.00
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
Found at i:2824958 original size:25 final size:24
Alignment explanation
Indices: 2824891--2824959 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
2824881 TAATCTAATC
*
2824891 CTAAACCATTTAA-ACAAAAAATA
1 CTAAACCATTTAACATAAAAAATA
* * * *
2824914 CTAAACCACTTCACTCTAAAAAATT
1 CTAAACCATTTAAC-ATAAAAAATA
2824939 CTAAACCAATTTAACATAAAA
1 CTAAACC-ATTTAACATAAAA
2824960 CCCTAACCCT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 11 0.31
25 19 0.54
26 5 0.14
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.25
Consensus pattern (24 bp):
CTAAACCATTTAACATAAAAAATA
Found at i:2831615 original size:19 final size:19
Alignment explanation
Indices: 2831587--2831623 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2831577 GTTAAAAATT
*
2831587 TAATGGTAATATTGACATC
1 TAATGATAATATTGACATC
*
2831606 TAATGATAATGTTGACAT
1 TAATGATAATATTGACAT
2831624 GTATCATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (19 bp):
TAATGATAATATTGACATC
Found at i:2843121 original size:210 final size:211
Alignment explanation
Indices: 2842759--2843174 Score: 809
Period size: 210 Copynumber: 2.0 Consensus size: 211
2842749 TAAGTAATAC
2842759 ATATATATCTATATATATAACAATTTGTTATTGTGTAATTTTTTATATAAAAAATACAATACATA
1 ATATATATCTATATATATAACAATTTGTTATTGTGTAATTTTTTATATAAAAAATACAATACATA
2842824 TACATTTTTTTCATATAAGATATACATATATCACACATAATTTAGGGACTCGACTTAAACTTGAA
66 TACATTTTTTTCATATAAGATATACATATATCACACATAATTTAGGGACTCGACTTAAACTTGAA
2842889 AATTCATCCAGTAATTACTAATTTTTTTTGAGTTATTCGAGTTGTA-TTTAC-AATCGATTAGAA
131 AATTCATCCAGTAATTACTAA-TTTTTTTGAGTTATTCGAGTTGTATTTTACAAATCGATTAGAA
2842952 CTTAAATTTTTTAAGTA
195 CTTAAATTTTTTAAGTA
2842969 ATATATATCTATATATATAACAATTTGTTATTGTGTAATTTTTTATATAAAAAATACAATACATA
1 ATATATATCTATATATATAACAATTTGTTATTGTGTAATTTTTTATATAAAAAATACAATACATA
2843034 TACATTTTTTTCATATAAGATATACATATATCACACATAATTTAGGGACTCGACTTAAACTTGAA
66 TACATTTTTTTCATATAAGATATACATATATCACACATAATTTAGGGACTCGACTTAAACTTGAA
2843099 AATTCATCCAGTAATTACTAATTTTTTTGAGTTATTCGAGTTGTATTTTACAAATCGATTAGAAC
131 AATTCATCCAGTAATTACTAATTTTTTTGAGTTATTCGAGTTGTATTTTACAAATCGATTAGAAC
2843164 TTAAATTTTTT
196 TTAAATTTTTT
2843175 TCGAGTCGAG
Statistics
Matches: 204, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
209 24 0.12
210 156 0.76
211 24 0.12
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (211 bp):
ATATATATCTATATATATAACAATTTGTTATTGTGTAATTTTTTATATAAAAAATACAATACATA
TACATTTTTTTCATATAAGATATACATATATCACACATAATTTAGGGACTCGACTTAAACTTGAA
AATTCATCCAGTAATTACTAATTTTTTTGAGTTATTCGAGTTGTATTTTACAAATCGATTAGAAC
TTAAATTTTTTAAGTA
Found at i:2843504 original size:41 final size:41
Alignment explanation
Indices: 2843425--2843504 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
2843415 TCAAGCCTTC
*
2843425 GGTATGGATATCCAATACTCGGTATGGAAACCATTTTATTT
1 GGTATGGATATCCAATACTCGGTATGGAAACCAGTTTATTT
* * * *
2843466 GGTATGGATA-CCAGTCCTCCGGTATGTATACCAGTTTAT
1 GGTATGGATATCCAATACT-CGGTATGGAAACCAGTTTAT
2843505 CCTGGATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 6 0.18
41 27 0.82
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (41 bp):
GGTATGGATATCCAATACTCGGTATGGAAACCAGTTTATTT
Found at i:2849499 original size:83 final size:82
Alignment explanation
Indices: 2849398--2849694 Score: 260
Period size: 83 Copynumber: 3.6 Consensus size: 82
2849388 ATACTTGAGC
* * * * * *
2849398 GGCGTTTTTTAAACAAACGCCGTAATATAGTGGTAATTTAGCGGTGTTTATAACTCCAACGCCGT
1 GGCGTTTGTTCAACAAACGCCGTAATATAGTAGTAATTTAGCGGCGTTTATAA-TCAAACGTCGT
2849463 AATAGAGTTGTTTATAGT
65 AATAGAGTTGTTTATAGT
* * * * * * * *
2849481 GGCATTTTTTCAACAAACGTCGTAATAGATTGGTAATTTAGCGGTGTTT-TTATACAAACGTCGT
1 GGCGTTTGTTCAACAAACGCCGTAATATAGTAGTAATTTAGCGGCGTTTATAAT-CAAACGTCGT
*
2849545 GATA-ATGTTGTTTATAGT
65 AATAGA-GTTGTTTATAGT
* * ** * *
2849563 GTCGTTTGTTCAACAAATGATGCT-AT-TGAGAAGTAATTTAGCGGCGTTTATCAAACAAACGTC
1 GGCGTTTGTTCAACAAACGCCG-TAATAT-AGTAGTAATTTAGCGGCGTTTAT-AATCAAACGTC
* *
2849626 GTAAAAGGGTTGTTTATAGT
63 GTAATAGAGTTGTTTATAGT
* * * * *
2849646 GGCGTTTGTGCAAAAAACGCCGCAATAAAGTAATAATTTAGCGGCGTTT
1 GGCGTTTGTTCAACAAACGCCGTAATATAGTAGTAATTTAGCGGCGTTT
2849695 GTCCCACAAA
Statistics
Matches: 170, Mismatches: 35, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
81 2 0.01
82 60 0.35
83 107 0.63
84 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (82 bp):
GGCGTTTGTTCAACAAACGCCGTAATATAGTAGTAATTTAGCGGCGTTTATAATCAAACGTCGTA
ATAGAGTTGTTTATAGT
Found at i:2849544 original size:41 final size:40
Alignment explanation
Indices: 2849403--2849540 Score: 113
Period size: 41 Copynumber: 3.3 Consensus size: 40
2849393 TGAGCGGCGT
* *
2849403 TTTTTAAACAAACGCCGTAATATAGTGGTAATTTAGCGGTG
1 TTTTT-AACAAACGCCGTAATAGATTGGTAATTTAGCGGTG
* * *
2849444 TTTATAACTCCAACGCCGTAATAGAGTT-GT--TTATAGTGGCAT-
1 TTTTTAA--CAAACGCCGTAATAGA-TTGGTAATT-TAGCGG--TG
*
2849486 TTTTTCAACAAACGTCGTAATAGATTGGTAATTTAGCGGTG
1 TTTTT-AACAAACGCCGTAATAGATTGGTAATTTAGCGGTG
2849527 TTTTTATACAAACG
1 TTTTTA-ACAAACG
2849541 TCGTGATAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
40 8 0.11
41 37 0.49
42 25 0.33
43 6 0.08
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (40 bp):
TTTTTAACAAACGCCGTAATAGATTGGTAATTTAGCGGTG
Found at i:2849872 original size:19 final size:19
Alignment explanation
Indices: 2849848--2849886 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2849838 TAGTCTTGTA
2849848 CTTATCTGGCGTTTGTGAT
1 CTTATCTGGCGTTTGTGAT
2849867 CTTATCTGGCGTTTGTGAT
1 CTTATCTGGCGTTTGTGAT
2849886 C
1 C
2849887 AAACGTCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (19 bp):
CTTATCTGGCGTTTGTGAT
Found at i:2850046 original size:42 final size:42
Alignment explanation
Indices: 2849965--2850046 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 42
2849955 GGCGTTTCTT
** * * *
2849965 TAATAAACGCCGCAGTAGTTTTGTCCTTTATGGGTGTTTTTG
1 TAATAAACGCCGCAAAAGTTTGGTCCCTTATGGGAGTTTTTG
*
2850007 TAATAAACTCCGCAAAAGTTTGGTCCCTTA-GTGGAGTTTT
1 TAATAAACGCCGCAAAAGTTTGGTCCCTTATG-GGAGTTTT
2850047 AATATAAACG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
41 1 0.03
42 32 0.97
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (42 bp):
TAATAAACGCCGCAAAAGTTTGGTCCCTTATGGGAGTTTTTG
Found at i:2853497 original size:21 final size:23
Alignment explanation
Indices: 2853457--2853504 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
2853447 TGATGATTAT
*
2853457 TTTTTAATATATATATATTTAAA
1 TTTTTAATATATATACATTTAAA
*
2853480 TTTTT-ATAT-TATACATTTATA
1 TTTTTAATATATATACATTTAAA
2853501 TTTT
1 TTTT
2853505 ATGTGTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 4 0.17
23 5 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTAATATATATACATTTAAA
Found at i:2859833 original size:42 final size:42
Alignment explanation
Indices: 2859784--2859949 Score: 190
Period size: 42 Copynumber: 3.9 Consensus size: 42
2859774 GTTTTTAGCA
2859784 AAAACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTAGG
1 AAAACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTAGG
* * * *
2859826 AAAACGCCACAAAACATCAACACCTACTGCTGCGTTTATGGG
1 AAAACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTAGG
** * *
2859868 AAAACGCTGCAAAACATCAACACCTACTGCGGCATTT-TAGAG
1 AAAACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTAG-G
* * * * *
2859910 AAAAACGCCGCTAAACATCATAACCTATTGCGACGTTTGT
1 -AAAACGCCACAAAACATCAAAACCTACTGCGGCGTTTGT
2859950 CTAAAAAACG
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
41 2 0.02
42 72 0.69
43 30 0.29
44 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (42 bp):
AAAACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTAGG
Found at i:2859929 original size:43 final size:43
Alignment explanation
Indices: 2859783--2860077 Score: 226
Period size: 43 Copynumber: 6.9 Consensus size: 43
2859773 CGTTTTTAGC
* * * *
2859783 AAAAACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTAG-G
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTT-TAGAG
* * * *
2859826 -AAAACGCCACAAAACATCAACACCTACTGCTGCG-TTTATG-G
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTTA-GAG
* * * * *
2859867 GAAAACGCTGCAAAACATCAACACCTACTGCGGCATTTTAGAG
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTTAGAG
* **
2859910 AAAAACGCCGCTAAACATCATA-ACCTATTGCGACGTTTGTCTA-
1 AAAAACGCCGCTAAACATCA-ACACCTATTGCGGCGTTT-TAGAG
* * ***
2859953 AAAAACGCCGCTAAATATCAACACCTATTGCGGTGTTTTTCTG
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTTAGAG
* * * * * *
2859996 ACAAACGCCGCTAAATATCAATACCTATTGCGGCATTTGT-CAC
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTT-TAGAG
* * *
2860039 ACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTTT
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTT
2860078 TTGTTAAAAA
Statistics
Matches: 216, Mismatches: 27, Indels: 19
0.82 0.10 0.07
Matches are distributed among these distances:
40 2 0.01
41 4 0.02
42 66 0.31
43 140 0.65
44 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTTAGAG
Found at i:2860002 original size:86 final size:86
Alignment explanation
Indices: 2859868--2860078 Score: 255
Period size: 86 Copynumber: 2.5 Consensus size: 86
2859858 CGTTTATGGG
* * * * * *** *
2859868 AAAACGCTGCAAAACATCAACACCTACTGCGGCATTTTAGAGAAAAACGCCGCTAAACATC-ATA
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCTGACAAACGCCGCTAAACATCAAT-
*
2859932 ACCTATTGCGACGTTTGTCTA-A
65 ACCTATTGCGACATTTGTC-ACA
* *
2859954 AAAACGCCGCTAAATATCAACACCTATTGCGGTGTTTTTCTGACAAACGCCGCTAAATATCAATA
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCTGACAAACGCCGCTAAACATCAATA
*
2860019 CCTATTGCGGCATTTGTCACA
66 CCTATTGCGACATTTGTCACA
* *
2860040 CAAACGCCGCTAAATATCAATACCTATTGCGGCGTTTTT
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT
2860079 TGTTAAAAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 1 0.01
86 104 0.97
87 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (86 bp):
AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCTGACAAACGCCGCTAAACATCAATA
CCTATTGCGACATTTGTCACA
Found at i:2864833 original size:23 final size:23
Alignment explanation
Indices: 2864807--2864866 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2864797 ATCAAGCACA
*
2864807 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
2864830 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
2864853 ATAATAAAATAGGT
1 ATAACATAATAGGT
2864867 TAATTACTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2864928 original size:158 final size:158
Alignment explanation
Indices: 2864631--2864937 Score: 528
Period size: 158 Copynumber: 1.9 Consensus size: 158
2864621 CATTTAACCG
* * *
2864631 GAAATATTATCAAGTTAAATAACATTTTAGGTAGCACTTATATAACGTAATAGATAGCGCTTATA
1 GAAACATTATCAAGTCAAATAACATATTAGGTAGCACTTATATAACGTAATAGATAGCGCTTATA
2864696 TAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTAC
66 TAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTAC
*
2864761 TAATGATAACATAACCGGTTAATTACTA
131 CAATGATAACATAACCGGTTAATTACTA
* *
2864789 GAAACATTATCAAG-CACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTAT
1 GAAACATTATCAAGTCA-AATAACATATTAGGTAGCACTTATATAACGTAATAGATAGCGCTTAT
2864853 ATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTA
65 ATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTA
2864918 CCAA-GAATAACATAACCGGT
130 CCAATG-ATAACATAACCGGT
2864938 AGCGCTTTAC
Statistics
Matches: 141, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
157 2 0.01
158 139 0.99
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (158 bp):
GAAACATTATCAAGTCAAATAACATATTAGGTAGCACTTATATAACGTAATAGATAGCGCTTATA
TAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTAC
CAATGATAACATAACCGGTTAATTACTA
Found at i:2870774 original size:47 final size:47
Alignment explanation
Indices: 2870685--2870774 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
2870675 TGGGGGGAAA
* ** * * *
2870685 TCTTATTTTTAATTATTTAAGTAGTGAGAGATTTGAAGAAAAAAATT
1 TCTTATTTTCAATTATTTAAGTAAAGAGAAATTAGAAAAAAAAAATT
2870732 TCTTATTTTCAATTATTTAAGTAAAGAGAAATTAGAAAAAAAA
1 TCTTATTTTCAATTATTTAAGTAAAGAGAAATTAGAAAAAAAA
2870775 TTATTCACGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (47 bp):
TCTTATTTTCAATTATTTAAGTAAAGAGAAATTAGAAAAAAAAAATT
Found at i:2871066 original size:33 final size:31
Alignment explanation
Indices: 2870953--2871066 Score: 88
Period size: 33 Copynumber: 3.4 Consensus size: 31
2870943 TTTTGATTAA
* *
2870953 AAAATGAAAAACGTGATAAAAGATGTCAACAAG
1 AAAATGAAAAACATGAT-AAAGATATCAA-AAG
* *
2870986 AAAATGGAAAAAAAAACTAGA-AAACGA-ATCAAAAA
1 AAAAT-G--AAAAACA-T-GATAAA-GATATCAAAAG
2871021 AAAATGAAAAACATGATAATAGATATCAAGAAG
1 AAAATGAAAAACATGATAA-AGATATCAA-AAG
2871054 AAAATGAAAAACA
1 AAAATGAAAAACA
2871067 ACTATTATCA
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
30 2 0.03
31 5 0.08
32 12 0.18
33 20 0.31
34 2 0.03
35 7 0.11
36 12 0.18
37 3 0.05
38 2 0.03
ACGTcount: A:0.65, C:0.08, G:0.14, T:0.13
Consensus pattern (31 bp):
AAAATGAAAAACATGATAAAGATATCAAAAG
Found at i:2873302 original size:64 final size:64
Alignment explanation
Indices: 2873223--2873362 Score: 192
Period size: 64 Copynumber: 2.2 Consensus size: 64
2873213 CGGATCTTGG
* * *
2873223 CAGGTCGGGTAAAATCGAGTACAGGTCA-ACTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
1 CAGGTCAGGTCAAATC-AGTACAGGTCATACTCAGATTGATTTGACACCAGATCCAGATCGGGTT
* * * **
2873287 CAGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGATTGATTTGACACCAGATCCAGATCGGGTT
1 CAGGTCAGGTCAAATCAGTACAGGTCATACTCAGATTGATTTGACACCAGATCCAGATCGGGTT
2873351 CAGGTCAGGTCA
1 CAGGTCAGGTCA
2873363 TTTTTAGTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 8 0.12
64 59 0.88
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (64 bp):
CAGGTCAGGTCAAATCAGTACAGGTCATACTCAGATTGATTTGACACCAGATCCAGATCGGGTT
Found at i:2874065 original size:19 final size:18
Alignment explanation
Indices: 2874033--2874083 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
2874023 AAAAAATATA
2874033 ATATATATAA-TATAAGTTT
1 ATATATA-AACTATAA-TTT
2874052 ATATATAAACTAT-ATTT
1 ATATATAAACTATAATTT
*
2874069 ATATTAGAAACTATA
1 ATA-TATAAACTATA
2874084 TAATTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 10 0.36
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (18 bp):
ATATATAAACTATAATTT
Found at i:2874069 original size:17 final size:18
Alignment explanation
Indices: 2874049--2874084 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2874039 ATAATATAAG
*
2874049 TTTATA-TATAAACTATA
1 TTTATATTAGAAACTATA
2874066 TTTATATTAGAAACTATA
1 TTTATATTAGAAACTATA
2874084 T
1 T
2874085 AATTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTATATTAGAAACTATA
Found at i:2874103 original size:2 final size:2
Alignment explanation
Indices: 2874098--2874204 Score: 53
Period size: 2 Copynumber: 53.5 Consensus size: 2
2874088 TATTATAAGT
* * *
2874098 TA TA TA TA TA TA T- TA TG TT TA TA TGA -A CTA TA TA TA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA -TA
* * * * *
2874141 TA TA TG TA AA CTA TA TA TG TA TA AA CTA TA -A TT TA TA T- TA -A
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
*
2874182 TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2874205 TATTCAAAGT
Statistics
Matches: 78, Mismatches: 17, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
1 5 0.06
2 68 0.87
3 5 0.06
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2874113 original size:13 final size:13
Alignment explanation
Indices: 2874097--2874207 Score: 55
Period size: 13 Copynumber: 8.3 Consensus size: 13
2874087 TTATTATAAG
2874097 TTATATATATATA
1 TTATATATATATA
* *
2874110 TTATGTTTATATGAA
1 TTATATATATAT--A
* *
2874125 CTATATATATAAA
1 TTATATATATATA
* * *
2874138 CTATATATGTAAA
1 TTATATATATATA
* *
2874151 CTATATATGTATA
1 TTATATATATATA
* *
2874164 -AACTATAATTTATA
1 TTA-TAT-ATATATA
2874178 TTA-ATATATATA
1 TTATATATATATA
*
2874190 TATATATACATATA
1 T-TATATATATATA
2874204 TTAT
1 TTAT
2874208 TCAAAGTGAG
Statistics
Matches: 78, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
12 8 0.10
13 45 0.58
14 15 0.19
15 10 0.13
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (13 bp):
TTATATATATATA
Found at i:2874184 original size:28 final size:29
Alignment explanation
Indices: 2874068--2874191 Score: 89
Period size: 28 Copynumber: 4.3 Consensus size: 29
2874058 AAACTATATT
* *
2874068 TATAT-TAGAAACTATATAATTAT-TATAA
1 TATATATATAAACTATATATTTATAT-TAA
* * *
2874096 GT-TATATATATA-TATTATGTTTATATGAA
1 -TATATATATAAACTA-TATATTTATATTAA
* * *
2874125 CTATATATATAAACTATATATGTAAACT-A
1 -TATATATATAAACTATATATTTATATTAA
*
2874154 TATATGTATAAACTATA-ATTTATATTAA
1 TATATATATAAACTATATATTTATATTAA
2874182 TATATATATA
1 TATATATATA
2874192 TATATACATA
Statistics
Matches: 72, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
27 6 0.08
28 31 0.43
29 16 0.22
30 17 0.24
31 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATATATAAACTATATATTTATATTAA
Found at i:2874308 original size:20 final size:19
Alignment explanation
Indices: 2874266--2874344 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
2874256 GTGAAAATTT
* *
2874266 TTTATAGGGAAATTGATAA
1 TTTAGAGGGAAATTGAAAA
2874285 TTTAGAGGGAAATTGAGAAA
1 TTTAGAGGGAAATTGA-AAA
*
2874305 TTTAGAGGG-AATAGAAAA
1 TTTAGAGGGAAATTGAAAA
* * *
2874323 TTTTGGAAGGAAATTGATAA
1 -TTTAGAGGGAAATTGAAAA
2874343 TT
1 TT
2874345 AGATTTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
18 3 0.06
19 29 0.58
20 18 0.36
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.32
Consensus pattern (19 bp):
TTTAGAGGGAAATTGAAAA
Found at i:2874537 original size:2 final size:2
Alignment explanation
Indices: 2874530--2874658 Score: 62
Period size: 2 Copynumber: 67.0 Consensus size: 2
2874520 TTTAATTTTC
* * * * *
2874530 TA TA TA TA TA TG TA TA TA AA CTA TA TA -A AA TA TA GTT TA TA AA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* *
2874573 T- TA T- TA -A TA TA GTA TA TA TA TG TA TG TA TA -A CTA -A TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
2874612 -A GTA -A TC TA TA GA T- 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
2874652 TA T- TA TA
1 TA TA TA TA
2874659 GAAATATTAT
Statistics
Matches: 95, Mismatches: 17, Indels: 30
0.67 0.12 0.21
Matches are distributed among these distances:
1 10 0.11
2 79 0.83
3 6 0.06
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2874646 original size:57 final size:52
Alignment explanation
Indices: 2874530--2874658 Score: 129
Period size: 57 Copynumber: 2.4 Consensus size: 52
2874520 TTTAATTTTC
*
2874530 TATATATATATGTA-TATAAACTATATAAAATATAGTTTATAAATTATTAATA
1 TATATATATATGTATTAT-AACTATATAAAATATAGATTATAAATTATTAATA
*
2874582 TAGTATATATATGTATGTATAACTAATATAAGTAATCTATAGATTATATA-TA-TATATA
1 TA-TATATATATGTAT-TATAACT-ATATAA--AA--TATAGATTATAAATTATTA-ATA
*
2874640 TATATATATATATATTATA
1 TATATATATATGTATTATA
2874659 GAAATATTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
52 2 0.03
53 12 0.18
54 4 0.06
55 9 0.14
56 4 0.06
57 16 0.25
58 7 0.11
59 11 0.17
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (52 bp):
TATATATATATGTATTATAACTATATAAAATATAGATTATAAATTATTAATA
Found at i:2874648 original size:59 final size:52
Alignment explanation
Indices: 2874530--2874658 Score: 134
Period size: 53 Copynumber: 2.3 Consensus size: 52
2874520 TTTAATTTTC
*
2874530 TATATATATATGTATATAAACTATATAAAATATAGTTTATAAATTATTAATA
1 TATATATATATGTATATAAACTATATAAAATATAGATTATAAATTATTAATA
* *
2874582 TAGTATATATATGTATGTATAACTAATATAAGTAATCTATAGATTATATATATATATATATA
1 TA-TATATATATGTATATA-AACT-ATATAA--AA--TATAGATTATAAAT-TAT-TA-ATA
2874644 TATATATATAT-TATA
1 TATATATATATGTATA
2874659 GAAATATTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
52 2 0.03
53 15 0.24
54 4 0.06
55 6 0.10
57 2 0.03
59 12 0.19
60 6 0.10
61 11 0.17
62 5 0.08
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (52 bp):
TATATATATATGTATATAAACTATATAAAATATAGATTATAAATTATTAATA
Found at i:2874718 original size:7 final size:7
Alignment explanation
Indices: 2874708--2874774 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
2874698 TAGTTTATAA
2874708 AAACCCT
1 AAACCCT
*
2874715 AAACTCT
1 AAACCCT
2874722 AAACCCT
1 AAACCCT
*
2874729 AAACTCT
1 AAACCCT
***
2874736 AAATTGT
1 AAACCCT
*
2874743 GAACCCT
1 AAACCCT
*
2874750 AAACCTT
1 AAACCCT
*
2874757 TAACCCT
1 AAACCCT
*
2874764 AACCCCT
1 AAACCCT
2874771 AAAC
1 AAAC
2874775 TATATATGTA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.40, C:0.34, G:0.03, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:2874727 original size:14 final size:14
Alignment explanation
Indices: 2874708--2874738 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2874698 TAGTTTATAA
2874708 AAACCCTAAACTCT
1 AAACCCTAAACTCT
2874722 AAACCCTAAACTCT
1 AAACCCTAAACTCT
2874736 AAA
1 AAA
2874739 TTGTGAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACCCTAAACTCT
Found at i:2875154 original size:22 final size:23
Alignment explanation
Indices: 2875128--2875172 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
2875118 TTTCTTTATA
2875128 TAAATTAAACTATA-TAATTTTC
1 TAAATTAAACTATATTAATTTTC
2875150 TAAATTAAACTATATTAATTTTC
1 TAAATTAAACTATATTAATTTTC
2875173 CTTTGCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTAAACTATATTAATTTTC
Found at i:2875291 original size:31 final size:31
Alignment explanation
Indices: 2875253--2875312 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2875243 AATTATCATA
2875253 ATATTTTTATT-ATAAAATTTAAAAAGTAATC
1 ATATTTTT-TTAATAAAATTTAAAAAGTAATC
* *
2875284 ATATTTTTTTAATTACATTTAAAAAGTAA
1 ATATTTTTTTAATAAAATTTAAAAAGTAA
2875313 ATAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATTTTTTTAATAAAATTTAAAAAGTAATC
Found at i:2876180 original size:158 final size:162
Alignment explanation
Indices: 2876005--2876328 Score: 575
Period size: 158 Copynumber: 2.0 Consensus size: 162
2875995 ATATAAACTA
2876005 TATATATATATATATAAAGTATATAAAGTATATTACTTATATAGTTTATAGAAACCCTAAATC-A
1 TATATATATATATATAAAGTATATAAAGTATATTACTTATATAGTTTATAGAAACCCTAAATCAA
2876069 ACCCTAAATCATAAACTTTAAACCATAAA-A-AAACCACAAACCCTAATGTAAATGGCTAGCAC-
66 ACCCTAAATCATAAACTTTAAACCATAAACACAAACCACAAACCCTAATGTAAATGGCTAGCACA
2876131 TGCATATATATTTGTAATAAAAGAGTGAGTTC
131 TGCATATATATTTGTAATAAAAGAGTGAGTTC
2876163 TATATATATATATATAAAGTATATAAAGTATATTACTTATATAGTTTATAGAAACCCTAAATCAT
1 TATATATATATATATAAAGTATATAAAGTATATTACTTATATAGTTTATAGAAACCCTAAATC--
2876228 AAACCCTAAATCATAAACTTTAAACCATAAACACTAAACCACAAACCCTAATGTAAATGGCTAGC
64 AAACCCTAAATCATAAACTTTAAACCATAAACAC-AAACCACAAACCCTAATGTAAATGGCTAGC
2876293 ACTAATGCATATATATTTGTAATAAAAGAGTGAGTT
128 AC--ATGCATATATATTTGTAATAAAAGAGTGAGTT
2876329 TATGTATTGG
Statistics
Matches: 157, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
158 63 0.40
161 30 0.19
162 1 0.01
164 32 0.20
167 31 0.20
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.31
Consensus pattern (162 bp):
TATATATATATATATAAAGTATATAAAGTATATTACTTATATAGTTTATAGAAACCCTAAATCAA
ACCCTAAATCATAAACTTTAAACCATAAACACAAACCACAAACCCTAATGTAAATGGCTAGCACA
TGCATATATATTTGTAATAAAAGAGTGAGTTC
Found at i:2876233 original size:14 final size:14
Alignment explanation
Indices: 2876214--2876278 Score: 76
Period size: 14 Copynumber: 4.6 Consensus size: 14
2876204 TAGTTTATAG
*
2876214 AAACCCTAAATCAT
1 AAACCCTAAACCAT
*
2876228 AAACCCTAAATCAT
1 AAACCCTAAACCAT
**
2876242 AAACTTTAAACCAT
1 AAACCCTAAACCAT
* *
2876256 AAACACTAAACCAC
1 AAACCCTAAACCAT
2876270 AAACCCTAA
1 AAACCCTAA
2876279 TGTAAATGGC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:2876251 original size:21 final size:21
Alignment explanation
Indices: 2876227--2876266 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2876217 CCCTAAATCA
*
2876227 TAAACCCTAAATCA-TAAACTT
1 TAAACCATAAA-CACTAAACTT
2876248 TAAACCATAAACACTAAAC
1 TAAACCATAAACACTAAAC
2876267 CACAAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCATAAACACTAAACTT
Found at i:2876481 original size:20 final size:19
Alignment explanation
Indices: 2876452--2876489 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2876442 GTGAATTAAC
*
2876452 CTAACATGCAACTAAAATA
1 CTAACATGCAAATAAAATA
2876471 CTAATCATGCAAATAAAAT
1 CTAA-CATGCAAATAAAAT
2876490 TAATATGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (19 bp):
CTAACATGCAAATAAAATA
Found at i:2876619 original size:13 final size:13
Alignment explanation
Indices: 2876587--2876613 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2876577 TAATTTACAT
2876587 TTAAATAATTTTA
1 TTAAATAATTTTA
2876600 TTAAATAATTTTA
1 TTAAATAATTTTA
2876613 T
1 T
2876614 ATAATATGTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:2876649 original size:20 final size:21
Alignment explanation
Indices: 2876612--2876671 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
2876602 AAATAATTTT
*
2876612 ATATAATATGTATGTATAAACC
1 ATAT-ATATGTATATATAAACC
* *
2876634 ATGTATA-GTATATATAAACT
1 ATATATATGTATATATAAACC
2876654 ATATATATGTATAGTATA
1 ATATATATGTATA-TATA
2876672 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.53
21 8 0.25
22 7 0.22
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
ATATATATGTATATATAAACC
Found at i:2876671 original size:13 final size:13
Alignment explanation
Indices: 2876637--2876679 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2876627 ATAAACCATG
2876637 TATAGTATATATA
1 TATAGTATATATA
* *
2876650 AACTA-TATATATG
1 TA-TAGTATATATA
2876663 TATAGTATATATA
1 TATAGTATATATA
2876676 TATA
1 TATA
2876680 TAAACTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (13 bp):
TATAGTATATATA
Found at i:2876688 original size:15 final size:15
Alignment explanation
Indices: 2876637--2876690 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
2876627 ATAAACCATG
2876637 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
2876653 TATATATATGTATAGTA-
1 TATATATA--TATA-AAC
2876670 TATATATATATAAAC
1 TATATATATATAAAC
2876685 TATATA
1 TATATA
2876691 AAATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.03
15 14 0.44
16 4 0.12
17 12 0.38
18 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:2876780 original size:49 final size:49
Alignment explanation
Indices: 2876679--2876783 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
2876669 ATATATATAT
* ** * **
2876679 ATAAACTATATAAAATAAATTACTTATATAATTTATAGAAATACTATGC
1 ATAAACTATATAAAATAAATAAAGTATATAATTTAAAGAAATACTAACC
* *
2876728 ATAAACTATATAAAGT-AATAAAGTATATAATTTAAAGAAATCCTAAACC
1 ATAAACTATATAAAATAAATAAAGTATATAATTTAAAGAAATACT-AACC
2876777 ATAAACT
1 ATAAACT
2876784 TTAAACCATA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 23 0.49
49 24 0.51
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAATAAATAAAGTATATAATTTAAAGAAATACTAACC
Found at i:2876795 original size:7 final size:7
Alignment explanation
Indices: 2876771--2876822 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
2876761 AAAGAAATCC
2876771 TAAACCA
1 TAAACCA
**
2876778 TAAACTT
1 TAAACCA
2876785 TAAACCA
1 TAAACCA
2876792 TAAA-CA
1 TAAACCA
2876798 CTAAA-CA
1 -TAAACCA
2876805 CTAAACCA
1 -TAAACCA
2876813 TAAACCA
1 TAAACCA
2876820 TAA
1 TAA
2876823 TATAAATGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 2 0.05
7 35 0.90
8 2 0.05
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:2876795 original size:21 final size:21
Alignment explanation
Indices: 2876771--2876822 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2876761 AAAGAAATCC
**
2876771 TAAACCATAAACTTTAAACCA
1 TAAACCATAAACACTAAACCA
2876792 TAAA-CACTAAACACTAAACCA
1 TAAACCA-TAAACACTAAACCA
2876813 TAAACCATAA
1 TAAACCATAA
2876823 TATAAATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCATAAACACTAAACCA
Found at i:2877034 original size:9 final size:9
Alignment explanation
Indices: 2877022--2877051 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
2877012 TACATTTAAA
2877022 TAATTTTAT
1 TAATTTTAT
2877031 TAATTTTAT
1 TAATTTTAT
2877040 TAATTTTAT
1 TAATTTTAT
2877049 TAA
1 TAA
2877052 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TAATTTTAT
Found at i:2877282 original size:16 final size:16
Alignment explanation
Indices: 2877261--2877327 Score: 107
Period size: 16 Copynumber: 4.2 Consensus size: 16
2877251 TCATTTACAT
*
2877261 GTCAGGCTAAAAACAG
1 GTCAGGTTAAAAACAG
2877277 GTCAGGTTAAAAACAG
1 GTCAGGTTAAAAACAG
*
2877293 GTCAGGTTAAAAACAT
1 GTCAGGTTAAAAACAG
*
2877309 GTCAGGTTGAAAACAG
1 GTCAGGTTAAAAACAG
2877325 GTC
1 GTC
2877328 GGGTAATACC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.19
Consensus pattern (16 bp):
GTCAGGTTAAAAACAG
Found at i:2881844 original size:74 final size:75
Alignment explanation
Indices: 2881715--2881890 Score: 173
Period size: 74 Copynumber: 2.4 Consensus size: 75
2881705 AACAATTACT
* * * *
2881715 AAAATAAATAAATGAAA-AAAAATAAACATCCTAAAAAATAGCTAAAAAAATAAAAATA-AAAGG
1 AAAAAAAATAAATGAAATAAAAATAAACAACCAAAAAAATAGCTAAAAAAATAAAAATATAAA-A
** *
2881778 CTAAATTAAAA
65 AAAAATCAAAA
* * **
2881789 AAAAGAAATAAATGAAATAAAAA-AAGA-AACCAAAAAAACTAGCTAACATTA-AAAAATATAAA
1 AAAAAAAATAAATGAAATAAAAATAA-ACAACCAAAAAAA-TAGCTAAAAAAATAAAAATATAAA
2881851 AAAAAATCAAAA
64 AAAAAATCAAAA
*
2881863 ATAAAAAAATAAAAGAAATAAAAATAAA
1 A-AAAAAAATAAATGAAATAAAAATAAA
2881891 AATAAGATTA
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
74 43 0.51
75 39 0.46
76 2 0.02
ACGTcount: A:0.73, C:0.06, G:0.05, T:0.15
Consensus pattern (75 bp):
AAAAAAAATAAATGAAATAAAAATAAACAACCAAAAAAATAGCTAAAAAAATAAAAATATAAAAA
AAAATCAAAA
Found at i:2881862 original size:8 final size:8
Alignment explanation
Indices: 2881838--2881886 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 8
2881828 TAGCTAACAT
2881838 TAAAAAATA
1 TAAAAAA-A
2881847 TAAAAAAA
1 TAAAAAAA
2881855 -AATCAAAAA
1 TAA--AAAAA
2881864 TAAAAAAA
1 TAAAAAAA
2881872 TAAAAGAAA
1 TAAAA-AAA
2881881 TAAAAA
1 TAAAAA
2881887 TAAAAATAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 2 0.06
8 12 0.33
9 20 0.56
10 2 0.06
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:2881868 original size:6 final size:6
Alignment explanation
Indices: 2881840--2881895 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
2881830 GCTAACATTA
*
2881840 AAAAAT ATAAAA- AAAAAT CAAAAAT AAAAA- AATAAA- AGAAAT AAAAAT
1 AAAAAT A-AAAAT AAAAAT -AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT
2881888 AAAAAT AA
1 AAAAAT AA
2881896 GATTAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
5 9 0.21
6 24 0.56
7 10 0.23
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAAAT
Done.