Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004116.1 Hibiscus syriacus cultivar Beakdansim tig00009006_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: 135206
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1283 original size:16 final size:16
Alignment explanation
Indices: 1262--1294 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1252 CCCATTTATC
1262 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
1278 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
1294 A
1 A
1295 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:3613 original size:20 final size:21
Alignment explanation
Indices: 3567--3627 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
3557 TTCCCTTGTG
3567 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
3590 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
3610 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
3628 TGCAGCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:12584 original size:3 final size:3
Alignment explanation
Indices: 12576--12601 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12566 ATGTGTAACT
12576 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12602 TAGTTAATTG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16192 original size:16 final size:16
Alignment explanation
Indices: 16119--16198 Score: 58
Period size: 16 Copynumber: 4.9 Consensus size: 16
16109 TATAAATTAA
16119 ATAAATATAATAATA-
1 ATAAATATAATAATAT
* *
16134 ATTAATAATATTAAT-T
1 ATAAAT-ATAATAATAT
*
16150 ATTAAATATACTAA-AT
1 A-TAAATATAATAATAT
16166 AATTAAAATATAATAATAT
1 -A-T-AAATATAATAATAT
*
16185 ATAAATATAGTAAT
1 ATAAATATAATAAT
16199 TAAAATAGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
15 5 0.10
16 26 0.50
17 8 0.15
18 11 0.21
19 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
ATAAATATAATAATAT
Found at i:19755 original size:20 final size:21
Alignment explanation
Indices: 19730--19774 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
19720 TGATTATAAA
19730 AAAATAAATT-TTAAAATT-TT
1 AAAAT-AATTATTAAAATTATT
*
19750 AAAATAATTATTAAATTTATT
1 AAAATAATTATTAAAATTATT
19771 AAAA
1 AAAA
19775 ACATCACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 12 0.55
21 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATAATTATTAAAATTATT
Found at i:20424 original size:23 final size:22
Alignment explanation
Indices: 20398--20445 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
20388 TATTTTTTCG
*
20398 AATTTATATTATTATAATATTAA
1 AATTTATAATATTATAA-ATTAA
*
20421 AATTTATAATATTATAAATTTA
1 AATTTATAATATTATAAATTAA
20443 AAT
1 AAT
20446 GATTTCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTATAATATTATAAATTAA
Found at i:20429 original size:15 final size:16
Alignment explanation
Indices: 20409--20442 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
20399 ATTTATATTA
20409 TTATAATATTA-AAAT
1 TTATAATATTATAAAT
20424 TTATAATATTATAAAT
1 TTATAATATTATAAAT
20440 TTA
1 TTA
20443 AATGATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATAATATTATAAAT
Found at i:23420 original size:7 final size:7
Alignment explanation
Indices: 23410--23441 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
23400 CCTTCAAGTT
*
23410 TTGGTTT
1 TTGGTTC
23417 TTGGTTC
1 TTGGTTC
23424 TTGGTTC
1 TTGGTTC
23431 TTGGTTC
1 TTGGTTC
23438 TTGG
1 TTGG
23442 CTCGTGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.09, G:0.31, T:0.59
Consensus pattern (7 bp):
TTGGTTC
Found at i:24503 original size:27 final size:27
Alignment explanation
Indices: 24466--24531 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
24456 TTAAAATTTT
*
24466 AAATAAGAATAAACTTA-TAA-AGATAAA
1 AAATAAAAATAAA-TTATTAATAGA-AAA
*
24493 AAATAAAAATATATTATTAATAGAAAA
1 AAATAAAAATAAATTATTAATAGAAAA
24520 AAATATAAAATA
1 AAATA-AAAATA
24532 TATGACACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 3 0.09
27 22 0.65
28 9 0.26
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (27 bp):
AAATAAAAATAAATTATTAATAGAAAA
Found at i:26845 original size:3 final size:3
Alignment explanation
Indices: 26837--26889 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
26827 AATATATATT
*
26837 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
26885 TAA TA
1 TAA TA
26890 TGGGTAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27572 original size:102 final size:107
Alignment explanation
Indices: 27459--27756 Score: 435
Period size: 118 Copynumber: 2.7 Consensus size: 107
27449 CTCATTATGA
*
27459 ACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTT-C-CTGGCAATGTTGA
1 ACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGTTGA
27522 TCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG-T-T
66 TCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTAT
27562 -CTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGTTGA
1 ACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGTTGA
27626 TCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTAT
66 TCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG---------TTAT
* *
27677 GAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGAT
1 --ACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGTT
27742 GATCCATCAAATGAT
64 GATCCATCAAATGAT
27757 AGATTTGAAT
Statistics
Matches: 176, Mismatches: 3, Indels: 17
0.90 0.02 0.09
Matches are distributed among these distances:
102 48 0.27
103 1 0.01
104 50 0.28
114 1 0.01
115 1 0.01
118 75 0.43
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (107 bp):
ACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGTTGA
TCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTAT
Found at i:27660 original size:220 final size:217
Alignment explanation
Indices: 27348--27756 Score: 678
Period size: 220 Copynumber: 1.9 Consensus size: 217
27338 CATTATGAAT
27348 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCA
* ** *
27413 AATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * *
27478 GATGATGAGTTCTTCTCATTATGAACTCTT-C-CTGGCAATGTTGATCCATCAAATGATGAATTC
131 GATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATGATGAATTC
27541 AAACAAAAAGTTGAACAAGTTC
196 AAACAAAAAGTTGAACAAGTTC
*
27563 TTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGTTGATC
1 TTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACT-TT-CTCTGGAAATGATGATC
*
27628 CATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT
61 CATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
27693 CTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATGAT
126 CTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATGAT
27757 AGATTTGAAT
Statistics
Matches: 178, Mismatches: 9, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
215 16 0.09
217 1 0.01
218 24 0.13
219 2 0.01
220 110 0.62
221 1 0.01
222 24 0.13
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (217 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCA
AATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATGATGAATTC
AAACAAAAAGTTGAACAAGTTC
Found at i:28595 original size:83 final size:83
Alignment explanation
Indices: 28495--28782 Score: 549
Period size: 83 Copynumber: 3.5 Consensus size: 83
28485 TCCTACCACT
28495 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
28560 GATTGATTCTGTCCAACC
66 GATTGATTCTGTCCAACC
28578 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
28643 GATTGATTCTGTCCAACC
66 GATTGATTCTGTCCAACC
* **
28661 ATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
28726 GATTGATTCTGTCCAACC
66 GATTGATTCTGTCCAACC
28744 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
28783 GAGTATATTG
Statistics
Matches: 201, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 201 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (83 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
GATTGATTCTGTCCAACC
Found at i:29961 original size:10 final size:9
Alignment explanation
Indices: 29939--29982 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
29929 GACCCCCCTC
29939 TTTTTTCTT
1 TTTTTTCTT
*
29948 TTTTCTCTT
1 TTTTTTCTT
29957 TTTTTTCATT
1 TTTTTTC-TT
29967 TTTTTTCTT
1 TTTTTTCTT
29976 TTCTTTT
1 TT-TTTT
29983 TTCTTCAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 18 0.58
10 13 0.42
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:29968 original size:19 final size:18
Alignment explanation
Indices: 29939--29982 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
29929 GACCCCCCTC
29939 TTTTTTCTTTTTTCTCTT
1 TTTTTTCTTTTTTCTCTT
*
29957 TTTTTTCATTTTTTTTCTT
1 TTTTTTC-TTTTTTCTCTT
29976 TTCTTTT
1 TT-TTTT
29983 TTCTTCAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 12 0.52
20 4 0.17
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTCTTTTTTCTCTT
Found at i:42854 original size:3 final size:3
Alignment explanation
Indices: 42846--42898 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
42836 AATATATATT
*
42846 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42894 TAA TA
1 TAA TA
42899 TGGGTAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43705 original size:40 final size:40
Alignment explanation
Indices: 43650--43734 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
43640 AGTTGTCACA
43650 TGATTATAAGGTGGATCCCTCGGAACTGAAACACGCTGGC
1 TGATTATAAGGTGGATCCCTCGGAACTGAAACACGCTGGC
43690 TGATTATAAGGTGGATCCCTCGGAACTGAAACACGCTGGC
1 TGATTATAAGGTGGATCCCTCGGAACTGAAACACGCTGGC
43730 TGATT
1 TGATT
43735 CTTTAGCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
TGATTATAAGGTGGATCCCTCGGAACTGAAACACGCTGGC
Found at i:52685 original size:21 final size:21
Alignment explanation
Indices: 52655--52695 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52645 CCGTGAACAG
*
52655 TGCTACAGTGTATCGATGCAC
1 TGCTACAGTGTACCGATGCAC
*
52676 TGCTATAGTGTACCGATGCA
1 TGCTACAGTGTACCGATGCA
52696 TAAAAACATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAC
Found at i:53453 original size:21 final size:21
Alignment explanation
Indices: 53404--53484 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
53394 TGAAATTTTA
* *
53404 TCCCGAAGGACCTGTGAATATG
1 TCCCGAAGGACCTATGAGT-TG
*
53426 TCTCGAAGGACCTATGAGTTG
1 TCCCGAAGGACCTATGAGTTG
*
53447 TCCCGAAGGACCTATGAGTTA
1 TCCCGAAGGACCTATGAGTTG
* *
53468 TCCCGAATGACCCATGA
1 TCCCGAAGGACCTATGA
53485 AGCCTTCGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
21 36 0.69
22 16 0.31
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
TCCCGAAGGACCTATGAGTTG
Found at i:64097 original size:18 final size:17
Alignment explanation
Indices: 64061--64095 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
64051 TATGCAGATG
64061 CTAAAATAAAAGAAAAA
1 CTAAAATAAAAGAAAAA
64078 CTAAAACTAAAATGAAAA
1 CTAAAA-TAAAA-GAAAA
64096 CTCACTGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.14
Consensus pattern (17 bp):
CTAAAATAAAAGAAAAA
Found at i:88007 original size:180 final size:180
Alignment explanation
Indices: 87700--88056 Score: 687
Period size: 180 Copynumber: 2.0 Consensus size: 180
87690 TGTACAAACT
87700 AGCAAATATATTCCATCATACTGTAAAAACAAAGTGATTGATTACAATAGAAAGAGATTTTTGTT
1 AGCAAATATATTCCATCATACTGTAAAAACAAAGTGATTGATTACAATAGAAAGAGATTTTTGTT
*
87765 TTTGCATTATTCGATCTCGAGATTGATATTGACTGAAGATTTAGCAGAGTCTTGCTTTAGTGGAA
66 TTTGCATTATTCGATCTCGAGATTGATATTGACTGAAGATTTAACAGAGTCTTGCTTTAGTGGAA
*
87830 CTTGTTAAAAATCATTGACACCATTAACAATTTGAAGCCATCTATCTTGA
131 CTTATTAAAAATCATTGACACCATTAACAATTTGAAGCCATCTATCTTGA
*
87880 AGCAGATATATTCCATCATACTGTAAAAACAAAGTGATTGATTACAATAGAAAGAGATTTTTGTT
1 AGCAAATATATTCCATCATACTGTAAAAACAAAGTGATTGATTACAATAGAAAGAGATTTTTGTT
87945 TTTGCATTATTCGATCTCGAGATTGATATTGACTGAAGATTTAACAGAGTCTTGCTTTAGTGGAA
66 TTTGCATTATTCGATCTCGAGATTGATATTGACTGAAGATTTAACAGAGTCTTGCTTTAGTGGAA
88010 CTTATTAAAAATCATTGACACCATTAACAATTTGAAGCCATCTATCT
131 CTTATTAAAAATCATTGACACCATTAACAATTTGAAGCCATCTATCT
88057 ATCTTGAAGA
Statistics
Matches: 174, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 174 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (180 bp):
AGCAAATATATTCCATCATACTGTAAAAACAAAGTGATTGATTACAATAGAAAGAGATTTTTGTT
TTTGCATTATTCGATCTCGAGATTGATATTGACTGAAGATTTAACAGAGTCTTGCTTTAGTGGAA
CTTATTAAAAATCATTGACACCATTAACAATTTGAAGCCATCTATCTTGA
Found at i:95747 original size:3 final size:3
Alignment explanation
Indices: 95739--95829 Score: 101
Period size: 3 Copynumber: 29.7 Consensus size: 3
95729 TTCATTTAAA
* * * *
95739 TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT AAT TAT AAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
95787 TAA TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
95830 CAAACGGGCC
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
3 68 0.92
4 6 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:97218 original size:25 final size:23
Alignment explanation
Indices: 97190--97241 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
97180 AAATATATAT
97190 AATAAATAATAATTT-ATATTTTTTC
1 AATAAAT--TAATTTAATA-TTTTTC
*
97215 AATAAATTATTTTAATATTTTTC
1 AATAAATTAATTTAATATTTTTC
97238 AATA
1 AATA
97242 TCGAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 15 0.60
24 3 0.12
25 7 0.28
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAAATTAATTTAATATTTTTC
Found at i:97925 original size:24 final size:22
Alignment explanation
Indices: 97875--97935 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
97865 CATATATTTA
97875 ATTTATAAT-TT-TTTTTATAT
1 ATTTATAATATTATTTTTATAT
*
97895 ATATATACATATTATTTTTATAGT
1 ATTTATA-ATATTATTTTTATA-T
97919 ATTTATATATATTATTT
1 ATTTATA-ATATTATTT
97936 CATTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.18
21 2 0.06
22 2 0.06
23 8 0.24
24 16 0.47
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTATAATATTATTTTTATAT
Found at i:99613 original size:15 final size:14
Alignment explanation
Indices: 99571--99623 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
99561 ATTTTAAATA
*
99571 ATTTACATTTACA-
1 ATTTACATTTGCAT
99584 ATTTTACATTTGCAT
1 A-TTTACATTTGCAT
99599 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
99614 CTTTGCATTT
1 ATTTACATTT
99624 TTATTGCACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.03
14 20 0.59
15 13 0.38
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:105307 original size:83 final size:82
Alignment explanation
Indices: 105034--105491 Score: 781
Period size: 82 Copynumber: 5.6 Consensus size: 82
105024 AATAGAACAA
** *
105034 ATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
105099 ATCATTGAGTTTAGAAG
66 ATCATTGAGTTTAGAAG
*
105116 ATGAATTTGCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
105181 ATCATTGAGTTTAGAAG
66 ATCATTGAGTTTAGAAG
* *
105198 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
* *
105263 AAGCATTGAGTTCAGAAG
65 AATCATTGAGTTTAGAAG
* *
105281 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
* * *
105346 AAGCATTGAATTTGGAAG
65 AATCATTGAGTTTAGAAG
105364 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
105429 ATCATTGAGTTTAGAAG
66 ATCATTGAGTTTAGAAG
105446 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
105492 AGTTTGATAT
Statistics
Matches: 358, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
82 200 0.56
83 158 0.44
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (82 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
ATCATTGAGTTTAGAAG
Found at i:105471 original size:248 final size:247
Alignment explanation
Indices: 105034--105489 Score: 822
Period size: 248 Copynumber: 1.8 Consensus size: 247
105024 AATAGAACAA
** * *
105034 ATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGATTGGACAGAACA
* *
105099 ATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGA
66 AGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGA
105164 TCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTG
131 TCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTG
105229 TTCTTTGAGTTATATGATCTGATTGGACAGAATCAAGCATTGAGTTCAGAAG
196 TTCTTTGAGTTATATGATCTGATTGGACAGAATCAAGCATTGAGTTCAGAAG
*
105281 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGATTGGACAGAA-C
* *
105346 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
65 AAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTG
105411 ATCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGT
130 ATCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGT
105476 GTTCTTTGAGTTAT
195 GTTCTTTGAGTTAT
105490 CTAGTTTGAT
Statistics
Matches: 199, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
247 58 0.29
248 141 0.71
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (247 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGATTGGACAGAACA
AGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGA
TCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTG
TTCTTTGAGTTATATGATCTGATTGGACAGAATCAAGCATTGAGTTCAGAAG
Found at i:107815 original size:40 final size:40
Alignment explanation
Indices: 107770--107845 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
107760 TGAGCAGAGT
*
107770 CCACAGCAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
* *
107810 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTA
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTA
107846 CATCTAAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
Found at i:108265 original size:22 final size:22
Alignment explanation
Indices: 108236--108290 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
108226 ATCTACACTC
*
108236 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
108258 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
108280 TTCAAAGATGA
1 TTCAAAGATGA
108291 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:108890 original size:113 final size:113
Alignment explanation
Indices: 108692--109012 Score: 443
Period size: 113 Copynumber: 2.8 Consensus size: 113
108682 AGCAAAGATA
** * ****
108692 TGAATTCATCATTTGATGATTCAACATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTTGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
**
108757 GAAAAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCGCT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCT
*
108805 TGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTTGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
*
108870 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
** * *
108918 CAAATCCATC-TCTTGATGGA-TCAGCT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 TGAATTCATCAT-TTGAT-GATTCAG-TATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT
108980 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
63 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
109013 CTCATTTGAA
Statistics
Matches: 187, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
112 1 0.01
113 178 0.95
114 8 0.04
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (113 bp):
TGAATTCATCATTTGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
Found at i:109009 original size:40 final size:40
Alignment explanation
Indices: 108954--109054 Score: 175
Period size: 40 Copynumber: 2.5 Consensus size: 40
108944 TTTCCAGAGA
**
108954 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
*
108994 AAGTTCATAATGAGAAGAACTCATTTGAAGAAAAAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
109034 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
109055 TGTTCAACTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.20
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
Found at i:109032 original size:153 final size:153
Alignment explanation
Indices: 108836--109165 Score: 479
Period size: 153 Copynumber: 2.2 Consensus size: 153
108826 CAGTATTTCC
* ** *
108836 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAAC
* *
108901 TTGTTCAACCTTTT-GCTCAAATCCATC-TCTTGATGGA-TCAGCT-TTTCCAGAGAAAGTTCAT
66 TTGTTCAA-CTTTTCGCTCAAATCCATCAT-TCGAT-GATTCAG-TATTTCCAGAAAAAGTTCAT
*
108962 AATGAGAAGAACTCATCTGAAGAAGGA
127 AATGAGAAGAACACATCTGAAGAAGGA
* *
108989 AGAAGAAGTTCATAATGAGAAGAACTCATTTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAAC
** *
109054 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATG
66 TTGTTCAACTTTTCGCTCAAATCCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATG
109119 AGAAGAACACATCTGAAGAAGGA
131 AGAAGAACACATCTGAAGAAGGA
*
109142 AGAAGAAATTCATAATGAGAAGAA
1 AGAAGAAGTTCATAATGAGAAGAA
109166 TTTGTTCAAC
Statistics
Matches: 160, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
152 8 0.05
153 151 0.94
154 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (153 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAAC
TTGTTCAACTTTTCGCTCAAATCCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATG
AGAAGAACACATCTGAAGAAGGA
Found at i:109111 original size:113 final size:113
Alignment explanation
Indices: 108989--109637 Score: 792
Period size: 113 Copynumber: 5.7 Consensus size: 113
108979 TGAAGAAGGA
* *
108989 AGAAGAAGTTCATAATGAGAAGAACTCATTTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
* *
109054 TTGTTCAA-CTTTTCGCTTGAATTCATCATTCGAT-GATTCAGTATTTCC
66 TTGTTCAACCTTTT-GCTTAAATTCATCATTTGATGGA-TCAGTATTTCC
* ** * *
109102 AGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
* *
109167 TTGTTCAACCTTTTGCTCAAATCCATC-TCTTGATGGATCAGCT-TTTCC
66 TTGTTCAACCTTTTGCTTAAATTCATCAT-TTGATGGATCAG-TATTTCC
* *
109215 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAAAAGAAGTTCATAATGAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
* *
109280 TTGTTCAA-CTTTTCGCTTGAATTCATCATTCGAT-GATTCAGTATTTCC
66 TTGTTCAACCTTTT-GCTTAAATTCATCATTTGATGGA-TCAGTATTTCC
**** ** * *
109328 AGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
* *
109393 TTGTTCAACCTTTTGCTCAAATCCATC-TCTTGATGGATCAGCT-TTTCC
66 TTGTTCAACCTTTTGCTTAAATTCATCAT-TTGATGGATCAG-TATTTCC
* ** *
109441 AAAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAA
1 -AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAA
* * ** *
109506 TTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCC
65 CTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGTATTTCC
* *
109555 AGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAG
1 AGAAAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAG
* *
109620 AGCTTATTCAACCTTTTG
63 AACTTGTTCAACCTTTTG
109638 AATGACTCTA
Statistics
Matches: 461, Mismatches: 57, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
112 10 0.02
113 286 0.62
114 114 0.25
115 2 0.00
116 49 0.11
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAGTATTTCC
Found at i:109203 original size:266 final size:266
Alignment explanation
Indices: 108729--109280 Score: 1050
Period size: 266 Copynumber: 2.1 Consensus size: 266
108719 TACCAGTTCG
*
108729 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
108794 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
*
108859 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
131 ACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
**
108924 CATCTCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
196 CATCTCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
*
108989 AGAAGA
261 AAAAGA
*
108995 AGTTCATAATGAGAAGAACTCATTTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
109060 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
109125 ACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
131 ACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
109190 CATCTCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
196 CATCTCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
109255 AAAAGA
261 AAAAGA
109261 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
109281 TGTTCAACTT
Statistics
Matches: 280, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 280 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (266 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
ACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
CATCTCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
AAAAGA
Found at i:109278 original size:226 final size:227
Alignment explanation
Indices: 108994--109637 Score: 988
Period size: 226 Copynumber: 2.8 Consensus size: 227
108984 AAGGAAGAAG
*
108994 AAGTTCATAATGAGAAGAACTCATTTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
109059 CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAG
66 CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAGAGTTCATAATGAGAAG
*
109124 AACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
131 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
* *
109189 CCATCTCTTGATGGATCAGCTTTTCC-AGAGA
196 CCATCTCTTGATGGATCAGCTTTTCCAAAAAA
*
109220 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAAAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
***
109285 CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAG
66 CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAGAGTTCATAATGAGAAG
109350 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
131 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
109415 CCATCTCTTGATGGATCAGCTTTTCCAAAAAA
196 CCATCTCTTGATGGATCAGCTTTTCCAAAAAA
** * *
109447 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * ** * *
109512 CAACCTTTT-GTTTAAATTCATCATTTGATGGA-TCAACATTGCCAGGAAGAGTTCATAATGAGA
66 CAA-CTTTTCGCTTGAATTCATCATTCGAT-GATTCAGTATTTCCAGAAAGAGTTCATAATGAGA
** * ** *
109575 AGAACTCGTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
129 AGAA--C-TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
109638 AATGACTCTA
Statistics
Matches: 383, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
226 214 0.56
227 112 0.29
228 7 0.02
229 1 0.00
230 49 0.13
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (227 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAGAGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
CCATCTCTTGATGGATCAGCTTTTCCAAAAAA
Found at i:109542 original size:340 final size:342
Alignment explanation
Indices: 108995--109636 Score: 951
Period size: 340 Copynumber: 1.9 Consensus size: 342
108985 AGGAAGAAGA
* *
108995 AGTTCATAATGAGAAGAACTCATTTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTTC
** * *
109060 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
66 AACTTTTCGCTCAAATCCATCATTCGATGATTCAGTATTTCCAAAAAAAGTTCATAATGAGAAGA
109125 ACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
131 ACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
* * *
109190 CATCTCTTGATGGATCAGCTTTTCCAGAGAA-AGTTCATAATGAGAAGAA-C-TCATCTGAAGAA
196 CATCTCTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAA
*
109252 AAAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGA
260 AAAAAAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTCGCTTGAATTCATCATTCGATGA
109316 TTCAGTATTTCCAGTTCG
325 TTCAGTATTTCCAGTTCG
** *
109334 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTTC
*
109399 AACCTTTT-GCTCAAATCCATC-TCTTGATGGA-TCAGCT-TTTCCAAAAAAAAGTTCATAATGA
66 AA-CTTTTCGCTCAAATCCATCAT-TCGAT-GATTCAG-TATTTCC-AAAAAAAGTTCATAATGA
* * * * *
109460 GAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
126 GAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
109525 AAATTCATCAT-TTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
191 AAATCCATC-TCTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAAC-CGTCATCT
* *
109589 GAAGAAAAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTT
254 GAAGAAAAAAAAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTT
109637 GAATGACTCT
Statistics
Matches: 270, Mismatches: 22, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
338 1 0.00
339 88 0.33
340 129 0.48
341 1 0.00
342 1 0.00
343 45 0.17
344 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (342 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTCAAATCCATCATTCGATGATTCAGTATTTCCAAAAAAAGTTCATAATGAGAAGA
ACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
CATCTCTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAA
AAAAAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTCGCTTGAATTCATCATTCGATGAT
TCAGTATTTCCAGTTCG
Found at i:109868 original size:3 final size:3
Alignment explanation
Indices: 109860--109950 Score: 92
Period size: 3 Copynumber: 29.7 Consensus size: 3
109850 TTCATTTAAA
* * * * *
109860 TAT TAT TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT AAT TAT AAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
109908 TAA TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
109951 CAAACGGGCC
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
3 68 0.92
4 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:111352 original size:25 final size:23
Alignment explanation
Indices: 111324--111375 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
111314 AAATATATAT
111324 AATAAATAATAATTT-ATATTTTTTC
1 AATAAAT--TAATTTAATA-TTTTTC
*
111349 AATAAATTATTTTAATATTTTTC
1 AATAAATTAATTTAATATTTTTC
111372 AATA
1 AATA
111376 TCGAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 15 0.60
24 3 0.12
25 7 0.28
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAAATTAATTTAATATTTTTC
Found at i:112231 original size:18 final size:19
Alignment explanation
Indices: 112208--112244 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
112198 AGTATCTTAC
*
112208 AGTGAAG-AACAAGGACAA
1 AGTGAAGAAACAAAGACAA
112226 AGTGAAGAAACAAAGACAA
1 AGTGAAGAAACAAAGACAA
112245 GAAGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.59, C:0.11, G:0.24, T:0.05
Consensus pattern (19 bp):
AGTGAAGAAACAAAGACAA
Found at i:117534 original size:55 final size:55
Alignment explanation
Indices: 117442--117548 Score: 187
Period size: 55 Copynumber: 1.9 Consensus size: 55
117432 ACATGGGTGA
*
117442 CCTGCACAAGGGGTATCATGGCACTCTAATAATATGTCGACATCCCTTTTTTCAC
1 CCTGCACAAGGGGTATCATGGCACTCTAATAAAATGTCGACATCCCTTTTTTCAC
* *
117497 CCTGCACAAGGGGTATCATGGCACTCTCATAAAATGTCGTCATCCCTTTTTT
1 CCTGCACAAGGGGTATCATGGCACTCTAATAAAATGTCGACATCCCTTTTTT
117549 TTTACAAGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (55 bp):
CCTGCACAAGGGGTATCATGGCACTCTAATAAAATGTCGACATCCCTTTTTTCAC
Found at i:117655 original size:14 final size:13
Alignment explanation
Indices: 117626--117651 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
117616 TCGAATATCA
117626 AAAAATATTTTTT
1 AAAAATATTTTTT
117639 AAAAATATTTTTT
1 AAAAATATTTTTT
117652 TAAACATCAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:118291 original size:20 final size:21
Alignment explanation
Indices: 118247--118291 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
118237 AAGATTCCTC
* * *
118247 CTAATTAACATAAATGAAGAT
1 CTAATTAAAACAAATGAAAAT
118268 CTAATTAAAACAAA-GAAAAT
1 CTAATTAAAACAAATGAAAAT
118288 CTAA
1 CTAA
118292 AGGTGTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (21 bp):
CTAATTAAAACAAATGAAAAT
Found at i:118490 original size:35 final size:35
Alignment explanation
Indices: 118436--118519 Score: 150
Period size: 35 Copynumber: 2.4 Consensus size: 35
118426 AAAAACTAAT
*
118436 AAAAACTAAAAGGACATTAAATTAAAATTTGACTAC
1 AAAAA-TAAAAGGAAATTAAATTAAAATTTGACTAC
118472 AAAAATAAAAGGAAATTAAATTAAAATTTGACTAC
1 AAAAATAAAAGGAAATTAAATTAAAATTTGACTAC
118507 AAAAATAAAAGGA
1 AAAAATAAAAGGA
118520 TTGAAGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 42 0.89
36 5 0.11
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.23
Consensus pattern (35 bp):
AAAAATAAAAGGAAATTAAATTAAAATTTGACTAC
Found at i:120113 original size:3 final size:3
Alignment explanation
Indices: 120105--120153 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
120095 AATATTTGTT
* * * * *
120105 TAA TAA TAA TGA TGA TGA TGA TAA TAA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
120153 T
1 T
120154 TTGGAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:122053 original size:2 final size:2
Alignment explanation
Indices: 122046--122084 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
122036 TTATGTAAGC
122046 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT CAT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A
122085 ATCATGTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:122066 original size:13 final size:12
Alignment explanation
Indices: 122046--122084 Score: 62
Period size: 11 Copynumber: 3.2 Consensus size: 12
122036 TTATGTAAGC
122046 ATATATATATAT
1 ATATATATATAT
122058 ATA-ATATATAT
1 ATATATATATAT
122069 ATATATCATATAT
1 ATATAT-ATATAT
122082 ATA
1 ATA
122085 ATCATGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATATATATAT
Found at i:122066 original size:15 final size:15
Alignment explanation
Indices: 122046--122084 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
122036 TTATGTAAGC
122046 ATATATATATATATA
1 ATATATATATATATA
*
122061 ATATATATATATATC
1 ATATATATATATATA
122076 ATATATATA
1 ATATATATA
122085 ATCATGTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:128614 original size:12 final size:12
Alignment explanation
Indices: 128597--128626 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
128587 TTTGTAATAC
128597 TGGAAATTTGGT
1 TGGAAATTTGGT
*
128609 TGGAAATTTGTT
1 TGGAAATTTGGT
128621 TGGAAA
1 TGGAAA
128627 CCAATTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (12 bp):
TGGAAATTTGGT
Done.